diff --git a/DESCRIPTION b/DESCRIPTION index c156032..a74bd83 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,12 @@ Package: jDMRgrid Type: Package -Title: A heuristic DMR caller for large-scale WGBS data -Version: 0.2.1 +Title: A heuristic DMR caller for large-scale WGBS data using grid approach +Version: 0.2.4 Authors@R: c( - person("Robert", "Piecyk", email = "robert.s.piecyk@gmail.com", role = c("cre","aut"), comment=c(ORCID="0000-0002-7962-2907")), - person("Rashmi", "Hazarika", email = "hazarika.rr@gmail.com", role = "aut"), - person("Yadollah", "Shahryary Dizaji", email = "shahryary@gmail.com", role = "aut"), - person("Frank", "Johannes", email = "frank@jlab.org", role = "aut")) + person(given = c("Robert", "Stefan"), family = "Piecyk", email = "robert.s.piecyk@gmail.com", role = c("cre","aut"), comment=c(ORCID="0000-0002-7962-2907")), + person(given = c("Rashmi", "Rekha"), family = "Hazarika", email = "hazarika.rr@gmail.com", role = "aut"), + person(given = "Yadollah", family = c("Shahryary", "Dizaji"), email = "shahryary@gmail.com", role = "aut"), + person(given = "Frank", family = "Johannes", email = "frank@jlab.org", role = "aut")) Description: jDMRgrid is a component of the jDMR toolkit, an essential tool for conducting efficient and heuristic DMR (Differentially Methylated Region) calling in large-scale epigenomic studies involving population-level analyses and control/treatment experiments. Its functionality relies on a grid-based methodology that involves dividing the genome into sliding windows or bins of customizable sizes. It determines methylation state calls for each individual sliding window based on a Hidden Markov Model (HMM) approach. @@ -17,7 +17,7 @@ Encoding: UTF-8 LazyData: false LazyLoad: yes Depends: - R (>= 4.3.0) + R (>= 4.0.0) Imports: ape (>= 5.6.3), GenomicRanges (>= 1.38.0), @@ -52,6 +52,6 @@ Suggests: rmarkdown, testthat (>= 3.0.0) biocViews: Epigenetics, FunctionalGenomics, Genetics, MathematicalBiology, HiddenMarkovModel -URL: https://github.com/robert-piecyk/jDMRgrid -BugReports: https://github.com/robert-piecyk/jDMRgrid +URL: https://github.com/jlab-code/jDMRgrid +BugReports: https://github.com/jlab-code/jDMRgrid Config/testthat/edition: 3 diff --git a/NAMESPACE b/NAMESPACE index 8c787f1..287b748 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,25 +1,12 @@ -export(annotate) export(annotateDMRs) export(filterDMRmatrix) export(filterEpiMAF) export(filterReplicateConsensus) -export(gff3.in) -export(gff3.out) export(makeDMRmatrix) -export(floorDec) export(context.specific.DMRs) -export(extract.context.DMRs) -export(statusStringCheck) -export(binGenome) -export(split.groups) -export(merge.bins) -export(merge_cols) +export(splitGroups) export(runjDMRgrid) -export(makeRegionsImpute) -export(modifiedExportMethylome) -export(modified.estimateTransDist) -export(makeMethimpute) - +export(makeMethimpute_foreach) import(ggplot2) import(utils) import(future) @@ -29,6 +16,7 @@ import(biocViews) import(future.apply) import(foreach) importFrom(GenomicRanges,GRanges) +importFrom(foreach, "%dopar%") importFrom(GenomicRanges,slidingWindows) importFrom(GenomicRanges,findOverlaps) importFrom(GenomicRanges,intersect) @@ -58,7 +46,7 @@ importFrom(stats,coefficients) importFrom(stats,na.omit) importFrom(stats,start) importFrom(stats,end) - +importFrom(foreach, "%dopar%") importFrom(stringr,str_remove_all) importFrom(stringr,str_replace_all) importFrom(tidyr,separate) @@ -73,7 +61,7 @@ importFrom(GenomicRanges,findOverlaps) importFrom(IRanges,CharacterList) importFrom(IRanges,ranges) importFrom(stats,aggregate) - +importFrom(Biostrings,readDNAStringSet) importFrom(S4Vectors,queryHits) importFrom(S4Vectors,subjectHits) importFrom(S4Vectors,elementMetadata) @@ -84,6 +72,9 @@ importFrom(S4Vectors,"elementMetadata<-") importFrom(S4Vectors,values) importFrom(Biostrings,type) importFrom(ape,read.gff) +importFrom(methimpute,importBismark) +importFrom(methimpute,extractCytosinesFromFASTA) +importFrom(methimpute,inflateMethylome) importFrom(data.table,uniqueN) importFrom(stats,ecdf) importFrom(stats,quantile) @@ -91,4 +82,4 @@ importFrom(R.utils,withTimeout) importFrom(methods,as) importFrom(parallel,makeCluster) importFrom(parallel,stopCluster) -importFrom(rlang,".data") \ No newline at end of file +importFrom(rlang,".data") diff --git a/NEWS b/NEWS index 1338c8d..fc4c68b 100644 --- a/NEWS +++ b/NEWS @@ -1,4 +1,18 @@ -# jDMRgrid 0.2.1 +# jDMRgrid 0.2.4 + +Changes in version 0.2.4 (2023-10-30) +* jDMRgrid accepts Bismark CX reports (together with FASTA file; used in Bismark analysis) +* fixed errors for R v4.0 and up + +Changes in version 0.2.3 (2023-10-24) +* New form of samplefile: samplelist (DataFrame needs to supplied directly) +* Meeting BiocCheck and R CMD check requirements +* Updated manuals for functions and intermediate datasets to run examples for single files +* Updated vignette +* Functions and package meeting good coding practices +* Faster filterDMRmatrix and findinig context specific DMRs +* Errors were corrected + Changes in version 0.2.2 (2023-10-19) * KISS & DRY code implementation diff --git a/R/annotateDMRs.R b/R/annotateDMRs.R index 3638714..d96f0e6 100644 --- a/R/annotateDMRs.R +++ b/R/annotateDMRs.R @@ -1,9 +1,9 @@ -#' -#' @param gff +#----------------------------------------------------------------------------- +#' Import gff files +#' @param gff Paths to gff files. (char) #' @importFrom rtracklayer import.gff3 -#' @export -#' @return merge all supplied gff3 annotations into one -#merge the input gff3 files into one +#' @return Merge all supplied gff3 annotations into one +#' gff3.in <- function(gff){ input.gff <- lapply(gff, function(x){ import.gff3(x, colnames=c("type", "ID")) @@ -12,25 +12,24 @@ gff3.in <- function(gff){ return(merged.gff) } -# Check Annotation levels here. Supply annotation terms for e.g genes, TEs -#levels(elementMetadata(merged.gff)[,"type"]) -#available annotations -#"chromosome","gene","mRNA","five_prime_UTR","exon","CDS", -#"three_prime_UTR","ncRNA_gene","lnc_RNA","miRNA","tRNA","ncRNA", -#"snoRNA","snRNA","rRNA","TE","promoters" - -#' @param gff -#' @param annotation -#' @param grangesObj -#' @param name -#' @param out.dir output directory +#----------------------------------------------------------------------------- +#' Find overlaps between annotation and DMRs; return as GRanges object and +#' save as gff file. The following annotation could be detected: +#' "chromosome","gene","mRNA","five_prime_UTR","exon","CDS", +#' "three_prime_UTR","ncRNA_gene","lnc_RNA","miRNA","tRNA","ncRNA", +#' "snoRNA","snRNA","rRNA","TE","promoters" +#' @param gff GenomicRanges object with set of regions/DMRs +#' (GenomicRanges object) +#' @param annotation Names of annotations to be detected in gff. (char) +#' @param grangesObj GRanges of regions/DMRs. (GRanges object) +#' @param gff GFF3 file with all annotations. (S4 object) +#' @param name Filename generated in annotation function. (char) +#' @param out.dir Path to the output directory. (char) #' @importFrom GenomicRanges findOverlaps #' @importFrom rtracklayer export.gff #' @importFrom S4Vectors values values<- elementMetadata<- -#' @export -#' @export -#' @return export output files in gff3 format -#output annotated gff3 files +#' @return Export output files in gff3 format +#' gff3.out <- function(annotation, grangesObj, gff, name, out.dir) { getgff3 <- lapply(annotation, function(x){ idx <- which(elementMetadata(gff)[,"type"] == x) @@ -50,19 +49,12 @@ gff3.out <- function(annotation, grangesObj, gff, name, out.dir) { out.dir,"/", name, "_annotation.gff3"), version="3") } -#' @inheritParams gff3.in -#' @param gff -#' @param annotation -#' @param grangesObj -#' @param name -#' @param out.dir output directory -#' @param getAnno -#' @param mygff -#' @param mygr -#' @param annotation -#' @param gff.files -#' @param gff3.out -#' @param input.dir +#----------------------------------------------------------------------------- +#' Extract annotated regions +#' @param getAnno Annotation terms used to annotate DMRs. (char) +#' @param mygff GFF objects corresponding to the annotation terms. (S4 object) +#' @param mygr GenomicRanges object with set of regions/DMRs +#' (GenomicRanges object) #' @import magrittr #' @importFrom dplyr mutate id #' @importFrom GenomicRanges findOverlaps subsetByOverlaps seqnames @@ -73,26 +65,30 @@ gff3.out <- function(annotation, grangesObj, gff, name, out.dir) { #' @importFrom methods as #' @importFrom rlang .data #' @importFrom tidyr unnest -#' @export -#' @return annotated list -#extract annotated regions +#' @return List of data frames; for each annotation term separately, subset +#' by the overlaps between corresponding GFF annotation and GRanges +#' regions object. +#' annotate <- function(getAnno, mygff, mygr){ + chr <- NULL + coord <- NULL + anno.str <- NULL lapply(getAnno, function(x){ idx <- which(elementMetadata(mygff)[,"type"] == x) - mygff <- mygff[idx,] - hits <- findOverlaps(mygr, mygff, ignore.strand=FALSE) - myranges <- subsetByOverlaps(mygr, mygff) + mygff_subset <- mygff[idx,] + hits <- findOverlaps(mygr, mygff_subset, ignore.strand=FALSE) + myranges <- subsetByOverlaps(mygr, mygff_subset) mcols(myranges)$id <- CharacterList( - split(mygff$ID[subjectHits(hits)],queryHits(hits))) + split(mygff_subset$ID[subjectHits(hits)],queryHits(hits))) mcols(myranges)$type <- CharacterList( - split(mygff$type[subjectHits(hits)],queryHits(hits))) + split(mygff_subset$type[subjectHits(hits)],queryHits(hits))) mcols(myranges)$chr <- CharacterList( - split(seqnames(mygff)[subjectHits(hits)],queryHits(hits))) + split(seqnames(mygff_subset)[subjectHits(hits)],queryHits(hits))) mcols(myranges)$coord <- CharacterList( - split(ranges(mygff)[subjectHits(hits)],queryHits(hits))) + split(ranges(mygff_subset)[subjectHits(hits)],queryHits(hits))) mcols(myranges)$anno.str <- CharacterList( - split(strand(mygff)[subjectHits(hits)],queryHits(hits))) + split(strand(mygff_subset)[subjectHits(hits)],queryHits(hits))) df <- as(myranges, "data.frame") df <- df %>% mutate(id = strsplit( as.character(id),","), type = strsplit( @@ -112,34 +108,87 @@ annotate <- function(getAnno, mygff, mygr){ }) } -#' Annotate DMRs -#' -#' This function takes gff3 files as input and -#' outputs annotated DMRs in text and gff3 format. -#' Additionally, a DMR count table is generated. -#' +#----------------------------------------------------------------------------- +#' Output annotations overlapping regions and DMR count table as txt files +#' @param d Data frame from annotate function containing overlapping +#' annotations. (DataFrame object) +#' @param gr GenomicRanges object with set of regions/DMRs +#' (GenomicRanges object) +#' @param annotation Annotation terms used to annotate DMRs. (char) +#' @param tmp.name Filename generated in annotation function. (char) +#' @param out.dir Path to the output directory. (char) +#' @import magrittr +#' @importFrom data.table fwrite uniqueN +#' @importFrom dplyr group_by summarize +#' @importFrom stats start end +#' @return Annotation and DMR counts txt files in the output directory. +#' +writeTxtAnnotations <- function( + d, gr, annotation, tmp.name, out.dir) +{ + anno.list <- list() + final.df <- list() + out <- d %>% + group_by(seqnames, start, end) %>% + summarize( + type = paste(type, collapse=","), + id = paste(id, collapse=","), + ) %>% as.data.frame() + if (NROW(out)!=0){ + for (k1 in seq_len(NROW(out))){ + out$unique.anno.type[k1] <- paste0(unlist(lapply( + strsplit(out$type[k1], ","), unique)), collapse=",") + } + } + # count the DMR overlaps; the output + out.1 <- out[which(unlist( + lapply(strsplit(out$type,','), uniqueN))==1),] + out.2 <- out[which(unlist( + lapply(strsplit(out$type,','), uniqueN))>=2),] + #counting unique annotations + for (k2 in seq_along(annotation)){ + anno.list[[k2]] <- NROW( + out.1[grep(annotation[k2], out.1$type),]) + names(anno.list)[[k2]] <- annotation[k2] + } + #also counting multiple overlaps + anno.list[length(annotation)+1] <- list(NROW(out.2)) + names(anno.list)[[length(annotation)+1]] <- "multiple.overlaps" + df.1 <- do.call(cbind, anno.list) + df <- cbind(sample=tmp.name, total.DMRs=NROW(gr), df.1) + final.df <- rbind(final.df, data.frame(df)) + out <- out[,-c(4,6)] + fwrite( + x=out, file=paste0(out.dir, "/", tmp.name, "_annotation.txt"), + quote=FALSE, row.names=FALSE, col.names=TRUE, sep="\t") + fwrite( + x=final.df, file=paste0(out.dir, "/DMR-counts.txt"), quote=FALSE, + row.names=FALSE, col.names=TRUE, sep="\t") +} + +#----------------------------------------------------------------------------- +#' Output annotated DMRs in text and gff3 format, and DMR count table #' @inheritParams gff3.in #' @inheritParams gff3.out #' @inheritParams annotate -#' @param out.dir output directory. -#' @param annotation annotation terms used to annotate DMRs. -#' @param gff.files multiple gff3 files can be supplied as a vector. -#' @param gff3.out a logical specifying whether output annotated files in gff3. -#' @param input.dir input directory containing filtered DMR matrix/matrices. -#' @import magrittr +#' @inheritParams writeTxtAnnotations +#' @param annotation Annotation terms used to annotate DMRs. (char) +#' @param gff.files Paths to the gff3 files can be supplied as a vector; +#' corresponding to the annotation terms. (char) +#' @param if.gff3 A logical specifying whether output annotated files in +#' gff3. (logical) +#' @param input.dir Path to the input directory containing (non)/filtered +#' DMR matrix/matrices. (char) +#' @param out.dir Path to the output directory. (char) #' @importFrom GenomicRanges GRanges -#' @importFrom IRanges IRanges -#' @importFrom stats start end -#' @importFrom data.table fwrite fread rbindlist uniqueN -#' @importFrom dplyr group_by summarize +#' @importFrom IRanges IRanges +#' @importFrom data.table fread rbindlist +#' @return Output files containing annotated DMRs and DMR counts table #' @export -#' @return output files containing annotated DMRs and DMR counts table. - +#' annotateDMRs <- function(annotation, gff.files, if.gff3, input.dir, out.dir) { - anno.list <- list(); final.df <- list() file.list <- list.files(input.dir, pattern="*.txt", full.names = TRUE) for (i in seq_along(file.list)){ - message("Running file ", file.list[i]) tmp.name <- gsub("\\.txt$", "", basename(file.list[i])) file <- fread(file.list[i], select=c(1,2,3)) @@ -149,59 +198,17 @@ annotateDMRs <- function(annotation, gff.files, if.gff3, input.dir, out.dir) { gr <- GRanges( seqnames=file$V1,ranges=IRanges(start=file$V2, end=file$V3)) gff <- gff3.in(gff.files) - if (if.gff3==TRUE) { gff3.out( annotation = annotation, gff = gff, grangesObj = gr, name = tmp.name, out.dir = out.dir) } - d <- rbindlist(annotate(getAnno=annotation, mygff=gff, mygr=gr)) - if (nrow(d) != 0){ - out <- d %>% - group_by(seqnames, start, end) %>% - summarize( - type = paste(type, collapse=","), - id = paste(id, collapse=","), - ) %>% as.data.frame() - - if (NROW(out)!=0){ - for (k1 in seq_len(NROW(out))){ - out$unique.anno.type[k1] <- paste0(unlist(lapply( - strsplit(out$type[k1], ","), unique)), collapse=",") - } - } - # count the DMR overlaps; the output - # can be used to make a barplot or pie-chart - # unique annotation overlaps - - out.1 <- out[which(unlist( - lapply(strsplit(out$type,','), uniqueN))==1),] - out.2 <- out[which(unlist( - lapply(strsplit(out$type,','), uniqueN))>=2),] - - #counting unique annotations - for (k2 in seq_along(annotation)){ - anno.list[[k2]] <- NROW( - out.1[grep(annotation[k2], out.1$type),]) - names(anno.list)[[k2]] <- annotation[k2] - } - #also counting multiple overlaps - anno.list[length(annotation)+1] <- list(NROW(out.2)) - names(anno.list)[[length(annotation)+1]] <- "multiple.overlaps" - df.1 <- do.call(cbind, anno.list) - - df <- cbind(sample=tmp.name, total.DMRs=NROW(gr), df.1) - final.df <- rbind(final.df, data.frame(df)) - - out <- out[,-c(4,6)] - fwrite(x=out, file=paste0( - out.dir, "/", tmp.name, "_annotation.txt" - ), quote=FALSE, row.names=FALSE, col.names=TRUE, sep="\t") + if (nrow(d) != 0) { + writeTxtAnnotations( + d = d, gr = gr, annotation = annotation, + tmp.name = tmp.name, out.dir = out.dir) } - fwrite(x=final.df, file=paste0( - out.dir, "/DMR-counts.txt" - ), quote=FALSE, row.names=FALSE, col.names=TRUE, sep="\t") } } } diff --git a/R/filterDMRmatrix.R b/R/filterDMRmatrix.R index 2d31bbc..d68901f 100644 --- a/R/filterDMRmatrix.R +++ b/R/filterDMRmatrix.R @@ -1,94 +1,107 @@ -#' -#' @param status.collect -#' @param rc.methlevel.collect -#' @param replicate.consensus -#' @param diff.ct +#------------------------------------------------------------------------------ +#' Bind list of replicates (as part of lapply function) +#' @param x Number of rows in state-calls file. (num) +#' @param status.collect DataFrame with state-calls. (DataFrame object) +#' @param sampleinfo Information about samples and their replicates in df +#' @param replicate.consensus Percentage of concordance in state calls in num +#' @param diffct Allowed difference between control and treatment groups in num +#' @return A logical if the following row meets replicate consensus criterion +#' and should be included in the filtered dataset. +#' +bindReplicateLists <- function( + x, mypattern, df.bind, sampleinfo, replicate.consensus, diff.ct, + max.iter) { + Sys.sleep(1/max.iter) + for (m in unique(df.bind$sample)){ + total.reps <- length(df.bind$mypattern[df.bind$sample==m]) + rval <- round(replicate.consensus * total.reps) + pattern.vals <- df.bind$mypattern[df.bind$sample==m] + df.bind$diff.count[df.bind$sample==m] <- length( + which(pattern.vals==1))/total.reps + tt <- table(pattern.vals) + if (max(tt) >= rval){ + df.bind$count[df.bind$sample==m] <- 0 + } else { + df.bind_rows <- apply(df.bind, 1, function(row) { + m <- row[which(colnames(df.bind) == 'sample')] + total.reps <- length( + df.bind$mypattern[df.bind$sample == m]) + rval <- round(replicate.consensus * total.reps) + pattern.vals <- df.bind$mypattern[df.bind$sample == m] + row[["diff.count"]] <- length( + which(pattern.vals == 1)) / total.reps + tt <- table(pattern.vals) + if (max(tt) >= rval) { + row[["count"]] <- 0 + } else { + row[["count"]] <- 1 } + return(row) }) + df.bind_rows <- as.data.frame(t(df.bind_rows)) + df.bind_rows$mypattern <- as.numeric( + df.bind_rows$mypattern) + df.bind_rows$diff.count <- as.numeric( + df.bind_rows$diff.count) + df.bind_rows$count <- as.numeric(df.bind_rows$count) + df.bind <- df.bind_rows + } + } + df.gp <- group_by(df.bind, sample) %>% + summarize(n = mean(.data$diff.count)) + cb <- combn(df.gp$n,2) + my.diff <- unlist(lapply(cb, function(x) abs(cb[1]-cb[2]))) + if ((min(my.diff) >= diff.ct) & (sum(df.bind$count)==0)) { + return(TRUE) + } else { + return(FALSE) + } +} + +#----------------------------------------------------------------------------- +#' Application of filtering using replicate consensus +#' @param status.collect DataFrame for state-calls. (DataFrame object) +#' @param rc.methlevel.collect DataFrame rc-methylation levels. +#' (DataFrame object) +#' @param replicate.consensus Percentage of concordance in state calls. (num) +#' @param diff.ct Allowed difference between control and treatment groups. (num) #' @import magrittr #' @importFrom data.table fread #' @importFrom data.table rbindlist #' @importFrom dplyr semi_join summarize #' @importFrom utils setTxtProgressBar txtProgressBar +#' @return List of data frames for rc-methylation level and state-calls using +#' replicate-consensus criterion. #' @export #' - filterReplicateConsensus <- function( - status.collect, rc.methlevel.collect, replicate.consensus, - diff.ct=0.5) { - + status.collect, rc.methlevel.collect, replicate.consensus, diff.ct) { if (!is.null(status.collect$epiMAF)){ - status.collect <- status.collect[,-c("epiMAF")] + status.collect <- as.data.frame(status.collect) + status.collect <- status.collect[,-nrow(status.collect)] } # deducing replicates info mycol <- names(status.collect)[4:NCOL(status.collect)] sampleinfo <- data.frame(do.call(rbind, strsplit(as.character(mycol),"_"))) - if (length(sampleinfo)==2){ colnames(sampleinfo) <- c("sample", "replicate") dt <- data.frame() pb1 <- txtProgressBar( - min = 1, - max = NROW(status.collect), - char = "=", style = 3, file = "") - - q <- lapply(seq_len(NROW(status.collect)), function(x){ - mypattern <- unlist(status.collect[x, 4:NCOL(status.collect)]) - df.bind <- cbind(sampleinfo, mypattern) - for (m in unique(df.bind$sample)){ - total.reps <- length(df.bind$mypattern[df.bind$sample==m]) - rval <- round(replicate.consensus * total.reps) - pattern.vals <- df.bind$mypattern[df.bind$sample==m] - df.bind$diff.count[df.bind$sample==m] <- length( - which(pattern.vals==1))/total.reps - tt <- table(pattern.vals) - if (max(tt) >= rval){ - df.bind$count[df.bind$sample==m] <- 0 - } else { - df.bind_rows <- apply(df.bind, 1, function(row) { - m <- row[which(colnames(df.bind) == 'sample')] - total.reps <- length( - df.bind$mypattern[df.bind$sample == m]) - rval <- round(replicate.consensus * total.reps) - pattern.vals <- df.bind$mypattern[df.bind$sample == m] - row[["diff.count"]] <- length( - which(pattern.vals == 1)) / total.reps - tt <- table(pattern.vals) - if (max(tt) >= rval) { - row[["count"]] <- 0 - } else { - row[["count"]] <- 1 - } - return(row) - }) - df.bind_rows <- as.data.frame(t(df.bind_rows)) - df.bind_rows$mypattern <- as.numeric( - df.bind_rows$mypattern) - df.bind_rows$diff.count <- as.numeric( - df.bind_rows$diff.count) - df.bind_rows$count <- as.numeric(df.bind_rows$count) - df.bind <- df.bind_rows - } - } - Sys.sleep(1/NROW(status.collect)) - setTxtProgressBar(pb1, x) - close(pb1) - - df.gp <- group_by(df.bind, sample) %>% - summarize(n = mean(.data$diff.count)) - cb <- combn(df.gp$n,2) - my.diff <- unlist(lapply(cb, function(x) abs(cb[1]-cb[2]))) - - # allowing 50% difference between control and treatment groups - if ((min(my.diff) >= diff.ct) & (sum(df.bind$count)==0)) { - dt <- rbind(dt, status.collect[x,]) - } - #print(df.bind) - #if (sum(df.bind$count)==0) { - # dt <- rbind(dt, status.collect[x,]) - #} - }) - out <- q[!unlist(lapply(q,is.null))] - #status.collect <- q[-which(sapply(q, is.null))] - df.status.collect <- rbindlist(out) + min = 1, max = nrow(status.collect), char = "=", + style = 3, file = "") + q <- lapply( + seq(NROW(status.collect)), function(iter) { + mypattern <- unlist( + status.collect[iter, 4:NCOL(status.collect)]) + df.bind <- cbind(sampleinfo, mypattern) + out.q <- bindReplicateLists( + x = iter, mypattern = mypattern, df.bind = df.bind, + sampleinfo = sampleinfo, + replicate.consensus = replicate.consensus, + diff.ct = diff.ct, max.iter = nrow(status.collect)) + setTxtProgressBar(pb1, iter) + return(out.q) + }) + close(pb1) + df.status.collect <- status.collect[unlist(q),] if (NROW(df.status.collect) !=0){ df.rc.methlevel.collect <- rc.methlevel.collect %>% semi_join( @@ -104,97 +117,90 @@ filterReplicateConsensus <- function( } } - #----------------------------------------------------------------------------- - -#' @param mat1 -#' @param mat2 -#' @param epiMAF +#' Application of filtering using epiMAF criterion +#' @param status.collect DataFrame for state-calls. (DataFrame object) +#' @param rc.methlevel.collect DataFrame rc-methylation levels. +#' (DataFrame object) +#' @param epiMAF Threshold to filter for minor epi-allele frequency. (num) #' @import magrittr #' @importFrom dplyr semi_join #' @importFrom utils setTxtProgressBar txtProgressBar +#' @return List of data frames for rc-methylation level and state-calls using +#' minor epi-allele frequency criterion. #' @export -#' - -filterEpiMAF <- function(mat1, mat2, epiMAF){ +#' +filterEpiMAF <- function(status.collect, rc.methlevel.collect, epiMAF){ floorDec <- function(valParm ,x){ y <- function(x, level=1) round(x - 5*10^(-level-1), level) res <-y(as.numeric(valParm),x) return(res) } pb2 <- txtProgressBar( - min = 1, max = NROW(mat1), char = "=", style = 3, file = "") - mypatterns <- mat1[, 4:(NCOL(mat1) - 1)] + min = 1, max = NROW(status.collect), char = "=", style = 3, file = "") + mypatterns <- status.collect[, 4:(NCOL(status.collect) - 1)] epiMAFs <- apply(mypatterns, 1, function(row) { mycount <- table(row) epiMAF.out <- min(mycount) / length(row) return(floorDec(as.numeric(as.character(epiMAF.out)), 5)) }) - mat1$epiMAF <- epiMAFs + status.collect$epiMAF <- epiMAFs - Sys.sleep(1 / NROW(mat1)) - setTxtProgressBar(pb2, NROW(mat1)) + Sys.sleep(1 / NROW(status.collect)) + setTxtProgressBar(pb2, NROW(status.collect)) close(pb2) - df.status.collect <- mat1[which(mat1$epiMAF < epiMAF),] + status.collect <- as.data.frame(status.collect) + rc.methlevel.collect <- as.data.frame(rc.methlevel.collect) + df.status.collect <- status.collect[which(status.collect$epiMAF < epiMAF),] if (NROW(df.status.collect) !=0){ - df.rc.methlevel.collect <- mat2 %>% semi_join( + df.rc.methlevel.collect <- rc.methlevel.collect %>% semi_join( df.status.collect, by=c("seqnames","start","end")) return(list(df.status.collect, df.rc.methlevel.collect)) } else { - message("Empty dataframe. Nothing to write!") + message("Empty data frame. Nothing to write!") return(NULL) } } #------------------------------------------------------------------------------ -#' -#' @param rcmethlvl_data -#' @param statecalls_data +#' Merge bins having the same state-calls and calculate mean of their +#' methylation levels +#' @param rcmethlvl_data DataFrame rc-methylation levels. +#' (DataFrame object) +#' @param statecalls_data DataFrame for state-calls. (DataFrame object) #' @import magrittr -#' @importFrom GenomicRanges makeGRangesFromDataFrame -#' @importFrom GenomicRanges reduce -#' @importFrom GenomicRanges findOverlaps -#' @importFrom data.table fread -#' @importFrom data.table fwrite -#' @importFrom data.table rbindlist -#' @export -#' +#' @importFrom GenomicRanges makeGRangesFromDataFrame reduce findOverlaps +#' @importFrom data.table fread fwrite rbindlist +#' @return List of data frames for rc-methylation level and state-calls with +#' merged neighbouring bins having similar state-call profile. +#' merge.bins <- function(rcmethlvl_data, statecalls_data) { - # split state call dataset into unique patterns of state calls among samples states.all <- split(statecalls_data, apply( statecalls_data[,4:NCOL(statecalls_data)],1,paste,collapse = "_")) rcmethlvl.all <- split( rcmethlvl_data, apply( statecalls_data[,4:NCOL(statecalls_data)],1,paste,collapse = "_")) - # merge overlapping bins having the same patterns among samples AND - # save the indices corresponding the merged windows + # merge overlapping bins having the same patterns among samples states.list <- lapply(states.all, function(x) { data.list <- list() - # create a GRanges object - data <- GenomicRanges::makeGRangesFromDataFrame( - x,keep.extra.columns = TRUE) + # create a GRanges object and merge overlapping bins + data <- makeGRangesFromDataFrame(x,keep.extra.columns = TRUE) # merge overlapping bins data.reduced <- reduce(data) # find the indices of the overlapping bins ovlps <- as.data.frame(findOverlaps(data, data.reduced)) - # prepare dataset for the final step - data.reduced <- as.data.frame(data.reduced) - data.reduced <- data.reduced[,c(1,2,3)] + data.reduced <- as.data.frame(data.reduced)[,c(1,2,3)] data.reduced <- cbind(data.reduced, x[1,4:NCOL(x)]) - data.list[[1]] <- ovlps - data.list[[2]] <- data.reduced + data.list[[1]] <- ovlps; data.list[[2]] <- data.reduced return(data.list) }) - # extract state calls and overlaps from the previous function overlaps.data <- lapply(states.list, function(x) x[[1]]) states.data <- lapply(states.list, function(x) x[[2]]) - - # calculate the average methylation for each previously merged bin by - # using the overlaps dataset from the previous function + # calculate the average methylation for each previously merged bin rcmethlvl.data <- lapply(seq_along(rcmethlvl.all), function(x) { # extract methylation levels and overlaps for a given run rcmethlvl.1 <- rcmethlvl.all[[x]] @@ -213,16 +219,26 @@ merge.bins <- function(rcmethlvl_data, statecalls_data) rbindlist(rcmethlvl.out)) return(rcmethlvl.out) }) - - # prepare dataset to get it through next step of analysis states.data <- rbindlist(states.data) states.data <- states.data[order(seqnames, start, end), ] rcmethlvl.data <- rbindlist(rcmethlvl.data) rcmethlvl.data <- rcmethlvl.data[order(seqnames, start, end), ] return(list(states.data, rcmethlvl.data)) } -#------------------------------------------------------------------------------ +#------------------------------------------------------------------------------ +#' Save methylation levels and state calls at a given context as txt file +#' @param out.rcmethlvl Output DataFrame rc-methylation levels. +#' (DataFrame object) +#' @param out.statecalls Output DataFrame for state-calls. (DataFrame object) +#' @param context Methylation context. (char) +#' @param out.name1 Name for the state-call file. (char) +#' @param out.name2 Name for the rc-methylation level file. (char) +#' @param data.out Path to the output directory. (char) +#' @import data.table fwrite +#' @return Output DMR matrices for state-calls and rc-methylation levels as +#' txt file. +#' export.out <- function( out.rcmethlvl,out.statecalls,context,out.name1,out.name2,data.out){ fwrite( @@ -237,35 +253,259 @@ export.out <- function( } #------------------------------------------------------------------------------ -#' filter DMR matrix +#' Remove non-polymorphic state-calls only by merging bins if applicable +#' @inheritParams merge.bins +#' @inheritParams export.out +#' @param status.collect DataFrame for state-calls. (DataFrame object) +#' @param rc.methlevel.collect DataFrame rc-methylation levels. +#' (DataFrame object) +#' @param context Methylation context. (char) +#' @param data.dir Path to the output directory. (char) +#' @param if.mergingBins Logical if bins with same state-calls profile among +#' samples should be merged. (logical) +#' @return Filtrated state-calls and methylation DMR matrices using +#' merging bins criterion. +#' +removeNonPolymorphicOnly <- function( + status.collect, rc.methlevel.collect, context, data.dir, + if.mergingBins) { + message("Both, epiMAF and replicate consensus set to NULL. + Merge corresponding bins") + out1 <- status.collect + out2 <- rc.methlevel.collect + if (if.mergingBins == TRUE) + { + out <- merge.bins(statecalls_data=out1, rcmethlvl_data=out2) + } else { + out <- list(statecalls=out1, rcmethlvl=out2) + } + export.out( + out.statecalls=out[[1]],out.rcmethlvl=out[[2]], + context=context,out.name1="StateCalls-filtered", + out.name2="rcMethlvl-filtered",data.out=data.dir) +} + +#------------------------------------------------------------------------------ +#' Apply epiMAF filtering and merging bins if applicable +#' @inheritParams filterEpiMAF +#' @inheritParams merge.bins +#' @inheritParams export.out +#' @param status.collect DataFrame for state-calls. (DataFrame object) +#' @param rc.methlevel.collect DataFrame rc-methylation levels. +#' (DataFrame object) +#' @param context Methylation context. (char) +#' @param data.dir Path to the output directory. (char) +#' @param epiMAF.cutoff Threshold to filter for +#' the minor epi-allele frequency. (num) +#' @param if.mergingBins Logical if bins with same state-calls profile among +#' samples should be merged. (logical) +#' @return Filtrated state-calls and methylation DMR matrices using epi-allele +#' frequency criterion and merging bins, if applicable +#' +populationFiltering <- function( + status.collect, rc.methlevel.collect, context, data.dir, + epiMAF.cutoff, if.mergingBins) { + message("Filtering for epiMAF: ", epiMAF.cutoff, '...') + mydf <- filterEpiMAF( + status.collect=status.collect, + rc.methlevel.collect=rc.methlevel.collect, epiMAF=epiMAF.cutoff) + if (!is.null(mydf)){ + # for population data remove the epiMAF column + out1 <- mydf[[1]][,-ncol(mydf[[1]])] + out2 <- mydf[[2]] + if (if.mergingBins == TRUE) + { + out <- merge.bins( + statecalls_data=out1, rcmethlvl_data=out2) + } else { + out <- list(statecalls=out1, rcmethlvl=out2) + } + export.out( + out.statecalls=out[[1]], out.rcmethlvl=out[[2]], + context=context, out.name1="StateCalls-filtered", + out.name2="rcMethlvl-filtered", data.out=data.dir) + } + else { + message('Filtering for epiMAF returns NULL dataset.') + out1 <- status.collect + out2 <- rc.methlevel.collect + if (if.mergingBins == TRUE) + { + out <- merge.bins( + statecalls_data=out1, rcmethlvl_data=out2) + } else { + out <- list(statecalls=out1, rcmethlvl=out2) + } + export.out( + out.statecalls=out[[1]], out.rcmethlvl=out[[2]], + context=context, out.name1="StateCalls-filtered", + out.name2="rcMethlvl-filtered", data.out=data.dir) + } +} + +#------------------------------------------------------------------------------ +#' Apply replicate consensus filtering and merging bins if applicable +#' @inheritParams filterReplicateConsensus +#' @inheritParams merge.bins +#' @inheritParams export.out +#' @param status.collect DataFrame for state-calls. (DataFrame object) +#' @param rc.methlevel.collect DataFrame rc-methylation levels. +#' (DataFrame object) +#' @param context Methylation context. (char) +#' @param data.dir Path to the output directory. (char) +#' @param replicate.consensus Percentage of concordance in state calls. (num) +#' @param if.mergingBins Logical if bins with same state-calls profile among +#' samples should be merged. (logical) +#' @param diff.ct Allowed difference between control and treatment groups. (num) +#' @return Filtrated state-calls and methylation DMR matrices using replicate +#' consensus and merging bins, if applicable +#' +replicateFiltering <- function( + status.collect, rc.methlevel.collect, context, data.dir, + replicate.consensus, if.mergingBins, diff.ct) { + message("Filtering for replicate consensus...") + mydf <- filterReplicateConsensus( + status.collect, rc.methlevel.collect, replicate.consensus, diff.ct) + if (!is.null(mydf)){ + out1 <- mydf[[1]] + out2 <- mydf[[2]] + if (if.mergingBins == TRUE) + { + out <- merge.bins( + statecalls_data=out1, rcmethlvl_data=out2) + } else { + out <- list(statecalls=out1, rcmethlvl=out2) + } + export.out( + out[[2]],out[[1]],context=context, + out.name1="StateCalls-filtered", + out.name2="rcMethlvl-filtered", data.out=data.dir) + } else { + message('Proceeding with the original dataset...') + out1 <- status.collect + out2 <- rc.methlevel.collect + if (if.mergingBins == TRUE) + { + out <- merge.bins( + statecalls_data=out1, rcmethlvl_data=out2) + } else { + out <- list(statecalls=out1, rcmethlvl=out2) + } + export.out( + out.statecalls=out[[1]], out.rcmethlvl=out[[2]], + context=context, out.name1="StateCalls-filtered", + out.name2="rcMethlvl-filtered", data.out=data.dir) + } +} + +#------------------------------------------------------------------------------ +#' Filter DMR matrix among contexts +#' @inheritParams removeNonPolymorphicOnly +#' @inheritParams populationFiltering +#' @inheritParams replicateFiltering +#' @param list.status Vector with the filenames for state-calls matrices. (char) +#' @param data.dir Path to the input/output directory for +#' raw/filtered DMR matrices. (char) +#' @param replicate.consensus Percentage of concordance in state calls. (num) +#' @param epiMAF.cutoff Threshold to filter for minor epi-allele frequency. +#' (num) +#' @param if.mergingBins Logical if bins with same state-calls profile among +#' samples should be merged. (logical) +#' @import magrittr +#' @importFrom data.table fread +#' @return Filtrated state-calls and methylation DMR matrices #' -#' Filters non-polymorphic patterns by default. -#' @param epiMAF.cutoff -#' @param replicate.consensus -#' @param data.dir -#' @param samplefiles -#' @param if.mergingBins +filteringAmongContexts <- function( + list.status, data.dir, replicate.consensus, epiMAF.cutoff, + if.mergingBins) { + for (i in seq_along(list.status)){ + # extract context for a given state calls file + context <- gsub("_StateCalls.txt", "", basename(list.status[i])) + message("Filtering DMR matrix for ", context, ' context.') + # read a given state calls file + if (file.exists(list.status[i])){ + status.collect <- fread(list.status[i], header=TRUE) + } else { + stop("Files do not exist or is non-readable!") + } + # remove non-polymorphic/unchanged patterns + message("Removing non-polymorphic patterns...") + # extract rows where state calls for each sample are NOT unchanged + index <- which(rowSums( + status.collect[,4:NCOL(status.collect)]) != 0 & rowSums( + status.collect[,4:NCOL( + status.collect)]) != NCOL(status.collect)-3) + # update state calls list with the changed patterns + status.collect <- status.collect[index,] + # read a corresponding methylation file and update it + rc.methlvl.name <- paste0(data.dir, "/", context, "_rcMethlvl.txt") + rc.methlevel.collect <- fread(rc.methlvl.name, header=TRUE) + rc.methlevel.collect <- rc.methlevel.collect[index,] + # we are only removing non-polymorphic patterns + if (is.null(epiMAF.cutoff) && is.null(replicate.consensus)) { + removeNonPolymorphicOnly( + status.collect = status.collect, + rc.methlevel.collect = rc.methlevel.collect, + context = context, data.dir = data.dir, + if.mergingBins = if.mergingBins)} + # filtering out regions with epiMAF < Minor Allele Frequency + if (!is.null(epiMAF.cutoff)) { + populationFiltering( + status.collect = status.collect, + rc.methlevel.collect = rc.methlevel.collect, + context = context, data.dir = data.dir, + epiMAF.cutoff = epiMAF.cutoff, + if.mergingBins = if.mergingBins)} + # retaining samples based on replicate.consensus + if (!is.null(replicate.consensus)) { + replicateFiltering( + status.collect = status.collect, + rc.methlevel.collect = rc.methlevel.collect, + context = context, data.dir = data.dir, + replicate.consensus = replicate.consensus, + if.mergingBins = if.mergingBins, diff.ct = 0.5)} + } +} + +#------------------------------------------------------------------------------ +#' Filter DMR matrix. Filters non-polymorphic patterns by default. +#' @inheritParams filteringAmongContexts +#' @param epiMAF.cutoff Threshold to filter for +#' minor epi-allele frequency. (num; default as NULL) +#' @param replicate.consensus Percentage of concordance in state calls. +#' (num; default as NULL) +#' @param data.dir Path to the directory containing DMR matrix files. (char) +#' @param samplelist DataFrame object containing information about +#' file, sample, replicate and group. (DataFrame object) +#' @param if.mergingBins Logical if bins with same state-calls profile among +#' samples should be merged. (logical; default as FALSE) #' @import magrittr #' @importFrom data.table fread +#' @return Filtrated state-calls and methylation DMR matrices using: +#' filtration for non-polymorphic patterns and +#' (epiMAF for population-based data or +#' replicate consensus for control/treatment data) +#' and/or merging neighbouring bins with same state calls profiles. #' @export #' filterDMRmatrix <- function( - epiMAF.cutoff=NULL,replicate.consensus=NULL,data.dir,samplefiles, - if.mergingBins=TRUE) - { - contexts <- unique(sub("_.*", "", list.files(data.dir, pattern = 'C'))) - ft <- data.table::fread(samplefiles) - if (!is.null(ft$group)){ - ft$name <- paste0(ft$sample,"_", ft$replicate) - gps <- ft$group[!ft$group %in% c('control')] + epiMAF.cutoff = NULL, replicate.consensus = NULL, data.dir, + samplelist, if.mergingBins = FALSE) +{ + contexts <- unique(sub("_.*", "", list.files(data.dir, pattern = '^C'))) + if (!is.null(samplelist$group)){ + samplelist$name <- paste0(samplelist$sample,"_", samplelist$replicate) + gps <- samplelist$group[!samplelist$group %in% c('control')] gps <- unique(gps) list.collect2 <- lapply(seq_along(gps), function(m) { myvec <- c("control", gps[m]) - gp1 <- ft$name[which(ft$group == myvec[1])] - gp2 <- ft$name[which(ft$group == myvec[2])] - gp1.sample <- unique(ft$sample[which(ft$name == gp1)]) - gp2.sample <- unique(ft$sample[which(ft$name == gp2)]) + gp1 <- samplelist$name[which(samplelist$group == myvec[1])] + gp2 <- samplelist$name[which(samplelist$group == myvec[2])] + gp1.sample <- unique( + samplelist$sample[which(samplelist$name == gp1)]) + gp2.sample <- unique( + samplelist$sample[which(samplelist$name == gp2)]) out.name <- paste0(gp1.sample, "_", gp2.sample) list.collect1 <- lapply(seq_along(contexts), function(cn) { @@ -281,157 +521,92 @@ filterDMRmatrix <- function( data.dir, pattern="_StateCalls.txt", full.names=TRUE) } if (length(list.status) != 0){ - for (i in seq_along(list.status)){ - # extract context for a given state calls file - context <- gsub("_StateCalls.txt", "", basename(list.status[i])) - message("Filtering DMR matrix for ", context, ' context.') - - # read a given state calls file - if (file.exists(list.status[i])){ - status.collect <- fread(list.status[i], header=TRUE) - } else { - stop("Files do not exist or is non-readable!") - } - - # remove non-polymorphic/unchanged patterns - message("Removing non-polymorphic patterns...") - - # extract rows for which state calls for each sample are NOT - # unchanged (either all 0 or 1) - index <- which(rowSums( - status.collect[,4:NCOL(status.collect)]) != 0 & rowSums( - status.collect[,4:NCOL( - status.collect)]) != NCOL(status.collect)-3) - - # update state calls list with the changed patterns - status.collect <- status.collect[index,] - - # read a corresponding methylation file and update it - # using indices from the previous step - rc.methlvl.name <- paste0(data.dir, "/", context, "_rcMethlvl.txt") - rc.methlevel.collect <- fread(rc.methlvl.name, header=TRUE) - rc.methlevel.collect <- rc.methlevel.collect[index,] - - # if epiMAP and replicate cutoffs are set to NULL, - # we are only removing non-polymorphic patterns - if (is.null(epiMAF.cutoff) && is.null(replicate.consensus)) { - message("Both, epiMAF and replicate consensus set to NULL. - Merge corresponding bins") - out1 <- status.collect - out2 <- rc.methlevel.collect - if (if.mergingBins == TRUE) - { - out <- merge.bins(statecalls_data=out1, rcmethlvl_data=out2) - } else { - out <- list(statecalls=out1, rcmethlvl=out2) - } - export.out( - out.statecalls=out[[1]],out.rcmethlvl=out[[2]], - context=context,out.name1="StateCalls-filtered", - out.name2="rcMethlvl-filtered",data.out=data.dir) - } - - # filtering out regions with epiMAF < Minor Allele Frequency - if (!is.null(epiMAF.cutoff)) { - message("Filtering for epiMAF: ", epiMAF.cutoff, '...') - mydf <- filterEpiMAF( - mat1=status.collect,mat2=rc.methlevel.collect, - epiMAF=epiMAF.cutoff) - if (!is.null(mydf)){ - # for population data remove the epiMAF column - out1 <- mydf[[1]][,-c("epiMAF")] - out2 <- mydf[[2]] - if (if.mergingBins == TRUE) - { - out <- merge.bins( - statecalls_data=out1, rcmethlvl_data=out2) - } else { - out <- list(statecalls=out1, rcmethlvl=out2) - } - export.out( - out.statecalls=out[[1]], out.rcmethlvl=out[[2]], - context=context, out.name1="StateCalls-filtered", - out.name2="rcMethlvl-filtered", data.out=data.dir) - } else { - message('Filtering for epiMAF returns NULL dataset.') - out1 <- status.collect - out2 <- rc.methlevel.collect - if (if.mergingBins == TRUE) - { - out <- merge.bins( - statecalls_data=out1, rcmethlvl_data=out2) - } else { - out <- list(statecalls=out1, rcmethlvl=out2) - } - export.out( - out.statecalls=out[[1]], out.rcmethlvl=out[[2]], - context=context, out.name1="StateCalls-filtered", - out.name2="rcMethlvl-filtered", data.out=data.dir) - } - } - # retaining samples based on replicate.consensus - if (!is.null(replicate.consensus)) { - message("Filtering for replicate consensus...") - mydf <- filterReplicateConsensus( - status.collect, rc.methlevel.collect, replicate.consensus) - if (!is.null(mydf)){ - out1 <- mydf[[1]] - out2 <- mydf[[2]] - if (if.mergingBins == TRUE) - { - out <- merge.bins( - statecalls_data=out1, rcmethlvl_data=out2) - } else { - out <- list(statecalls=out1, rcmethlvl=out2) - } - export.out( - out[[2]],out[[1]],context=context, - out.name1="StateCalls-filtered", - out.name2="rcMethlvl-filtered", data.out=data.dir) - } else { - message('Proceeding with the original dataset...') - out1 <- status.collect - out2 <- rc.methlevel.collect - if (if.mergingBins == TRUE) - { - out <- merge.bins( - statecalls_data=out1, rcmethlvl_data=out2) - } else { - out <- list(statecalls=out1, rcmethlvl=out2) - } - export.out( - out.statecalls=out[[1]], out.rcmethlvl=out[[2]], - context=context, out.name1="StateCalls-filtered", - out.name2="rcMethlvl-filtered", data.out=data.dir) - } - } - } + filteringAmongContexts( + list.status = list.status, data.dir = data.dir, + replicate.consensus = replicate.consensus, + epiMAF.cutoff = epiMAF.cutoff, if.mergingBins = if.mergingBins) } else { message("DMR matrix files do not exist!") } } #------------------------------------------------------------------------------ -#' -#' write DMR out list -#' @param context.df -#' @param out.name -#' @param data.out +#' Read state calls files for each context and create their GRanges objects +#' @param file.list Path to the DMR matrices with state calls for +#' CG, CHG and CHH contexts. (char) #' @importFrom data.table fread +#' @importFrom GenomicRanges GRanges +#' @importFrom IRanges subsetByOverlaps +#' @return List of data frames and GRanges objects of state calls; for each +#' methylation contexts separately. +#' +DMR.list.in <- function(file.list) { + contexts <- c('CG','CHG','CHH') + data.out <- lapply(file.list, function(x) fread(x, header = TRUE)) + gr.out <- lapply(data.out, function(x) GRanges( + seqnames=x$seqnames,ranges=IRanges(x$start,end=x$end))) + names(data.out) <- contexts + names(gr.out) <- contexts + return(list(data.out = data.out, gr.out = gr.out)) +} + +#------------------------------------------------------------------------------ +#' Save DataFrame with context-specific DMRs as txt file +#' @param context.df DataFrame with filtrated context-specific DMRs +#' (DataFrame object). +#' @param out.name Name sample_replicate_context_group-of-analysis OR +#' context_group-of-analysis. (char) +#' @param data.out Path to the output directory. (char) +#' @importFrom data.table fwrite +#' @return Context-specific DMRs saved as the txt files in the output directory. #' DMR.list.out <- function(context.df, out.name, data.out){ fwrite( - x=context.df, file=paste0(data.out, "/", out.name,".txt"),quote=FALSE, + x=context.df, file=paste0(data.out, "/", out.name,".txt"), quote=FALSE, row.names=FALSE, col.names=TRUE, sep="\t") } #------------------------------------------------------------------------------ +#' Identify DMRs which are occuring only at a given context +#' (for non-CG and multi-context DMRs) +#' @param context Methylation context for which unique DMRs are identified; +#' "CG", "CHG" or "CHH". (char) +#' @param list.out List of state calls and their GRanges for each context. +#' (list) +#' @param data.dir Path to the output directory. (char) +#' @param tmp.name For group-specific analysis: vector with with +#' sample_replicate names. (char) +#' @import magrittr +#' @importFrom dplyr semi_join +#' @return #' -#' @param file1 -#' @param file2 -#' @param file3 -#' @param tmp.name -#' @param data.dir +DMR.onlyContext <- function(context, list.out, data.dir, tmp.name) { + message('Generating ', context, '-only DMRs...') + sel.line <- ifelse(context == 'CG', 1, ifelse(context=='CHG', 2, 3)) + out.line <- setdiff(seq(1,3), sel.line) + out.1 <- subsetByOverlaps( + list.out[[2]][[sel.line]], list.out[[2]][[out.line[1]]], invert = TRUE) + out.2 <- subsetByOverlaps( + out.1, list.out[[2]][[out.line[2]]], invert = TRUE) + out.only <- as.data.frame(out.2) + out.only $seqnames <- as.integer(as.character(out.only$seqnames)) + out.only <- out.only %>% semi_join( + out.only, by = c("seqnames","start","end")) + DMR.list.out( + context.df=out.only, out.name=paste0(tmp.name, context, "-only-DMRs"), + data.out=data.dir) + message("Done!") +} + +#------------------------------------------------------------------------------ +#' Main function to extract context-specific DMRs +#' for the provided list of state-calls paths +#' @param file1 Path to the DMR matrix state calls for CG context. (char) +#' @param file2 Path to the DMR matrix state calls for CHG context. (char) +#' @param file3 Path to the DMR matrix state calls for CHH context. (char) +#' @param tmp.name For group-specific analysis: vector with with +#' sample_replicate names. (char) +#' @param data.dir Path to the output directory. (char) #' @import magrittr #' @importFrom IRanges subsetByOverlaps #' @importFrom dplyr semi_join @@ -448,175 +623,87 @@ DMR.list.out <- function(context.df, out.name, data.out){ #' @importFrom utils setTxtProgressBar txtProgressBar #' @importFrom IRanges setTxtProgressBar txtProgressBar subsetByOverlaps #' @importFrom rlang .data -#' @export +#' @return Output files containing context-specific DMRs in txt format #' - extract.context.DMRs <- function(file1, file2, file3, tmp.name, data.dir) { - if (file.exists(file1) && file.exists(file2) && file.exists(file3)){ - CG.out <- fread(file1, header=TRUE) - CHG.out <- fread(file2, header=TRUE) - CHH.out <- fread(file3, header=TRUE) - - CG.gr <- GRanges(seqnames=CG.out$seqnames,ranges=IRanges( - CG.out$start,end=CG.out$end)) - CHG.gr <- GRanges(seqnames=CHG.out$seqnames,ranges=IRanges( - CHG.out$start,end=CHG.out$end)) - CHH.gr <- GRanges(seqnames=CHH.out$seqnames,ranges=IRanges( - CHH.out$start,end=CHH.out$end)) - - #CG.only - message("Generating CG-only DMRs...") - out1 <- subsetByOverlaps(CG.gr, CHG.gr, invert = TRUE) - CG.1 <- subsetByOverlaps(out1, CHH.gr, invert = TRUE) - CG.1 <- as.data.frame(CG.1) - CG.1$seqnames <- as.integer(as.character(CG.1$seqnames)) - CG.only <- CG.out %>% semi_join(CG.1,by = c("seqnames","start","end")) - DMR.list.out( - context.df=CG.only,out.name=paste0(tmp.name,"CG-only-DMRs"), - data.out=data.dir) - message("Done!") - - #CHG.only - message("Generating CHG-only DMRs...") - out2 <- subsetByOverlaps(CHG.gr, CG.gr, invert = TRUE) - CHG.1 <- subsetByOverlaps(out2, CHH.gr, invert = TRUE) - CHG.1 <- as.data.frame(CHG.1) - CHG.1$seqnames <-as.integer(as.character(CHG.1$seqnames)) - CHG.only <- CHG.out %>% semi_join(CHG.1,by=c("seqnames","start","end")) - DMR.list.out( - context.df=CHG.only,out.name=paste0(tmp.name,"CHG-only-DMRs"), - data.out=data.dir) - message("Done!") - - #CHH.only - message("Generating CHH-only DMRs...") - out3 <- subsetByOverlaps(CHH.gr, CG.gr, invert = TRUE) - CHH.1 <- subsetByOverlaps(out3, CHG.gr, invert = TRUE) - CHH.1 <- as.data.frame(CHH.1) - CHH.1$seqnames <-as.integer(as.character(CHH.1$seqnames)) - CHH.only <- CHH.out %>% semi_join(CHH.1,by=c("seqnames","start","end")) - DMR.list.out( - context.df=CHH.only, out.name=paste0(tmp.name, "CHH-only-DMRs"), - data.out=data.dir) - message("Done!") - + if (file.exists(file1) && file.exists(file2) && file.exists(file3)) { + list.out <- DMR.list.in(c(file1, file2, file3)) + # context-only + DMR.onlyContext( + 'CG', list.out = list.out, data.dir = data.dir, + tmp.name = tmp.name) #CG + DMR.onlyContext( + 'CHG', list.out = list.out, data.dir = data.dir, + tmp.name = tmp.name) #CHG + DMR.onlyContext( + 'CHH', list.out = list.out, data.dir = data.dir, + tmp.name = tmp.name) #CHH #non-CG message("Generating non-CG DMRs...") - overlaps.nonCG <- findOverlaps(CHG.gr, CHH.gr, ignore.strand=TRUE) - overlaps.hits.nonCG <- subsetByOverlaps(CHG.gr, CHH.gr) - mcols(overlaps.hits.nonCG)$DMRs.CHH.coord <- CharacterList( - split( - CHH.gr[subjectHits(overlaps.nonCG)], queryHits(overlaps.nonCG))) - out.nonCG <- subsetByOverlaps( - overlaps.hits.nonCG, CG.gr, invert = TRUE) - nonCG <- data.frame(out.nonCG) %>% - mutate(DMRs.CHH.coord = strsplit( - as.character(.data$DMRs.CHH.coord),",")) %>% - unnest(c(.data$DMRs.CHH.coord)) - nonCG.clean <- data.frame(lapply(nonCG, function(k) - gsub ("[\\c]|[()]|\"|^ .", "", k))) - nonCG.clean <- nonCG.clean %>% - separate( - .data$DMRs.CHH.coord, c("CHH.seqnames","CHH.start","CHH.stop"), - sep = '([-:])') - nonCG.clean <- nonCG.clean[-c(4,5)] - colnames(nonCG.clean)[1] <- "CHG.seqnames" - colnames(nonCG.clean)[2] <- "CHG.start" - colnames(nonCG.clean)[3] <- "CHG.stop" - - b <- makeGRangesFromDataFrame( - nonCG.clean[, c("CHG.seqnames","CHG.start","CHG.stop")]) - c <- makeGRangesFromDataFrame( - nonCG.clean[, c("CHH.seqnames","CHH.start","CHH.stop")]) - out0 <- data.frame(GenomicRanges::intersect(b, c)) - nonCG.collect <- data.frame(matrix(NA, nrow(out0), 0)) - nonCG.collect$merged.seqnames <- out0$seqnames - nonCG.collect$merged.start <- out0$start - nonCG.collect$merged.stop <- out0$end + gr.nonCG <- subsetByOverlaps(list.out[[2]][[2]], list.out[[2]][[3]]) + gr.nonCG <- subsetByOverlaps( + gr.nonCG, list.out[[2]][[1]], invert = TRUE, type = 'any') + nonCG <- as.data.frame(reduce(gr.nonCG)) + nonCG$seqnames <- as.integer(as.character(nonCG$seqnames)) + nonCG <- nonCG %>% semi_join(nonCG, by = c("seqnames","start","end")) DMR.list.out( - context.df=nonCG.collect,out.name=paste0(tmp.name,"nonCG-DMRs"), + context.df=nonCG, out.name=paste0(tmp.name, "nonCG-DMRs"), data.out=data.dir) message("Done!") - #multi-context message("Generating multi-context DMRs...") - overlaps.1 <- findOverlaps(CG.gr, CHG.gr, ignore.strand=TRUE) - overlaps.hits.1 <- subsetByOverlaps(CG.gr, CHG.gr) - mcols(overlaps.hits.1)$DMRs.CHG.coord <- CharacterList( - split(CHG.gr[subjectHits(overlaps.1)], queryHits(overlaps.1))) - overlaps.2 <- findOverlaps(overlaps.hits.1, CHH.gr, ignore.strand=TRUE) - overlaps.hits.2 <- subsetByOverlaps(overlaps.hits.1, CHH.gr) - if (NROW(overlaps.hits.2)!=0){ - mcols(overlaps.hits.2)$DMRs.CHH.coord <- CharacterList( - split(CHH.gr[subjectHits(overlaps.2)], queryHits(overlaps.2))) - multi.context.1 <- data.frame(overlaps.hits.2) %>% - mutate(DMRs.CHG.coord = strsplit( - as.character(.data$DMRs.CHG.coord), ",")) %>% - unnest(c(.data$DMRs.CHG.coord)) - multi.context.1.clean <- data.frame(lapply( - multi.context.1,function(k) gsub ("[\\c]|[()]|\"|^ .", "", k))) - multi.context.1.clean <- multi.context.1.clean %>% - separate( - .data$DMRs.CHG.coord, c("CHG.seqnames","CHG.start", - "CHG.stop"), sep = '([-:])') - multi.context.2.clean <- data.frame(multi.context.1.clean) %>% - mutate(DMRs.CHH.coord = strsplit(as.character( - .data$DMRs.CHH.coord), ",")) %>% - unnest(c(.data$DMRs.CHH.coord)) - multi.context.2.clean <- multi.context.2.clean %>% - separate( - .data$DMRs.CHH.coord, c("CHH.seqnames","CHH.start", - "CHH.stop"), sep = '([-:])') - multi.context.2.clean <- multi.context.2.clean[-c(4,5)] - colnames(multi.context.2.clean)[1] <- "CG.seqnames" - colnames(multi.context.2.clean)[2] <- "CG.start" - colnames(multi.context.2.clean)[3] <- "CG.stop" - - a <- makeGRangesFromDataFrame(multi.context.2.clean[, c( - "CG.seqnames", "CG.start", "CG.stop")]) - b <- makeGRangesFromDataFrame(multi.context.2.clean[, c( - "CHG.seqnames", "CHG.start", "CHG.stop")]) - c <- makeGRangesFromDataFrame(multi.context.2.clean[, c( - "CHH.seqnames", "CHH.start", "CHH.stop")]) - out2 <- data.frame(intersect(intersect(a, b), c)) - multi.context.collect <- data.frame(matrix(NA, nrow(out2), 0)) - multi.context.collect$merged.seqnames <- out2$seqnames - multi.context.collect$merged.start <- out2$start - multi.context.collect$merged.stop <- out2$end + CG.gr <- list.out[[2]][[1]] + CHG.gr <- list.out[[2]][[2]] + CHH.gr <- list.out[[2]][[3]] + multi <- as.data.frame(intersect(CG.gr, intersect(CHG.gr, CHH.gr))) + if (nrow(multi) != 0) { + multi$seqnames <- as.integer(as.character(multi$seqnames)) + multi <- multi %>% semi_join( + multi, by = c("seqnames","start","end")) DMR.list.out( - context.df=multi.context.collect,out.name=paste0( + context.df=multi,out.name=paste0( tmp.name, "multi-context-DMRs"), data.out=data.dir) } else { message("No multi-context DMRs found!") } - message("Done!") } else { - stop("Filtered DMR matrix files for all contexts donot exist!") + stop("Filtered DMR matrix files for all contexts do not exist!") } } #------------------------------------------------------------------------------ +#' Output context-specific DMRs (only for a given context, nonCG or all context) +#' @param samplelist DataFrame object containing information about +#' file, sample, replicate and group. (DataFrame object) +#' @param input.dir Path to the input directory with DMR matrices. (char) +#' @param output.dir Path to the output directory. (char) +#' @param if.filtered Logical to specify if we should use filtered or +#' non-filtered matrices. (logical) +#' @importFrom data.table fread +#' @return Output files containing context-specific DMRs for five categories: +#' CG-only, +#' CHG-only, +#' CHH-only, +#' non-CG (occurs for CHG and/or CHH, but not for CG context), +#' multi-context (occurs for CG and CHG and CHH contexts) +#' @export #' -#' @param samplefiles -#' @param input.dir -#' @param output.dir -#' @param if.filtered -#' - -context.specific.DMRs <- function(samplefiles, input.dir, output.dir, if.filtered = FALSE){ - ft <- fread(samplefiles) - if (!is.null(ft$group)){ - ft$name <- paste0(ft$sample,"_", ft$replicate) - gps <- ft$group[!ft$group %in% c('control')] +context.specific.DMRs <- function( + samplelist, input.dir, output.dir, if.filtered = FALSE) { + if (!is.null(samplelist$group)){ + samplelist$name <- paste0(samplelist$sample,"_", samplelist$replicate) + gps <- samplelist$group[!samplelist$group %in% c('control')] gps <- unique(gps) for (m in seq_along(gps)){ myvec <- c("control", gps[m]) - gp1 <- ft$name[which(ft$group==myvec[1])] - gp2 <- ft$name[which(ft$group==myvec[2])] + gp1 <- samplelist$name[which(samplelist$group==myvec[1])] + gp2 <- samplelist$name[which(samplelist$group==myvec[2])] - gp1.sample <- unique(ft$sample[which(ft$name==gp1)]) - gp2.sample <- unique(ft$sample[which(ft$name==gp2)]) + gp1.sample <- unique( + samplelist$sample[which(samplelist$name==gp1)]) + gp2.sample <- unique( + samplelist$sample[which(samplelist$name==gp2)]) message("Generating context specific DMRs for ", gp1.sample, "-", gp2.sample,"\n") name_string <- ifelse( @@ -642,6 +729,3 @@ context.specific.DMRs <- function(samplefiles, input.dir, output.dir, if.filtere tmp.name="",data.dir=output.dir) } } - - - diff --git a/R/globFun.R b/R/globFun.R index 9caa0bd..841c944 100644 --- a/R/globFun.R +++ b/R/globFun.R @@ -1,15 +1,23 @@ -# Take 5 digit of decimal value and cut the numbers -floorDec <- function(valParm ,x){ +#------------------------------------------------------------------------------ +#' Take x digit of decimal value and cut the numbers +#' @param valParm Numeric input. (num) +#' @param x Number of digits to be taken into account. (num) +#' @return Numeric input cut by x digits +floorDec <- function(valParm, x){ y <- function(x, level=1) round(x - 5*10^(-level-1), level) res <-y(as.numeric(valParm),x) return(res) } -#' @param file_A +#------------------------------------------------------------------------------ +#' Replace methylation status by U, I and M states +#' @param file_A DataFrame with state-calls object; must contain status with +#' 'Intermediate', 'Unmethylated' or 'Methylated' calls +#' (DataFrame object) #' @importFrom utils #' @importFrom stringr str_replace_all -#' @export -#' +#' @return DataFrame with state-calls object; status calls replaced by U, I or +#' M state calls statusStringCheck <- function(file_A){ list_status <- c("Unmethylated", "Intermediate", "Methylated") strTocheckFileA <- head(file_A$status[1]) @@ -22,5 +30,4 @@ statusStringCheck <- function(file_A){ file_A$status,pattern = "Methylated",replacement = "M") } return(file_A) -} - +} \ No newline at end of file diff --git a/R/jDMRReg.R b/R/jDMRReg.R index 73ff6fb..33cf439 100644 --- a/R/jDMRReg.R +++ b/R/jDMRReg.R @@ -1,109 +1,97 @@ +#-------------------------------------------------------------------------- #' -#' @param model -#' @param out.dir -#' @param name -#' @param distcor -#' @param skip -#' @param plot.parameters -#' @param df -#' @param refRegion -#' @param context Cytosine context -#' @param fit.plot -#' @param fit.name -#' @param refRegion -#' @param include.intermediate -#' @param probability -#' @param mincov -#' @param nCytosines +#' @param contexts Methylation context(s) to be analysed. (vector) +#' @param c1 Index of the first context. (num) +#' @param c2 Index of the second context. (num) +#' @param cor.array Correlation array gained from the distanceCorrelation. +#' @param dfs +#' @param maxweights +#' @param param.list +#' @param miny +#' @importFrom minpack.lm nlsLM +#' @importFrom stats na.omit coefficients +#' @return +#' +calculateDecayingConstance <- function( + contexts, c1, c2, cor.array, dfs, maxweights, params.list, miny, skip) +{ + context.transition <- paste0(contexts[c1], '-', contexts[c2]) + if (c1 <= c2) { + df <- data.frame( + distance = as.numeric(dimnames(cor.array)[[3]]), + correlation = cor.array[c1,c2,,'correlation'], + weight = cor.array[c1,c2,,'weight'], + from = contexts[c1], to = contexts[c2]) + y <- df$correlation[(skip + 1):nrow(df)] + x <- df$distance[(skip + 1):nrow(df)] + weight <- df$weight[(skip + 1 ):nrow(df)] + startvalues <- list(a0 = na.omit(y)[1], D = 50) + p <- NULL + if (is.null(p)) { + startvalues <- list(a0 = na.omit(y)[1]) + p <- tryCatch({ + fit <- nlsLM( + y ~ a0 * exp(-x/Inf), start=startvalues, + weights=weight) + s <- summary(fit) + c <- coefficients(s) + params <- c[seq_along(startvalues)] + names(params) <- names(startvalues) + params <- as.list(params) + params$D <- Inf + params + }, error = function(e) { + startvalues$D <- Inf + startvalues + }) + } + if (p$D <= 0) { + p$D <- Inf } + params.list[[context.transition]] <- p + df$correlation.fit <- p$a0 * exp(-df$distance/p$D) + df$logweight <- log(df$weight+1) + dfs[[context.transition]] <- df + maxweights[context.transition] <- max( + df$logweight, na.rm = TRUE) + } + return(list(maxweights = maxweights, dfs = dfs, params.list = params.list)) +} + +#-------------------------------------------------------------------------- +#' Obtain an estimate for the transDist parameter by fitting an exponential +#' function to the supplied correlations from distanceCorrelation. +#' Modified function from the methIMPUTE package. +#' @inheritParams calculateDecayingConstance +#' @param distcor The output produced by distanceCorrelation. +#' @param skip Skip the first n cytosines for the fitting. +#' @param plot.parameters Whether to plot fitted params on to the plot or not. #' @import ggplot2 #' @import magrittr #' @importFrom minpack.lm nlsLM #' @importFrom grDevices dev.off pdf -#' @importFrom data.table fread -#' @importFrom data.table fwrite +#' @importFrom data.table fread fwrite #' @importFrom stringr str_replace_all #' @importFrom dplyr bind_rows filter #' @importFrom stats na.omit coefficients #' @importFrom GenomicRanges GRanges findOverlaps #' @importFrom S4Vectors queryHits subjectHits -#' @importFrom methimpute callMethylation -#' @importFrom methimpute distanceCorrelation -#' @importFrom stats coefficients -#' @export - -modified.estimateTransDist <- function(distcor, skip=2, plot.parameters=TRUE) { - - ## Context correlation fits and plots +#' @return +#' +modified.estimateTransDist <- function(distcor, skip, plot.parameters=TRUE) { contexts <- dimnames(distcor$data)[[1]] cor.array <- distcor$data - maxweights <- numeric() - params.list <- list() + params.list <- list(); dfs <- list(); maxweights <- numeric() miny <- min(cor.array, na.rm = TRUE) - dfs <- list() for (c1 in seq_along(contexts)) { for (c2 in seq_along(contexts)) { - context.transition <- paste0(contexts[c1], '-', contexts[c2]) - if (distcor$separate.contexts) { - if (c1 != c2) { - next - } - } - if (c1 <= c2) { - df <- data.frame( - distance = as.numeric(dimnames(cor.array)[[3]]), - correlation = cor.array[c1,c2,,'correlation'], - weight = cor.array[c1,c2,,'weight'], - from = contexts[c1], to = contexts[c2]) - - ## Fit - y <- df$correlation[(skip+1):nrow(df)] - x <- df$distance[(skip+1):nrow(df)] - weight <- df$weight[(skip+1):nrow(df)] - startvalues <- list(a0 = stats::na.omit(y)[1], D = 50) - p <- NULL - - if (is.null(p)) { - startvalues <- list(a0 = stats::na.omit(y)[1]) - p <- tryCatch({ - fit <- nlsLM( - y ~ a0 * exp(-x/Inf), start=startvalues, - weights=weight) - s <- summary(fit) - c <- coefficients(s) - params <- c[seq_along(startvalues)] - names(params) <- names(startvalues) - params <- as.list(params) - params$D <- Inf - params - }, error = function(e) { - startvalues$D <- Inf - startvalues - }) - } - - ## Check if we have negative D - if (p$D <= 0) { - p$D <- Inf - } - params.list[[context.transition]] <- p - - ## Plot - df$correlation.fit <- p$a0 * exp(-df$distance/p$D) - df$logweight <- log(df$weight+1) - dfs[[context.transition]] <- df - maxweights[context.transition] <- max( - df$logweight, na.rm = TRUE) - } + output.list <- calculateDecayingConstance( + contexts, c1, c2, cor.array, dfs, maxweights, params.list, + miny, skip) } } - maxweight <- max(maxweights, na.rm = TRUE) - - ## Plot correlation - df <- do.call(rbind, dfs) - #df$a0 <- round( - # sapply(params.list[paste0(df$from, '-', df$to)], '[[', 'a0'), 2) - #df$D <- round( - # sapply(params.list[paste0(df$from, '-', df$to)], '[[', 'D'), 0) + maxweight <- max(output.list$maxweights, na.rm = TRUE) + df <- do.call(rbind, output.list$dfs) #plot correlations + params.list <- output.list$params.list df$a0 <- vapply( params.list[paste0(df$from, '-', df$to)], function(x) round(x$a0, 2), numeric(1)) @@ -133,17 +121,19 @@ modified.estimateTransDist <- function(distcor, skip=2, plot.parameters=TRUE) { ggplt <- ggplt + geom_hline(aes_string( 'yintercept'=0), linetype=2, alpha=0.5) } - - #transDist <- sapply(params.list, '[[', 'D') transDist <- vapply(params.list, function(x) x$D, numeric(1)) return(list(transDist=transDist, plot=ggplt)) } #-------------------------------------------------------------------------- #' +#' @param model +#' @param out.dir +#' @param context +#' @param name #' @import magrittr #' @importFrom data.table fwrite fread -#' @export +#' @return #' modifiedExportMethylome <- function(model, out.dir, context, name) { #data <- model$data @@ -178,7 +168,48 @@ modifiedExportMethylome <- function(model, out.dir, context, name) { } #-------------------------------------------------------------------------- -#' +#' How many cytosines are methylated and unmethylated in methimpute file +#' @param overlaps +#' @param overlaps.hits +#' @param data_gr +#' @importFrom stats aggregate +#' @importFrom dplyr bind_rows +#' @return +#' +findMethylatedOrUnmethylated <- function(overlaps, overlaps.hits, data_gr) +{ + counts <- array( + NA, dim=c(length(data_gr), 2), + dimnames=list(NULL, c("methylated", "total"))) + methylated <- aggregate( + overlaps.hits$methylated, list(subjectHits(overlaps)), FUN=sum) + total <- aggregate( + overlaps.hits$total, list(subjectHits(overlaps)), FUN=sum) + if (NROW(methylated) != NROW(counts) ){ + missingr <- which( + !rownames(data.frame(data_gr)) %in% methylated$Group.1) + methylated <- bind_rows( + data.frame(Group.1=missingr, x=0), methylated) + methylated <- methylated[order(methylated$Group.1),] + total <- bind_rows( + data.frame(Group.1=missingr,x=0), total) + total <- total[order(total$Group.1),] + } + counts[,"methylated"] <- methylated$x + counts[,"total"] <- total$x + data_gr$counts <- counts + return(data_gr) +} + +#-------------------------------------------------------------------------- +#' Transform methimpute dataset with single cytosine according to the bins +#' @param df +#' @param context +#' @param refRegion +#' @param mincov +#' @param nCytosines +#' @param if.Bismark +#' @param cyt.pos.all #' @import magrittr #' @importFrom dplyr filter #' @importFrom data.table fread @@ -186,89 +217,95 @@ modifiedExportMethylome <- function(model, out.dir, context, name) { #' @importFrom S4Vectors queryHits subjectHits #' @importFrom stats aggregate #' @importFrom dplyr bind_rows -makeRegionsImpute <- function(df, context, refRegion, mincov, nCytosines) { +#' @importFrom methimpute importBismark extractCytosinesFromFASTA +#' @importFrom mehtimpute inflateMethylome +#' @return +#' +makeRegionsImpute <- function( + df, context, refRegion, mincov, nCytosines, if.Bismark, cyt.pos.all) { tmp_reg <- refRegion data <- as.data.frame(tmp_reg$reg.obs) data <- data %>% filter(data$chr != "M" & data$chr != "C") - #reference methimpute file - ref_data <- fread(df, skip = 1, select = c("V1","V2","V3","V4","V5","V6")) - + if (if.Bismark == TRUE) { + ref_data <- importBismark(df) + cytosine.positions <- cyt.pos.all[cyt.pos.all$context == context] + ref_data <- inflateMethylome(ref_data, cytosine.positions) + ref_data <- as.data.frame(ref_data) + ref_data <- ref_data[,-c(3,4)] + colnames(ref_data) <- c('V1','V2','V3','V4','V5','V6') + } else { + ref_data <- fread( + df, skip = 1, select = c("V1","V2","V3","V4","V5","V6")) + } + ref_data$V4 <- as.character(ref_data$V4) #remove Mt and chloroplast coordinates. Following is for Arabidopsis only ref_data <- ref_data %>% filter(ref_data$V1 != "M" & ref_data$V1 != "C") - #filtering by coverage - if (mincov>0){ + if (mincov > 0) { message("Filtering for coverage: ", mincov) - ref_data <- ref_data[which(ref_data$V6 >= mincov),] - } - - ref_data <- ref_data[which(ref_data$V4==context),] - + ref_data <- ref_data[which(ref_data$V6 >= mincov),] } + ref_data <- ref_data[which(ref_data$V4 == context),] + #create GRanges objects for the methimpute and binned genome files data_gr <- GRanges( seqnames=data$chr, ranges=IRanges(start=data$start, end=data$end), clusterlen=data$cluster.length, context=as.factor(context)) - ref_gr <- GRanges( seqnames=ref_data$V1, ranges=IRanges(start=ref_data$V2, width=1), context=as.factor(context), methylated=ref_data$V5, total=ref_data$V6) - + #count number of overlapping cytosines within bin data_gr$cytosineCount <- countOverlaps(data_gr, ref_gr) - - counts <- array( - NA, dim=c(length(data_gr), 2), - dimnames=list(NULL, c("methylated", "total"))) - + #find overlaps between binned genome and methimpute dataset overlaps <- findOverlaps(ref_gr, data_gr) - overlaps.hits <- ref_gr[queryHits(overlaps)] if (NROW(overlaps.hits) != 0){ - - methylated <- aggregate( - overlaps.hits$methylated, list(subjectHits(overlaps)), FUN=sum) - total <- aggregate( - overlaps.hits$total, list(subjectHits(overlaps)), FUN=sum) - - if (NROW(methylated) != NROW(counts) ){ - missingr <- which( - !rownames(data.frame(data_gr)) %in% methylated$Group.1) - - methylated <- bind_rows( - data.frame(Group.1=missingr, x=0), methylated) - methylated <- methylated[order(methylated$Group.1),] - - total <- bind_rows( - data.frame(Group.1=missingr,x=0), total) - total <- total[order(total$Group.1),] - } - counts[,"methylated"] <- methylated$x - counts[,"total"] <- total$x - data_gr$counts <- counts + data_gr <- findMethylatedOrUnmethylated( + overlaps = overlaps, overlaps.hits = overlaps.hits, + data_gr = data_gr) } rm(ref_data, ref_gr, overlaps, overlaps.hits) return(data_gr) } #-------------------------------------------------------------------------- +#' Perform HMM for state calling within binned genome +#' @inheritParams modified.estimateTransDist +#' @inheritParams modifiedExportMethylome +#' @param df DataFrame with binned genome. () +#' @param context Methylation contexts. (char) +#' @param fit.plot +#' @param fit.name +#' @param refRegion +#' @param include.intermediate +#' @param probability +#' @param out.dir +#' @param name +#' @param mincov +#' @param if.Bismark +#' @param cyt.pos.all +#' @importFrom methimpute distanceCorrelation callMethylation +#' @return +#' makeMethimpute <- function( df, context, fit.plot, fit.name, refRegion, include.intermediate, - probability, out.dir, name, mincov) + probability, out.dir, name, mincov, if.Bismark, + cyt.pos.all) { - methylome.data <- makeRegionsImpute(df, context, refRegion, mincov) + methylome.data <- makeRegionsImpute( + df=df, context=context, refRegion=refRegion, mincov=mincov, + if.Bismark=if.Bismark, cyt.pos.all=cyt.pos.all) if (!is.null(methylome.data$counts)) { quant.cutoff <- as.numeric( quantile( methylome.data$counts[,"total"], probs = c(0.96), na.rm=TRUE)) - distcor <- distanceCorrelation(methylome.data, distances=0:100) - fit <- modified.estimateTransDist(distcor) - + distcor <- distanceCorrelation(data=methylome.data, distances=0:100) + fit <- modified.estimateTransDist(distcor=distcor, skip=2) if (fit.plot==TRUE){ message("Generating fit plot for ", name) pdf(paste0(out.dir, "/", fit.name, "-fit.pdf", sep = "")) message(fit) dev.off() } - model <- callMethylation( data = methylome.data, transDist = fit$transDist, count.cutoff = quant.cutoff, max.time = Inf, max.iter = Inf, diff --git a/R/makeDMRmatrix.R b/R/makeDMRmatrix.R index 4250cb9..0ae885f 100644 --- a/R/makeDMRmatrix.R +++ b/R/makeDMRmatrix.R @@ -1,18 +1,16 @@ - -#' @param filepath -#' @param colm -#' @param include.intermediate -#' @param mincov -#' @param nCytosines +#------------------------------------------------------------------------------ +#' Merge state calls (col6) and rc.meth.lvl (col7) for all samples into the +#' single DataFrame; make a list of these two dataframes +#' @param filepath Paths to the methylome outputs for single samples. (char) +#' @param colm Column indices to be included in the final dataset. (num) +#' @param include.intermediate Logical if intermediate calls should be used; +#' default as FALSE. (logical) #' @import magrittr #' @importFrom data.table fread #' @importFrom dplyr inner_join -#' @export -#' - -# This function will merge (column 6) state calls and (column 7) -# rc.meth.lvl from all samples into one dataframe -# makes list of 2 dataframes +#' @return List of two data frames (for state calls and rc.meth.lvl) with +#' merged columns +#' merge_cols <- function(filepath, colm, include.intermediate) { mylist <- list() for (l in seq_along(colm)){ @@ -38,136 +36,154 @@ merge_cols <- function(filepath, colm, include.intermediate) { return(mylist) } -write.out <- function(out.df, data.dir, out.name, contexts){ +#------------------------------------------------------------------------------ +#' Write DMR matrix data as txt file +#' @param out.df Output DataFrame with the dataset to be saved as txt file. +#' (DataFrame object) +#' @param data.dir Path to the output directory. (char) +#' @param out.name Name of the file to be saved. (char) +#' @param contexts Methylation context; 'CG' or 'CHG' or 'CHH' . (char) +#' @importFrom data.table fwrite +#' @return DMR matrix saved in the output directory for the given context and +#' data type given in the out.name +#' +write.out <- function(out.df, data.dir, out.name, contexts) { fwrite(x=out.df, file=paste0( - data.dir,"/",contexts,"_",out.name,".txt" - ),quote=FALSE, row.names=FALSE, col.names=TRUE, sep="\t") + data.dir, "/", contexts,"_", out.name, ".txt"), quote=FALSE, + row.names=FALSE, col.names=TRUE, sep="\t") +} + +#------------------------------------------------------------------------------ +#' Builds a combined matrix for a given dataset (s-c, rcmthlvl or postMax) +#' @inheritParams write.out +#' @param data DataFrame with the dataset to be saved as txt file. +#' (DataFrame object) +#' @param data.type Type of the data; "postMax" or "StateCalls" or "rcMethlvl" +#' (char) +#' @param flist List of the full.path.MethReg to be saved as the columns; +#' gained from the prepareFlist function. (DataFrame object) +#' @param out.dir Path to the output directory. (char) +#' @param context Methylation context "CG" or "CHG" or "CHH". (char) +#' @return Saved DMR matrix in output directory for a given context and type +#' +writeDMRmatrix <- function(data, data.type, flist, out.dir, context) { + for (a in 4:ncol(data)) { + for (n in seq_along(flist$name)) { + if (colnames(data)[a] == basename(flist$full.path.MethReg)[n]) { + colnames(data)[a] <- flist$name[n] + } + } + } + + names(data)[1] <- "seqnames" + names(data)[2] <- "start" + names(data)[3] <- "end" + + write.out(data, out.dir, data.type, context) } +#------------------------------------------------------------------------------ +#' Extract filenames and match them to the methylation contexts +#' @param context Methylation context; "CG" or "CHG" or "CHH". (char) +#' @param extractflist Vector with the files +#' listed in the input directory. (char) +#' @param samplelist DataFrame object containing information about +#' file, sample, replicate and group. (DataFrame object) +#' @importFrom data.table rbindlist +#' @return Path to the methylome input files matching a given context +#' +prepareFlist <- function(context, extractflist, samplelist) { + mynames <- gsub( + paste0("_", context,".txt$"), "", basename(extractflist)) + selectlist <- list() + message("Extracting filenames and matching them...") + for (a1 in seq_along(mynames)){ + pat1 <- paste0( + "_",mynames[a1],"_","|","_",mynames[a1],"|",mynames[a1]) + as <- samplelist[grepl(pat1, samplelist$file),] + if (NROW(as)==1){ + as$full.path.MethReg <- grep( + paste0( + "/", mynames[a1], "_",context, ".txt", sep="" + ), extractflist, value = TRUE) + message(basename(as$full.path.MethReg)," found!") + selectlist[[a1]] <- as + } else { + message( + "Multiple files with match ", mynames[a1]," found!") + as$full.path.MethReg <- grep( + paste0( + "/", mynames[a1], "_",context, ".txt", sep="" + ), extractflist, value = TRUE) + message(basename(as$full.path.MethReg)," found!") + selectlist[[a1]] <- as + } + } + flist <- rbindlist(selectlist) + return(flist) +} + +#------------------------------------------------------------------------------ #' Builds a DMR matrix for all samples -#' #' This function generates a binary matrix, a matrix of #' recalibrated methylation levels and posterior probabilities for all samples. -#' -#' @param context Vector of cytosine contexts. (character vector) -#' @param samplefiles Path to the text file. (character) -#' @param include.intermediate A logical if intermediate calls should be used. -#' @param input.dir Path to the methylome calls. (character) -#' @param out.dir Path to output directory. (character) +#' @inheritParams prepareFlist +#' @inheritParams merge_cols +#' @inheritParams writeDMRmatrix +#' @param context Vector of cytosine contexts; default c('CG','CHG','CHH'). +#' (char) +#' @param postMax.out Logical if DMR matrix with postMax probabilities +#' should be output; default as FALSE. (logical) +#' @param samplelist DataFrame object containing information about +#' file, sample, replicate and group. (DataFrame object) +#' @param input.dir Path to the input directory with methylome calls +#' after jDMRgrid function. (char) +#' @param out.dir Path to the output directory. (char) +#' @param include.intermediate Logical if intermediate calls should be used; +#' default as FALSE. (logical) #' @import magrittr -#' @importFrom data.table fread -#' @importFrom data.table fwrite -#' @importFrom data.table rbindlist +#' @importFrom data.table fread fwrite rbindlist +#' @return Saved state-calls, rc-methylation and postMax DMR matrices +#' as txt files. #' @export -#' makeDMRmatrix <- function( - contexts=c("CG","CHG","CHH"), postMax.out=FALSE, samplefiles, + contexts=c("CG","CHG","CHH"), postMax.out=FALSE, samplelist, input.dir, out.dir, include.intermediate=FALSE) { - # Read the sample file with filenames - samplelist <- fread(samplefiles, header=TRUE) for (j in seq_along(contexts)){ - # list all files in the input directory extractflist <- list.files( input.dir,pattern=paste0(contexts[j],".txt"),full.names=TRUE) - - #extract file subsets for construction of DMRmatrix if (length(extractflist) != 0){ - mynames <- gsub( - paste0("_", contexts[j],".txt$"), "",basename(extractflist)) - selectlist <- list() - message("Extracting filenames and matching them...") - for (a1 in seq_along(mynames)){ - pat1 <- paste0( - "_",mynames[a1],"_","|","_",mynames[a1],"|",mynames[a1]) - #pat1 <- paste0("_",mynames[a1],"_") - as <- samplelist[grepl(pat1, samplelist$file),] - if (NROW(as)==1){ - as$full.path.MethReg <- grep( - paste0( - "/", mynames[a1], "_",contexts[j], ".txt", sep="" - ),extractflist, value=TRUE) - message(basename(as$full.path.MethReg)," found!") - selectlist[[a1]] <- as - } else { - message( - "Multiple files with match ", mynames[a1]," found!") - } - } - flist <- rbindlist(selectlist) - #print(flist) - + # Prepare flist to read files out of it + flist <- prepareFlist( + context = contexts[j], extractflist = extractflist, + samplelist = samplelist) # Assign unique names for samples with or without replicate data if (!is.null(flist$replicate)) { message( - "Running context ", contexts[j], " for replicates...") + "Running context ", contexts[j], " for replicates...") flist$name <- paste0(flist$sample,"_", flist$replicate) } else { flist$name <- flist$sample } - message("Now, constructing DMR matrix for ", contexts[j]) - # merge samples by Chr coordinates - #(column 6) state-calls and (column 7) rc.meth.lvl mydf <- merge_cols( flist$full.path.MethReg,include.intermediate,colm=c(5, 6, 7)) - # list containing state calls - status.collect <- mydf[[2]] - # renaming file names with sample names - for (a in 4:length(colnames(status.collect))) { - for (n in seq_along(flist$name)) { - if (colnames(status.collect)[a] == - basename(flist$full.path.MethReg)[n]) { - colnames(status.collect)[a] <- flist$name[n] - } - } - } + writeDMRmatrix( + data = mydf[[2]], data.type = "StateCalls", flist = flist, + out.dir = out.dir, context = contexts[j]) # list containing rcmethlvls - rc.methlevel.collect <- mydf[[3]] - # renaming file names with sample names - for (a in 4:length(colnames(rc.methlevel.collect))) { - for (n in seq_along(flist$name)) { - if (colnames(rc.methlevel.collect)[a] == - basename(flist$full.path.MethReg)[n]) { - colnames(rc.methlevel.collect)[a] <- flist$name[n] - } - } - } - if (postMax.out==TRUE){ - # list containing postmax - postMax.collect <- mydf[[1]] - # renaming file names with sample names - for (a in 4:length(colnames(postMax.collect))) { - for (n in seq_along(flist$name)) { - if (colnames(postMax.collect)[a] == - basename(flist$full.path.MethReg)[n]) { - colnames(postMax.collect)[a] <- flist$name[n] - } - } - } - names(postMax.collect)[1] <- "seqnames" - names(postMax.collect)[2] <- "start" - names(postMax.collect)[3] <- "end" - write.out( - postMax.collect,out.dir,"postMax",contexts[j]) - } - - names(status.collect)[1] <- "seqnames" - names(status.collect)[2] <- "start" - names(status.collect)[3] <- "end" - - names(rc.methlevel.collect)[1] <- "seqnames" - names(rc.methlevel.collect)[2] <- "start" - names(rc.methlevel.collect)[3] <- "end" - - - write.out(status.collect,out.dir,"StateCalls",contexts[j]) - write.out(rc.methlevel.collect,out.dir,"rcMethlvl",contexts[j]) - - + writeDMRmatrix( + data = mydf[[3]], data.type = "rcMethlvl", flist = flist, + out.dir = out.dir, context = contexts[j]) + # list containing postMax + if (postMax.out == TRUE) { + writeDMRmatrix( + data = mydf[[1]], data.type = "postMax", flist = flist, + out.dir = out.dir, context = contexts[j])} message("Done!") } else{ message("Files for context ", contexts[j], " do not exist!") diff --git a/R/runjDMR.R b/R/runjDMR.R index edef7a2..169c932 100644 --- a/R/runjDMR.R +++ b/R/runjDMR.R @@ -1,3 +1,12 @@ +#----------------------------------------------------------------------------- +#' Export bins from the list and save it as RData file using dput +#' @param mylist List of two DataFrame objects : binned genome and statistics +#' meeting minC criterion. (list of DataFrame objects) +#' @param out.dir Path to the output directory. (char) +#' @param runName Character defining the name of the run; +#' default as GridGenome. (char) +#' @return Binned genome saved in output directory +#' export.bins <- function(mylist, out.dir, runName) { names_mylist <- names(mylist) @@ -14,32 +23,126 @@ export.bins <- function(mylist, out.dir, runName) }) } -#' +#----------------------------------------------------------------------------- +#' Main function to bin genome using non/sliding window approach +#' @param x1 Index of the set of window/step size to be checked; in single-mode +#' it is set to 1. (num) +#' @param window Bin size in non/sliding window approach. (num) +#' @param step Step size in non/sliding window approach. (num) +#' @param gr GenomicRanges object of the start-end positions within genome. +#' (GenomicRanges object) +#' @param cyt_gr GenomicRanges object of cytosines for all contexts. +#' (GenomicRanges object) +#' @param contexts Vector of cytosine contexts; +#' default as c('CG','CHG','CHH'). (char) +#' @param min.C Percentile threshold based on EDF. (num; between 0 and 100) #' @importFrom data.table fread #' @importFrom stats quantile ecdf #' @importFrom IRanges countOverlaps -#' @export +#' @return List of two DataFrame objects with binned genome and statistics +#' how many regions is meeting minC criterion. +#' +binGenomeLoop <- function(x1, window, step, gr, cyt_gr, contexts, min.C) { + window.size <- window[x1] + step.size <- step[x1] + # Binning genome + binned.g <- slidingWindows(gr, window.size, step.size) + message("Binning genome with windows of: ", window.size, + "bp and step-size of: ", step.size, "bp.") + # Creating a data frame from the binned data + dd <- data.frame(unlist(binned.g)) + names(dd) <- c("chr", "start", "end", "cluster.length", "strand") + # Storing the data frame in a list + new <- list(dd) + names(new) <- as.numeric(as.character(window.size)) + # Creating a GRange object + data_gr <- GRanges( + seqnames = dd$chr, ranges = IRanges( + start = dd$start, end = dd$end), + clusterlen = dd$cluster.length) + # Creating a data frame for bin and step sizes + mydf <- data.frame(bin.size = window.size, step.size = step.size) + # Process each context using lapply and combine the results + results <- lapply(contexts, function(cx) { + message("Extracting cytosines for ", cx, ".") + # Filtering cytosines + ref_gr <- cyt_gr[which(cyt_gr$context == cx),] + # Counting cytosines in GRanges + dat.collect <- countOverlaps(data_gr, ref_gr) + # Create a empirical distribution of cytosines within bins and + # find a threshold based on its min.C percentile + #new.dat.collect <- dat.collect[which(dat.collect >= min.C)] + new.dat.collect <- dat.collect[which(dat.collect >= as.numeric( + quantile(ecdf(dat.collect),min.C/100)))] + non.empty.bins <- length(new.dat.collect) / length(dat.collect) + # Create a filtrated data frame + data.out <- dd[which(dat.collect >= as.numeric(quantile( + ecdf(dat.collect),min.C/100))),] + return(list(non.empty.bins, data.out)) + }) + new.one <- lapply(results, function(x) x[[2]]) + names(new.one) <- paste0(contexts, '_', window.size, '_', step.size) + # Add the results to the mydf data frame + mydf <- cbind(mydf,data.frame(context = contexts, ratio = unlist( + lapply(results, function(x) x[[1]])))) + return(list(mydf = mydf, collect.bins = new.one)) +} + +#----------------------------------------------------------------------------- +#' Bin genome using non/sliding window approach +#' @inheritParams binGenomeLoop +#' @inheritParams export.bins +#' @param methimputefiles Vector of paths to text files of the sample reads. +#' (char) +#' @param contexts Vector of cytosine contexts; +#' default as c('CG','CHG','CHH'). (char) +#' @param window Bin size in non/sliding window approach. (num) +#' @param step Step size in non/sliding window approach. (num) +#' @param min.C Percentile threshold based on EDF. (num; between 0 and 100) +#' @param out.dir Path to the output directory. (char) +#' @param runName Character defining the name of the run; +#' default as GridGenome. (char) +#' @param if.Bismark Logical if Bismark inputs (CX reports in txt format) +#' are used. Default as FALSE. (logical) +#' @param FASTA.file Path to the FASTA file; required if Bismark outputs are +#' used. Default as NULL. (char) +#' @importFrom data.table fread rbindlist fwrite +#' @importFrom stats quantile ecdf +#' @importFrom IRanges countOverlaps +#' @importFrom GenomicRanges GRanges +#' @importFrom Biostrings readDNAStringSet +#' @return Binned genome saved in the output directory using non/sliding +#' window approach. #' binGenome <- function( - methimputefiles, contexts, window, step, min.C, out.dir,runName) + methimputefiles, contexts, window, step, min.C, out.dir, runName, + if.Bismark, FASTA.file) { # message about creating grid - message('Creating grid...') - cyt.collect <- list() + message('Creating grid...'); cyt.collect <- list() # from one of the methIMPUTE file extract all cytosines positions meth.out <- fread(methimputefiles[1],showProgress=FALSE) - all.cyt.pos <- meth.out[,c('seqnames','start','strand','context')] + if (if.Bismark == FALSE) { + all.cyt.pos <- meth.out[,c('seqnames','start','strand','context')] + } else { + all.cyt.pos <- meth.out[,c(1,2,3,6)] + } colnames(all.cyt.pos) <- c('chr','pos','strand','context') # create a GRanges object from the cytosines positions cyt_gr <- GRanges(seqnames=all.cyt.pos$chr,ranges=IRanges( start=all.cyt.pos$pos, width=1),context=all.cyt.pos$context, strand=all.cyt.pos$strand) - # get length of chromosomesś - chr.names <- unique(meth.out$seqnames) - chr.lengths <- unlist( - lapply(chr.names, function(x) max( - meth.out$start[meth.out$seqnames == x]))) - names(chr.lengths) <- chr.names + # get length of chromosomes + if (is.null(FASTA.file)) { + chr.names <- unique(meth.out$seqnames) + chr.lengths <- unlist( + lapply(chr.names, function(x) max( + meth.out$start[meth.out$seqnames == x]))) + names(chr.lengths) <- chr.names + } else { + fasta.out <- readDNAStringSet(FASTA.file) + chr.lengths <- unlist(lapply(fasta.out, length)) + } # create a GRanges object from the chromosome (fasta) start-end positions gr <- GRanges(seqnames=names(chr.lengths),ranges=IRanges( start=1, end=chr.lengths)) @@ -47,51 +150,9 @@ binGenome <- function( if (length(window) != length(step)) { message('Window and step vectors sizes must have same length.') } else { - results <- lapply(seq_along(window), function(x1) { - window.size <- window[x1] - step.size <- step[x1] - # Binning genome - binned.g <- slidingWindows(gr, window.size, step.size) - message("Binning genome with windows of: ", window.size, - "bp and step-size of: ", step.size, "bp.") - # Creating a data frame from the binned data - dd <- data.frame(unlist(binned.g)) - names(dd) <- c("chr", "start", "end", "cluster.length", "strand") - # Storing the data frame in a list - new <- list(dd) - names(new) <- as.numeric(as.character(window.size)) - # Creating a GRange object - data_gr <- GRanges( - seqnames = dd$chr, ranges = IRanges( - start = dd$start, end = dd$end), - clusterlen = dd$cluster.length) - # Creating a data frame for bin and step sizes - mydf <- data.frame(bin.size = window.size, step.size = step.size) - # Process each context using lapply and combine the results - results <- lapply(contexts, function(cx) { - message("Extracting cytosines for ", cx, ".") - # Filtering cytosines - ref_gr <- cyt_gr[which(cyt_gr$context == cx),] - # Counting cytosines in GRanges - dat.collect <- countOverlaps(data_gr, ref_gr) - # Create a empirical distribution of cytosines within bins and - # find a threshold based on its min.C percentile - #new.dat.collect <- dat.collect[which(dat.collect >= min.C)] - new.dat.collect <- dat.collect[which(dat.collect >= as.numeric( - quantile(ecdf(dat.collect),min.C/100)))] - non.empty.bins <- length(new.dat.collect) / length(dat.collect) - # Create a filtrated data frame - data.out <- dd[which(dat.collect >= as.numeric(quantile( - ecdf(dat.collect),min.C/100))),] - return(list(non.empty.bins, data.out)) - }) - new.one <- lapply(results, function(x) x[[2]]) - names(new.one) <- paste0(contexts, '_', window.size, '_', step.size) - # Add the results to the mydf data frame - mydf <- cbind(mydf,data.frame(context = contexts, ratio = unlist( - lapply(results, function(x) x[[1]])))) - return(list(mydf = mydf, collect.bins = new.one)) - }) + results <- lapply( + seq_along(window), binGenomeLoop, window = window, step = step, + gr = gr, cyt_gr = cyt_gr, contexts = contexts, min.C = min.C) out <- rbindlist(lapply(results, function(x) x$mydf)) out <- out[order(out$context, out$bin.size, out$step.size),] fwrite(out,file = paste0( @@ -100,29 +161,185 @@ binGenome <- function( #mybins <- lapply(out, function(x) x[which.min(x$ratio),]) collect.bins <- lapply(results, function(x) x$collect.bins) message("Exporting regions...") - lapply( - collect.bins, function(x) export.bins( - mylist=x, out.dir=out.dir,runName=runName)) + lapply(collect.bins, function(x) export.bins( + mylist=x, out.dir=out.dir,runName=runName)) return(list.files(out.dir, pattern=paste0( - ".*", runName, ".*\\.Rdata$"),full.names=TRUE)) + ".*", runName, ".*\\.Rdata$"), full.names=TRUE)) } - message("Done!") } + #----------------------------------------------------------------------------- -#' Run jDMR on binned genome +#' Run makeMethimpute using future_apply parallel method +#' @inheritParams makeMethimpute +#' @param out.samplelist DataFrame consisting of: contexts, methImpute files, +#' sample names (from methImpute files) and IDs +#' corresponding to the binned genome. (DataFrame object) +#' @param merge_list List of DataFrames with binned regions; for each context +#' separately (list of DataFrame objects) +#' @param include.intermediate Logical if intermediate calls should be used; +#' default as FALSE. (logical) +#' @param out.dir Path to the output directory. (char) +#' @param mincov Minimum read coverage; default as 0. (num; between 0 and 1) +#' @param if.Bismark Logical if Bismark inputs (CX reports in txt format) +#' are used. Default as FALSE. (logical) +#' @param cyt.pos.all GRanges object from extractCytosinesFromFASTA. (GRanges) +#' @import magrittr +#' @import future +#' @import future.apply +#' @import doParallel +#' @return Methylome for regions taken out grid genome from non/sliding window +#' approach +#' +makeMethimpute_future <- function( + out.samplelist, merge_list, include.intermediate, out.dir, mincov, + if.Bismark, cyt.pos.all) +{ + plan(multisession) + info_lapply <- future_lapply( + seq_along(out.samplelist$context), function(j) { + refRegion <- list(reg.obs = merge_list[[out.samplelist$id[j]]]) + message("Running file: ",out.samplelist$methfn[j]," for context: ", + out.samplelist$context[j], "\n") + grid.out <- makeMethimpute( + df = as.character(out.samplelist$file[j]), + context = out.samplelist$context[j], + refRegion = refRegion, fit.plot = FALSE, + include.intermediate = include.intermediate, + probability = "constrained", out.dir = out.dir, + fit.name = paste0( + basename(out.samplelist$methfn[j]), "_", + out.samplelist$context[j]), + name = basename(out.samplelist$methfn[j]), mincov = mincov, + if.Bismark = if.Bismark, cyt.pos.all = cyt.pos.all)}, + future.seed = NULL) +} + +#----------------------------------------------------------------------------- +#' Run makeMethimpute using future_apply parallel method +#' @inheritParams makeMethimpute +#' @param out.samplelist DataFrame consisting of: contexts, methImpute files, +#' sample names (from methImpute files) and IDs +#' corresponding to the binned genome. (DataFrame object) +#' @param merge_list List of DataFrames with binned regions; for each context +#' separately (list of DataFrame objects) +#' @param include.intermediate Logical if intermediate calls should be used; +#' default as FALSE. (logical) +#' @param out.dir Path to the output directory. (char) +#' @param mincov Minimum read coverage; default as 0. (num; between 0 and 1) +#' @param numCores Number of cores to be used if for_each method should be +#' performed; default as NULL. (num) +#' @param if.Bismark Logical if Bismark inputs (CX reports in txt format) +#' are used. Default as FALSE. (logical) +#' @param cyt.pos.all GRanges object from extractCytosinesFromFASTA. (GRanges) +#' @import magrittr +#' @import foreach +#' @import doParallel +#' @importFrom foreach %dopar% +#' @importFrom parallel makeCluster stopCluster +#' @return Methylome for regions taken out grid genome from non/sliding window +#' approach +#' @export #' -#' this function runs a HMM model on a genome binned -#' using a sliding/non-sliding window approach -#' @param out.dir Output directory. (character) -#' @param window Bin size. (numeric) -#' @param step Step size. (numeric) -#' @param samplefiles Path to the text file. (character) -#' @param contexts Vector of cytosine contexts. (character vector) -#' @param min.C Percentile threshold based on EDF. (numeric between 0 and 100) -#' @param mincov Minimum read coverage. (numeric value between 0 and 1) -#' @param include.intermediate A logical if intermediate calls should be used. -#' @param numCores Number of cores. (numeric) -#' @param parallelApply A logical if futureapply method should be performed. +makeMethimpute_foreach <- function( + out.samplelist, merge_list, include.intermediate, out.dir, mincov, + numCores, if.Bismark, cyt.pos.all) +{ + cl <- makeCluster(numCores) + registerDoParallel(cl) + runMethimputeJ <- function(jj) { + refRegion <- list(reg.obs = merge_list[[out.samplelist$id[jj]]]) + message("Running file: ", out.samplelist$methfn[jj], + " for context: ", out.samplelist$context[jj], "\n") + grid.out <- makeMethimpute( + df = as.character(out.samplelist$file[jj]), + context = out.samplelist$context[jj], + refRegion = refRegion, fit.plot = FALSE, + include.intermediate = include.intermediate, + probability = "constrained",out.dir = out.dir, + fit.name = paste0( + basename(out.samplelist$methfn[jj]), "_", + out.samplelist$context[jj]), + name = basename(out.samplelist$methfn[jj]), mincov = mincov, + if.Bismark = if.Bismark, cyt.pos.all = cyt.pos.all) + return(grid.out) + } + jk <- NULL + info_lapply <- foreach( + jk = seq_along(out.samplelist$context), .combine = "c", .packages = c( + 'methimpute'), .export = "jk") %dopar% + { + runMethimputeJ(jk) + } + stopCluster(cl) +} + + +#----------------------------------------------------------------------------- +#' Run makeMethimpute using single-core method +#' @inheritParams makeMethimpute +#' @param out.samplelist DataFrame consisting of: contexts, methImpute files, +#' sample names (from methImpute files) and IDs +#' corresponding to the binned genome. (DataFrame object) +#' @param merge_list List of DataFrames with binned regions; for each context +#' separately (list of DataFrame objects) +#' @param include.intermediate Logical if intermediate calls should be used; +#' default as FALSE. (logical) +#' @param out.dir Path to the output directory. (char) +#' @param mincov Minimum read coverage; default as 0. (num; between 0 and 1) +#' @param if.Bismark Logical if Bismark inputs (CX reports in txt format) +#' are used. Default as FALSE. (logical) +#' @param cyt.pos.all GRanges object from extractCytosinesFromFASTA. (GRanges) +#' @return Methylome for regions taken out grid genome from non/sliding window +#' approach +#' +makeMethImpute_normal <- function( + out.samplelist, merge_list, include.intermediate, out.dir, mincov, + if.Bismark, cyt.pos.all) +{ + info_lapply <- lapply(seq_along(out.samplelist$context), function(jn) { + refRegion <- list(reg.obs = merge_list[[out.samplelist$id[jn]]]) + message( + "Running file: ", out.samplelist$methfn[jn], " for context: ", + out.samplelist$context[jn], "\n") + grid.out <- makeMethimpute( + df = as.character(out.samplelist$file[jn]), + context = out.samplelist$context[jn], + refRegion = refRegion, fit.plot = FALSE, + include.intermediate = include.intermediate, + probability = "constrained", out.dir = out.dir, + fit.name = paste0( + basename(out.samplelist$methfn[jn]), "_", + out.samplelist$context[jn]), name = basename( + out.samplelist$methfn[jn]), mincov = mincov, + if.Bismark = if.Bismark, cyt.pos.all = cyt.pos.all) + }) +} + +#----------------------------------------------------------------------------- +#' Run jDMR on binned genome +#' this function runs a HMM model on a genome binned using +#' a sliding/non-sliding window approach +#' @param out.dir Path to the output directory. (char) +#' @param window Bin size in non/sliding window approach. (num) +#' @param step Step size in non/sliding window approach. (num) +#' @param samplelist DataFrame object containing information about +#' file, sample, replicate and group. (DataFrame object) +#' @param contexts Vector of cytosine contexts; +#' default as c('CG','CHG','CHH'). (char) +#' @param min.C Percentile threshold based on EDF. (num; between 0 and 100) +#' @param mincov Minimum read coverage; default as 0. (num; between 0 and 1) +#' @param include.intermediate Logical if intermediate calls should be used; +#' default as FALSE. (logical) +#' @param runName Character defining the name of the run; +#' default as GridGenome. (char) +#' @param numCores Number of cores to be used if for_each method should be +#' performed; default as NULL. (num) +#' @param parallelApply Logical if futureapply method should be performed; +#' default as FALSE. (logical) +#' @param if.Bismark Logical if Bismark inputs (CX reports in txt format) +#' are used; default as FALSE. (logical) +#' @param FASTA.file Path to the FASTA file; required if Bismark outputs are +#' used; default as NULL. (char) #' @import magrittr #' @import future.apply #' @import doParallel @@ -131,123 +348,57 @@ binGenome <- function( #' @importFrom foreach %dopar% #' @importFrom data.table fread fwrite #' @importFrom stringr str_remove_all -#' @importFrom data.table fwrite #' @importFrom IRanges slidingWindows #' @importFrom parallel makeCluster stopCluster +#' @importFrom methimpute extractCytosinesFromFASTA #' @importFrom rlang .data +#' @return Output methylome files for the regions using grid genome from +#' non/sliding window approach. #' @export #' -runjDMRgrid <- function(out.dir, - window, - step, - samplefiles, - contexts=c('CG','CHG','CHH'), - min.C, - mincov=0, - include.intermediate=FALSE, - runName='GridGenome', - numCores = NULL, - parallelApply = FALSE) +runjDMRgrid <- function( + out.dir, window, step, samplelist, contexts=c('CG','CHG','CHH'), + min.C, mincov=0, include.intermediate=FALSE, runName='GridGenome', + numCores = NULL, parallelApply = FALSE, if.Bismark = FALSE, + FASTA.file = NULL) { - # Step 1: Bin genome according to the window and step size + methimputefiles <- samplelist$file bin.genome.files <- binGenome( - methimputefiles=data.table::fread(samplefiles)$file, - contexts=contexts, - window=window, - step=step, - min.C=min.C, - out.dir=out.dir, - runName=runName) - # Step 2: Extract RData for binned regions and name them as contexts + methimputefiles = methimputefiles, contexts = contexts, + window = window, step = step, min.C = min.C, out.dir = out.dir, + runName = runName, if.Bismark = if.Bismark, FASTA.file = FASTA.file) bin.select <- lapply(seq_along(contexts), function(x) { b <- bin.genome.files[grep(contexts[x], bin.genome.files)] if (length(b) != 0) { names(b) <- contexts[x] - return(b) - } - }) + return(b) }}) bin.select <- Filter(Negate(is.null), bin.select) names(bin.select) <- unlist(lapply(bin.select, function(x) names(x)[1])) - # Step 3: Read all RData binned regions merge_list <- lapply(bin.select, function(x) dget(x)) - # Step 4: Read names of methImpute files which needs to be binned - filelist <- data.table::fread(samplefiles, header=TRUE) - # Step 5: Create data frame consisting of: contexts, methImpute files, - # sample names (from methImpute files) - # and IDs corresponding to the binned genome - out.filelist <- expand.grid(file = filelist$file, context = contexts) - out.filelist <- merge(out.filelist, data.frame( + out.samplelist <- expand.grid(file = samplelist$file, context = contexts) + out.samplelist <- merge(out.samplelist, data.frame( context = names(bin.select), id = seq(1,length(names(bin.select))))) - out.filelist$methfn <- unlist(lapply( - seq_along(out.filelist$file),function(xi) - { - gsub(".*methylome_|\\.txt|_All.txt$", "", out.filelist$file[xi])})) - # Step 6: Run makeMethimpute for files in out.filelist - if (parallelApply == TRUE) - { - plan(multisession) - info_lapply <- future_lapply( - seq_along(out.filelist$context), function(j) { - refRegion <- list(reg.obs = merge_list[[out.filelist$id[j]]]) - message("Running file: ", out.filelist$methfn[j], " for context: ", - out.filelist$context[j], "\n") - grid.out <- makeMethimpute( - df = as.character(out.filelist$file[j]), - context = out.filelist$context[j], - refRegion = refRegion, fit.plot = FALSE, - include.intermediate = include.intermediate, - probability = "constrained", out.dir = out.dir, - fit.name = paste0( - basename(out.filelist$methfn[j]), "_", - out.filelist$context[j]), - name = basename(out.filelist$methfn[j]), mincov = mincov) - }) - } - if (is.numeric(numCores) == TRUE) - { - cl <- makeCluster(numCores) - registerDoParallel(cl) - runMethimputeJ <- function(jj) { - refRegion <- list(reg.obs = merge_list[[out.filelist$id[jj]]]) - message("Running file: ", out.filelist$methfn[jj], - " for context: ", out.filelist$context[jj], "\n") - grid.out <- makeMethimpute( - df = as.character(out.filelist$file[jj]), - context = out.filelist$context[jj], - refRegion = refRegion, fit.plot = FALSE, - include.intermediate = include.intermediate, - probability = "constrained",out.dir = out.dir, - fit.name = paste0( - basename(out.filelist$methfn[jj]), "_", - out.filelist$context[jj]), - name = basename(out.filelist$methfn[jj]), mincov = mincov) - return(grid.out) - } - info_lapply <- foreach( - jk = seq_along(out.filelist$context), .combine = "c", .packages = c( - 'jDMRgrid','magrittr', 'methimpute')) %dopar% - { - runMethimputeJ(.data$jk) - } - stopCluster(cl) - } - if (is.null(numCores) & parallelApply == FALSE) - { - info_lapply <- lapply(seq_along(out.filelist$context), function(jn) { - refRegion <- list(reg.obs = merge_list[[out.filelist$id[jn]]]) - message( - "Running file: ", out.filelist$methfn[jn], " for context: ", - out.filelist$context[jn], "\n") - grid.out <- makeMethimpute( - df = as.character(out.filelist$file[jn]), - context = out.filelist$context[jn], - refRegion = refRegion, fit.plot = FALSE, - include.intermediate = include.intermediate, - probability = "constrained", out.dir = out.dir, - fit.name = paste0( - basename(out.filelist$methfn[jn]), "_", - out.filelist$context[jn]), name = basename( - out.filelist$methfn[jn]), mincov = mincov) - }) - } + if (if.Bismark == FALSE) { + out.samplelist$methfn<-unlist(lapply(out.samplelist$file,function(xi){ + gsub(".*methylome_|\\.txt|_All.txt$","",xi)})) + cyt.pos.all<-NULL} else { + out.samplelist$methfn<-unlist(lapply(out.samplelist$file,function(xi){ + gsub("|\\.txt|.CX_report.txt$","",xi)})) + cyt.pos.all<-extractCytosinesFromFASTA( + file = FASTA.file, contexts = contexts)} + if (parallelApply == TRUE) { + makeMethimpute_future( + out.samplelist=out.samplelist,merge_list=merge_list,mincov=mincov, + include.intermediate=include.intermediate,out.dir=out.dir, + if.Bismark=if.Bismark,cyt.pos.all=cyt.pos.all) } + if (is.numeric(numCores) == TRUE) { + makeMethimpute_foreach( + out.samplelist=out.samplelist,merge_list=merge_list,mincov=mincov, + include.intermediate=include.intermediate,out.dir=out.dir, + numCores=numCores,if.Bismark=if.Bismark,cyt.pos.all=cyt.pos.all) } + if (is.null(numCores) & parallelApply == FALSE) { + makeMethImpute_normal( + out.samplelist=out.samplelist,merge_list=merge_list,mincov=mincov, + include.intermediate=include.intermediate,out.dir=out.dir, + if.Bismark=if.Bismark,cyt.pos.all=cyt.pos.all) } } diff --git a/R/split.groups.R b/R/split.groups.R deleted file mode 100644 index a8c248e..0000000 --- a/R/split.groups.R +++ /dev/null @@ -1,66 +0,0 @@ -#' @param samplefiles -#' @param postMax.out -#' @param contexts -#' @param input.dir -#' @param out.dir -#' @import magrittr -#' @importFrom data.table fread fwrite -#' @importFrom dplyr inner_join -#' @export -#' -split.groups <- function( - samplefiles,postMax.out=FALSE,contexts=c("CG","CHG","CHH"),input.dir, - out.dir) - { - ft <- fread(samplefiles) - ft$name <- paste0(ft$sample,"_", ft$replicate) - gps <- ft$group[!ft$group %in% c('control')] - gps <- unique(gps) - for (m in seq_along(gps)){ - myvec <- c("control", gps[m]) - gp1 <- ft$name[which(ft$group==myvec[1])] - gp2 <- ft$name[which(ft$group==myvec[2])] - gp1.sample <- unique(ft$sample[which(ft$name==gp1)]) - gp2.sample <- unique(ft$sample[which(ft$name==gp2)]) - out.name <- paste0(gp1.sample, "_", gp2.sample) - for (cn in seq_along(contexts)){ - fn1 <- paste0(input.dir, '/', contexts[cn], "_StateCalls.txt") - if (file.exists(fn1)) { - StateCall <- fread(fn1) - df1 <- subset( - StateCall,, which(colnames(StateCall) %in% c( - 'seqnames','start','end', gp1, gp2))) - fwrite(x=df1, file=paste0( - out.dir, "/", contexts[cn], "_", - out.name, "_StateCalls.txt"), quote=FALSE, row.names=FALSE, - col.names=TRUE, sep="\t") - } - - fn2 <- paste0(input.dir, '/', contexts[cn], "_rcMethlvl.txt") - if (file.exists(fn2)) { - rcMethlvl <- fread(fn2) - df2 <- subset( - rcMethlvl,, which(colnames(rcMethlvl) %in% c( - 'seqnames', 'start', 'end', gp1, gp2))) - fwrite(x=df2, file=paste0( - out.dir, "/", contexts[cn], "_", out.name, - "_rcMethlvl.txt"), quote=FALSE, row.names=FALSE, - col.names=TRUE, sep="\t") - } - if (postMax.out==TRUE){ - fn3 <- paste0(input.dir, '/', contexts[cn], "_postMax.txt") - if (file.exists(fn3)) { - postMax <- fread(fn3) - df3 <- subset( - postMax,, which(colnames(postMax) %in% c( - 'seqnames', 'start', 'end', gp1, gp2))) - fwrite( - x=df3,file=paste0( - out.dir, "/", contexts[cn], "_", - out.name, "_postMax.txt"), quote=FALSE, - row.names=FALSE, col.names=TRUE, sep="\t") - } - } - } - } -} diff --git a/R/splitGroups.R b/R/splitGroups.R new file mode 100644 index 0000000..6d6b037 --- /dev/null +++ b/R/splitGroups.R @@ -0,0 +1,80 @@ +#------------------------------------------------------------------------------ +#' Save subset dataset by control/treatment for the next analyses +#' @param input.dir Path to the input directory. (char) +#' @param context Methylation context; 'CG' or 'CHG' or 'CHH'. (char) +#' @param gp1 Filename for group 1. (char) +#' @param gp2 Filename for group 2. (char) +#' @param out.name Group name, as the part of the output filename +#' sample_treatment. (char) +#' @param type.name Type name, as the part of the output filename +#' (_StateCalls.txt or _rcMethlvl.txt or _postMax.txt). (char) +#' @import magrittr +#' @importFrom dplyr inner_join +#' @importFrom data.table fread fwrite +#' @return Dataset split by the sample/treatment pairs +#' saved in the output directory +#' +saveSplitDataset <- function( + input.dir, context, gp1, gp2, out.dir, out.name, type.name) +{ + fname <- paste0(input.dir, '/', context, type.name) + if (file.exists(fname)) { + data <- fread(fname) + df1 <- subset( + data,, which(colnames(data) %in% c( + 'seqnames','start','end', gp1, gp2))) + fwrite(x=df1, file=paste0( + out.dir, "/", context, "_", out.name, type.name), quote=FALSE, + row.names=FALSE, col.names=TRUE, sep="\t") + } +} + +#------------------------------------------------------------------------------ +#' Split into control/treatment groups according to the sample and replicates +#' @inheritParams saveSplitDataset +#' @param samplelist DataFrame object containing information about +#' file, sample, replicate and group. (DataFrame object) +#' @param postMax.out Logical if postMax matrices should be included. (logical) +#' @param contexts Vector of cytosine contexts; default as c('CG','CHG','CHH'). +#' (char) +#' @param input.dir Path to the input directory with DMR matrices. (char) +#' @param out.dir Path to the output directory for DMR matrices. (char) +#' @import magrittr +#' @importFrom data.table fread +#' @importFrom dplyr inner_join +#' @return DMR matrices split by sample/treatment groups, saved in the same +#' directory with DMR matrices. +#' @export +#' +splitGroups <- function( + samplelist, postMax.out=FALSE, contexts=c("CG","CHG","CHH"), input.dir, + out.dir) +{ + samplelist$name <- paste0(samplelist$sample,"_", samplelist$replicate) + gps <- samplelist$group[!samplelist$group %in% c('control')] + gps <- unique(gps) + for (m in seq_along(gps)){ + myvec <- c("control", gps[m]) + gp1 <- samplelist$name[which(samplelist$group==myvec[1])] + gp2 <- samplelist$name[which(samplelist$group==myvec[2])] + gp1.sample <- unique(samplelist$sample[which(samplelist$name==gp1)]) + gp2.sample <- unique(samplelist$sample[which(samplelist$name==gp2)]) + out.name <- paste0(gp1.sample, "_", gp2.sample) + for (cn in seq_along(contexts)){ + saveSplitDataset( + input.dir = input.dir, context = contexts[cn], gp1 = gp1, + gp2 = gp2, out.name = out.name, out.dir = out.dir, + type.name = "_StateCalls.txt") + saveSplitDataset( + input.dir = input.dir, context = contexts[cn], gp1 = gp1, + gp2 = gp2, out.dir = out.dir, out.name = out.name, + type.name = "_rcMethlvl.txt") + if (postMax.out==TRUE) { + saveSplitDataset( + input.dir = input.dir, context = contexts[cn], gp1 = gp1, + gp2 = gp2, out.dir = out.dir, out.name = out.name, + type.name = "_postMax.txt") + } + } + } +} \ No newline at end of file diff --git a/README.md b/README.md index ff6ae1b..3a15760 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # jDMRgrid ## Description -...jDMRgrid is a component of the jDMR toolkit, an essential tool for conducting efficient and heuristic DMR (Differentially Methylated Region) calling in large-scale epigenomic studies involving population-level analyses and control/treatment experiments. Its functionality relies on a grid-based methodology that involves dividing the genome into sliding windows or bins of customizable sizes. It determines methylation state calls for each individual sliding window based on a Hidden Markov Model (HMM) approach. Subsequently, these calls are consolidated into a matrix format by merging data from all samples. Additionally, user can perform a filtration of DMR matrix to remove non-polymorphic patterns from the merged matrix. +jDMRgrid is a tool for conducting efficient and heuristic DMR (Differentially Methylated Region) calling in population-level or control/treatment WGBS data. Its functionality relies on a grid-based methodology that involves dividing the genome into sliding windows or bins of customizable sizes. For each sample and sliding window methylation state calls are obtained via a Hidden Markov Model (HMM). These calls are then consolidated into a DMR matrix format. ## Installing from the Github @@ -13,14 +13,15 @@ To install from GitHub (development version), follow the steps given below. ```sh install.packages("devtools") library(devtools) -devtools::install_github("robert-piecyk/jDMRgrid") +devtools::install_github("jlab-code/jDMRgrid") ``` ## How to use? -Please open the [vignette](https://github.com/robert-piecyk/jDMRgrid/blob/main/vignettes/manual.pdf) file. +Please open the [vignette](https://github.com/jlab-code/jDMRgrid/blob/master/vignettes/manual.pdf) file. ## Contributors ##### Robert Piecyk - robert.piecyk@tum.de ##### Rashmi Hazarika - rashmi.hazarika@tum.de ##### Yadi Shahryary - y.shahryary@tum.de ##### Frank Johannes - frank@johanneslab.org +##### Ming Zhou - ming.zhou@tum.de diff --git a/data/listFiles1.RData b/data/listFiles1.RData new file mode 100644 index 0000000..f64364d Binary files /dev/null and b/data/listFiles1.RData differ diff --git a/data/listFiles2.RData b/data/listFiles2.RData new file mode 100644 index 0000000..9e2d06a Binary files /dev/null and b/data/listFiles2.RData differ diff --git a/inst/extdata/Run_script_jDMRgrid.R b/inst/extdata/Run_script_jDMRgrid.R deleted file mode 100644 index e5a6c62..0000000 --- a/inst/extdata/Run_script_jDMRgrid.R +++ /dev/null @@ -1,115 +0,0 @@ -#------------------------------------------------------------------------------- -# Install jDMRgrid -#------------------------------------------------------------------------------- -rm(list=ls()) -library(devtools) -devtools::install_github("robert-piecyk/jDMRgrid") -library(jDMRgrid) -home_dir <- getwd() -#------------------------------------------------------------------------------- -# Step 1: Run jDMR using grid approach -#------------------------------------------------------------------------------- -sample.files.1 <- system.file("extdata", "listFiles1.fn", package="jDMRgrid") -sample.files.2 <- system.file("extdata", "listFiles2.fn", package="jDMRgrid") -runjDMRgrid(out.dir = 'jDMRgrid_test/folder_population/grid', - window = 200, - step = 50, - samplefiles = sample.files.1, - contexts = c("CG", "CHG", "CHH"), - min.C = 10, - mincov = 0, - include.intermediate = FALSE, - runName = "Arabidopsis") - -runjDMRgrid(out.dir = 'jDMRgrid_test/folder_replicate/grid', - window = 200, - step = 50, - samplefiles = sample.files.2, - contexts = c("CG", "CHG", "CHH"), - min.C = 10, - mincov = 0, - include.intermediate = TRUE, - runName = "Arabidopsis") - -#------------------------------------------------------------------------------- -# Step 2: Generate DMR matrix -#------------------------------------------------------------------------------- -makeDMRmatrix(contexts = c("CG", "CHG", "CHH"), - postMax.out = TRUE, - samplefiles = sample.files.1, - input.dir = 'jDMRgrid_test/folder_population/grid', - out.dir = 'jDMRgrid_test/folder_population/matrix', - include.intermediate = FALSE) - -makeDMRmatrix(contexts = c("CG", "CHG", "CHH"), - postMax.out = TRUE, - samplefiles = sample.files.2, - input.dir = 'jDMRgrid_test/folder_replicate/grid', - out.dir = 'jDMRgrid_test/folder_replicate/matrix', - include.intermediate = FALSE) - -#------------------------------------------------------------------------------- -# Run this step only if you have multiple treatment groups and -# you want to perform pairwise comparisons with -# each of the treatment groups with control. -# This function will split the DMR matrix into -# pairwise control-treatment groups. -# Refer to section 1.2 in the manual. -# The metadata file requires an additional column "group" -#------------------------------------------------------------------------------- -split.groups(samplefiles = sample.files.2, - input.dir = "jDMRgrid_test/folder_replicate/matrix", - out.dir = "jDMRgrid_test/folder_replicate/matrix") - -#------------------------------------------------------------------------------- -# Step 3: Filter the DMR matrix -#------------------------------------------------------------------------------- -filterDMRmatrix(epiMAF.cutoff = 0.33, - replicate.consensus = NULL, - data.dir = "jDMRgrid_test/folder_population/matrix", - samplefiles = sample.files.1) - -filterDMRmatrix(epiMAF.cutoff = NULL, - replicate.consensus = 0.8, - data.dir = "jDMRgrid_test/folder_replicate/matrix", - samplefiles = sample.files.2) - -#------------------------------------------------------------------------------- -# Step 4: Generate context-specific DMRs -#------------------------------------------------------------------------------- -output.dir.1 <- "jDMRgrid_test/folder_population/context_DMRs" -output.dir.2 <- "jDMRgrid_test/folder_replicate/context_DMRs" -context.specific.DMRs(samplefiles = sample.files.1, - output.dir = output.dir.1, - input.dir = "jDMRgrid_test/folder_population/matrix") - -context.specific.DMRs(samplefiles = sample.files.2, - output.dir = output.dir.2, - input.dir = "jDMRgrid_test/folder_replicate/matrix") - -#------------------------------------------------------------------------------- -# Step 5: Annotate DMRs. Please create a new folder and move all files to -# be annotated into the new folder -#------------------------------------------------------------------------------- -data.dir.pop <- "jDMRgrid_test/folder_population/annotate_DMRs" -data.dir.rep <- "jDMRgrid_test/folder_replicate/annotate_DMRs" -gff.file_promoters <- system.file("extdata/toyData", - "TAIR10_promoters.gff3", - package="jDMRgrid") -gff.file_TE <- system.file("extdata/toyData", - "TAIR10_TE.gff3", - package="jDMRgrid") -gff.file_genes <- system.file("extdata/toyData", - "TAIR10.gene.chr1.gff3", - package="jDMRgrid") - -annotateDMRs(gff.files = c(gff.file_promoters, gff.file_TE, gff.file_genes), - annotation = c("promoters", "TE", "gene"), - input.dir = "jDMRgrid_test/folder_population/context_DMRs", - gff3.out = FALSE, - out.dir = data.dir.pop) -annotateDMRs(gff.files = c(gff.file_promoters, gff.file_TE, gff.file_genes), - annotation = c("promoters", "TE", "gene"), - input.dir = "jDMRgrid_test/folder_replicate/context_DMRs", - gff3.out = FALSE, - out.dir = data.dir.rep) diff --git a/inst/extdata/grid_population/Arabidopsis_Win200_Step50_CG.Rdata b/inst/extdata/grid_population/Arabidopsis_Win200_Step50_CG.Rdata new file mode 100644 index 0000000..acc1c50 --- /dev/null +++ b/inst/extdata/grid_population/Arabidopsis_Win200_Step50_CG.Rdata @@ -0,0 +1,2509 @@ +structure(list(chr = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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start end context posteriorMax status rc.meth.lvl +1 1 200 CG 0.99926 U 0.0552 +1 51 250 CG 0.76587 U 0.15819 +1 101 300 CG 0.76587 U 0.15819 +1 151 350 CG 0.6289 M 0.73853 +1 201 400 CG 0.6289 M 0.73853 +1 251 450 CG 0.6289 M 0.73853 +1 301 500 CG 0.6289 M 0.73853 +1 351 550 CG 0.33333 U 0.48454 +1 401 600 CG 0.33333 U 0.48454 +1 451 650 CG 0.6289 M 0.73853 +1 501 700 CG 0.77849 M 0.81782 +1 551 750 CG 0.77849 M 0.81782 +1 601 800 CG 0.84641 U 0.12087 +1 651 850 CG 0.97985 U 0.06354 +1 701 900 CG 0.99767 U 0.05588 +1 751 950 CG 0.99962 U 0.05505 +1 801 1000 CG 0.85986 U 0.11537 +1 851 1050 CG 0.85986 U 0.11537 +1 901 1100 CG 0.85986 U 0.11537 +1 1151 1350 CG 0.44734 M 0.50804 +1 1201 1400 CG 0.33333 U 0.48454 +1 1251 1450 CG 0.61118 U 0.24578 +1 1301 1500 CG 0.61118 U 0.24578 +1 1351 1550 CG 0.76587 U 0.15819 +1 1401 1600 CG 0.76587 U 0.15819 +1 1451 1650 CG 0.85986 U 0.11537 +1 1501 1700 CG 0.85986 U 0.11537 +1 1551 1750 CG 0.76587 U 0.15819 +1 1601 1800 CG 0.76587 U 0.15819 +1 1651 1850 CG 0.33333 U 0.48454 +1 1701 1900 CG 0.33333 U 0.48454 +1 1751 1950 CG 0.33333 U 0.48454 +1 1801 2000 CG 0.33333 U 0.48454 +1 1851 2050 CG 0.33333 U 0.48454 +1 1901 2100 CG 0.33333 U 0.48454 +1 1951 2150 CG 0.33333 U 0.48454 +1 2001 2200 CG 0.65713 I 0.51457 +1 2051 2250 CG 0.65713 I 0.51457 +1 2101 2300 CG 0.65713 I 0.51457 +1 2151 2350 CG 0.65713 I 0.51457 +1 2201 2400 CG 0.61118 U 0.24578 +1 2251 2450 CG 0.61118 U 0.24578 +1 2301 2500 CG 0.61118 U 0.24578 +1 2351 2550 CG 0.61118 U 0.24578 +1 2401 2600 CG 0.33333 U 0.48454 +1 2451 2650 CG 0.33333 U 0.48454 +1 2501 2700 CG 0.33333 U 0.48454 +1 2551 2750 CG 0.33333 U 0.48454 +1 2601 2800 CG 0.33333 U 0.48454 +1 2651 2850 CG 0.33333 U 0.48454 +1 2701 2900 CG 0.99917 M 0.91384 +1 2751 2950 CG 0.99956 M 0.91401 +1 2801 3000 CG 0.99999 M 0.9142 +1 2851 3050 CG 0.99999 M 0.9142 +1 2901 3100 CG 0.99999 M 0.9142 +1 2951 3150 CG 0.99999 M 0.9142 +1 3001 3200 CG 0.99998 M 0.91419 +1 3051 3250 CG 0.99997 M 0.91419 +1 3101 3300 CG 0.99993 M 0.91417 +1 3151 3350 CG 0.99976 M 0.9141 +1 3201 3400 CG 0.61879 I 0.63582 +1 3251 3450 CG 0.61879 I 0.63582 +1 3301 3500 CG 0.65713 I 0.51457 +1 3351 3550 CG 0.61118 U 0.24578 +1 3401 3600 CG 0.61118 U 0.24578 +1 3451 3650 CG 0.61118 U 0.24578 +1 3501 3700 CG 0.77849 M 0.81782 +1 3551 3750 CG 0.9995 M 0.91399 +1 3601 3800 CG 0.90368 M 0.87282 +1 3651 3850 CG 0.60964 M 0.74648 +1 3701 3900 CG 0.54711 I 0.67913 +1 3751 3950 CG 0.70122 U 0.18329 +1 3801 4000 CG 0.69778 I 0.38603 +1 3851 4050 CG 0.65713 I 0.51457 +1 3901 4100 CG 0.61118 U 0.24578 +1 3951 4150 CG 0.6289 M 0.73853 +1 4001 4200 CG 0.92684 M 0.88276 +1 4051 4250 CG 0.92684 M 0.88276 +1 4101 4300 CG 0.92684 M 0.88276 +1 4151 4350 CG 0.87023 M 0.85836 +1 4201 4400 CG 0.33333 U 0.48454 +1 4251 4450 CG 0.33333 U 0.48454 +1 4301 4500 CG 0.33333 U 0.48454 +1 4351 4550 CG 0.6289 M 0.73853 +1 4401 4600 CG 0.6289 M 0.73853 +1 4451 4650 CG 0.6289 M 0.73853 +1 4501 4700 CG 0.6289 M 0.73853 +1 4551 4750 CG 0.6289 M 0.73853 +1 4601 4800 CG 0.6289 M 0.73853 +1 4651 4850 CG 0.6289 M 0.73853 +1 4701 4900 CG 0.6289 M 0.73853 +1 4751 4950 CG 0.33333 U 0.48454 +1 4801 5000 CG 0.33333 U 0.48454 +1 4851 5050 CG 0.33333 U 0.48454 +1 4901 5100 CG 0.33333 U 0.48454 +1 4951 5150 CG 0.33333 U 0.48454 +1 5001 5200 CG 0.96393 M 0.8987 +1 5051 5250 CG 0.96393 M 0.8987 +1 5101 5300 CG 0.96393 M 0.8987 +1 5151 5350 CG 0.96393 M 0.8987 +1 5201 5400 CG 0.6289 M 0.73853 +1 5251 5450 CG 0.6289 M 0.73853 +1 5301 5500 CG 0.6289 M 0.73853 +1 5351 5550 CG 0.77849 M 0.81782 +1 5401 5600 CG 0.6289 M 0.73853 +1 5451 5650 CG 0.77849 M 0.81782 +1 5501 5700 CG 0.77849 M 0.81782 +1 5551 5750 CG 0.6289 M 0.73853 +1 5601 5800 CG 0.6289 M 0.73853 +1 5651 5850 CG 0.6289 M 0.73853 +1 5701 5900 CG 0.6289 M 0.73853 +1 5751 5950 CG 0.6289 M 0.73853 +1 5801 6000 CG 0.6289 M 0.73853 +1 5851 6050 CG 0.85986 U 0.11537 +1 5901 6100 CG 0.85986 U 0.11537 +1 5951 6150 CG 0.58582 I 0.31097 +1 6001 6200 CG 0.58582 I 0.31097 +1 6051 6250 CG 0.6289 M 0.73853 +1 6101 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+1 218451 218650 CHG 0.85849 U 0.13072 +1 218501 218700 CHG 0.76322 U 0.17229 +1 218551 218745 CHG 0.76322 U 0.17229 diff --git a/inst/extdata/grid_population/methimpute_p1_CHH.txt b/inst/extdata/grid_population/methimpute_p1_CHH.txt new file mode 100644 index 0000000..a5f091b --- /dev/null +++ b/inst/extdata/grid_population/methimpute_p1_CHH.txt @@ -0,0 +1,3964 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CHH 0.99999 I 0.49604 +1 51 250 CHH 0.99999 I 0.49604 +1 101 300 CHH 0.99996 I 0.49605 +1 151 350 CHH 0.99961 M 0.83576 +1 201 400 CHH 0.99999 M 0.83589 +1 251 450 CHH 0.99966 M 0.83578 +1 301 500 CHH 0.99117 M 0.83289 +1 351 550 CHH 0.99887 I 0.49642 +1 401 600 CHH 0.99999 I 0.49604 +1 451 650 CHH 0.99999 I 0.49604 +1 501 700 CHH 0.99999 I 0.49604 +1 551 750 CHH 0.99671 M 0.83478 +1 601 800 CHH 0.99999 M 0.83589 +1 651 850 CHH 0.99999 M 0.83589 +1 701 900 CHH 0.99999 M 0.83589 +1 751 950 CHH 0.99999 M 0.83589 +1 801 1000 CHH 0.8629 I 0.46676 +1 851 1050 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0.49637 +1 216301 216500 CHH 0.99999 I 0.49604 +1 216351 216550 CHH 0.99997 I 0.49605 +1 216401 216600 CHH 0.94911 U 0.17348 +1 216451 216650 CHH 0.96053 U 0.1696 +1 216501 216700 CHH 0.97093 I 0.48616 +1 216551 216750 CHH 0.99999 U 0.15618 +1 216601 216800 CHH 0.97672 I 0.49137 +1 216651 216850 CHH 0.67399 I 0.60018 +1 216701 216900 CHH 0.91703 I 0.49885 +1 216751 216950 CHH 0.99986 M 0.83585 +1 216801 217000 CHH 0.99999 M 0.83589 +1 216851 217050 CHH 0.99999 M 0.83589 +1 216901 217100 CHH 0.99999 M 0.83589 +1 216951 217150 CHH 0.99941 M 0.83569 +1 217001 217200 CHH 0.89214 I 0.53263 +1 217051 217250 CHH 0.74027 U 0.24446 +1 217101 217300 CHH 0.97403 U 0.16501 +1 217151 217350 CHH 0.87583 U 0.19838 +1 217201 217400 CHH 0.78808 U 0.2282 +1 217251 217450 CHH 0.96774 I 0.48612 +1 217301 217500 CHH 0.67399 I 0.60018 +1 217351 217550 CHH 0.99999 M 0.83589 +1 217401 217600 CHH 0.99999 M 0.83589 +1 217451 217650 CHH 0.99999 M 0.83589 +1 217501 217700 CHH 0.99999 M 0.83589 +1 217551 217750 CHH 0.91186 I 0.51804 +1 217601 217800 CHH 0.99984 U 0.15624 +1 217651 217850 CHH 0.61437 I 0.36498 +1 217751 217950 CHH 0.93414 I 0.47366 +1 217801 218000 CHH 0.61437 I 0.36498 +1 217851 218050 CHH 0.99999 U 0.15618 +1 217901 218100 CHH 0.99999 U 0.15618 +1 217951 218150 CHH 0.99999 U 0.15618 +1 218001 218200 CHH 0.99999 U 0.15618 +1 218051 218250 CHH 0.99999 U 0.15618 +1 218101 218300 CHH 0.99991 U 0.15621 +1 218151 218350 CHH 0.972 I 0.5032 +1 218201 218400 CHH 0.98451 I 0.50004 +1 218251 218450 CHH 0.99695 M 0.83486 +1 218301 218500 CHH 0.99883 M 0.8355 +1 218401 218600 CHH 0.99982 M 0.83583 +1 218451 218650 CHH 0.57743 I 0.63935 +1 218501 218700 CHH 0.56356 U 0.30603 +1 218551 218745 CHH 0.7294 I 0.58797 diff --git a/inst/extdata/grid_population/methimpute_p2_CG.txt b/inst/extdata/grid_population/methimpute_p2_CG.txt new file mode 100644 index 0000000..d97366f --- /dev/null +++ b/inst/extdata/grid_population/methimpute_p2_CG.txt @@ -0,0 +1,4248 @@ +seqnames start end context 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0.37512 +1 187651 187850 CHG 0.6709 I 0.37512 +1 187701 187900 CHG 0.53351 I 0.30071 +1 187751 187950 CHG 0.86892 U 0.12338 +1 187801 188000 CHG 0.7769 U 0.16489 +1 187851 188050 CHG 0.99818 U 0.06678 +1 187901 188100 CHG 0.99659 U 0.06748 +1 187951 188150 CHG 0.97462 U 0.07708 +1 188001 188200 CHG 0.98633 U 0.07196 +1 188051 188250 CHG 0.6709 I 0.37512 +1 188101 188300 CHG 0.89975 I 0.49908 +1 188151 188350 CHG 0.89256 I 0.46088 +1 188201 188400 CHG 0.98207 U 0.07382 +1 188251 188450 CHG 0.98207 U 0.07382 +1 188301 188500 CHG 0.99932 U 0.06628 +1 188351 188550 CHG 0.99968 U 0.06613 +1 188401 188600 CHG 0.6709 I 0.37512 +1 188451 188650 CHG 0.6709 I 0.37512 +1 188501 188700 CHG 0.67955 I 0.49667 +1 188551 188750 CHG 0.67955 I 0.49667 +1 188601 188800 CHG 0.99659 U 0.06748 +1 188651 188850 CHG 0.55404 U 0.26091 +1 188701 188900 CHG 0.92021 I 0.4682 +1 188751 188950 CHG 0.98897 U 0.07081 +1 188801 189000 CHG 0.99757 I 0.50414 +1 188851 189050 CHG 0.99962 I 0.50324 +1 188901 189100 CHG 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201050 CHG 0.99787 I 0.50215 +1 200901 201100 CHG 0.99822 U 0.06677 +1 200951 201150 CHG 0.99999 U 0.06599 +1 201001 201200 CHG 0.99998 U 0.066 +1 201051 201250 CHG 0.99999 U 0.06599 +1 201101 201300 CHG 0.90696 I 0.53742 +1 201151 201350 CHG 0.84901 I 0.5683 +1 201201 201400 CHG 0.99475 I 0.50495 +1 201251 201450 CHG 0.96337 M 0.92416 +1 201301 201500 CHG 0.88278 M 0.88894 +1 201351 201550 CHG 0.90158 I 0.5461 +1 201401 201600 CHG 0.80119 M 0.85327 +1 201451 201650 CHG 0.89975 I 0.49908 +1 201501 201700 CHG 0.6709 I 0.37512 +1 201551 201750 CHG 0.33333 U 0.50308 +1 201601 201800 CHG 0.62653 U 0.24677 +1 201651 201850 CHG 0.86892 U 0.12338 +1 201701 201900 CHG 0.99497 M 0.93797 +1 201751 201950 CHG 0.99497 M 0.93797 +1 201801 202000 CHG 0.99939 M 0.9399 +1 201851 202050 CHG 0.99999 M 0.94017 +1 201901 202100 CHG 0.62653 U 0.24677 +1 201951 202150 CHG 0.7769 U 0.16489 +1 202001 202200 CHG 0.86892 U 0.12338 +1 202051 202250 CHG 0.86892 U 0.12338 +1 202101 202300 CHG 0.7769 U 0.16489 +1 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CHH 0.99999 U 0.17242 +1 209301 209500 CHH 0.99999 U 0.17242 +1 209351 209550 CHH 0.99999 U 0.17242 +1 209401 209600 CHH 0.99999 U 0.17242 +1 209451 209650 CHH 0.9966 U 0.17355 +1 209501 209700 CHH 0.99675 U 0.1735 +1 209551 209750 CHH 0.99888 U 0.17279 +1 209601 209800 CHH 0.99979 M 0.83662 +1 209651 209850 CHH 0.99993 M 0.83666 +1 209701 209900 CHH 0.99946 I 0.50473 +1 209751 209950 CHH 0.99311 I 0.50227 +1 209801 210000 CHH 0.99999 U 0.17242 +1 209851 210050 CHH 0.99999 U 0.17242 +1 209901 210100 CHH 0.99999 U 0.17242 +1 209951 210150 CHH 0.91488 U 0.20069 +1 210001 210200 CHH 0.55916 I 0.35821 +1 210051 210250 CHH 0.54714 I 0.35453 +1 210101 210300 CHH 0.79912 I 0.49574 +1 210301 210500 CHH 0.99999 I 0.50456 +1 210351 210550 CHH 0.99999 I 0.50456 +1 210401 210600 CHH 0.99999 I 0.50456 +1 210451 210650 CHH 0.99996 M 0.83668 +1 210501 210700 CHH 0.99999 I 0.50456 +1 210551 210750 CHH 0.99999 I 0.50456 +1 210601 210800 CHH 0.99999 I 0.50456 +1 210651 210850 CHH 0.99999 U 0.17242 +1 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0.43168 +1 212051 212250 CHH 0.80156 U 0.23834 +1 212101 212300 CHH 0.79391 U 0.24087 +1 212151 212350 CHH 0.94957 U 0.18917 +1 212201 212400 CHH 0.59105 U 0.30851 +1 212251 212450 CHH 0.60041 U 0.30654 +1 212301 212500 CHH 0.88105 U 0.21201 +1 212351 212550 CHH 0.9963 U 0.17365 +1 212401 212600 CHH 0.99989 U 0.17246 +1 212451 212650 CHH 0.99989 U 0.17246 +1 212501 212700 CHH 0.99999 U 0.17242 +1 212551 212750 CHH 0.99999 U 0.17242 +1 212601 212800 CHH 0.64995 I 0.38829 +1 212651 212850 CHH 0.64995 I 0.38829 +1 212701 212900 CHH 0.93933 M 0.81654 +1 212751 212950 CHH 0.99998 M 0.83668 +1 212801 213000 CHH 0.99535 M 0.83514 +1 212851 213050 CHH 0.99944 M 0.8365 +1 212901 213100 CHH 0.92019 M 0.81018 +1 212951 213150 CHH 0.96681 I 0.50289 +1 213001 213200 CHH 0.97 I 0.51017 +1 213051 213250 CHH 0.9949 M 0.835 +1 213251 213450 CHH 0.66601 I 0.43329 +1 213301 213500 CHH 0.69022 I 0.49316 +1 213551 213750 CHH 0.99999 I 0.50456 +1 213601 213800 CHH 0.99999 I 0.50456 +1 214001 214200 CHH 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215800 CHH 0.71654 U 0.2669 +1 215651 215850 CHH 0.53396 I 0.35185 +1 215701 215900 CHH 0.53396 I 0.35185 +1 215751 215950 CHH 0.76571 I 0.43168 +1 215801 216000 CHH 0.99999 U 0.17242 +1 215851 216050 CHH 0.99999 U 0.17242 +1 215901 216100 CHH 0.99999 U 0.17242 +1 215951 216150 CHH 0.99999 U 0.17242 +1 216001 216200 CHH 0.57988 U 0.31201 +1 216051 216250 CHH 0.91527 I 0.47673 +1 216101 216300 CHH 0.94981 I 0.48807 +1 216151 216350 CHH 0.96452 I 0.51605 +1 216201 216400 CHH 0.7247 U 0.26386 +1 216251 216450 CHH 0.99996 U 0.17243 +1 216301 216500 CHH 0.77608 U 0.2468 +1 216351 216550 CHH 0.97372 I 0.49583 +1 216401 216600 CHH 0.99956 I 0.5047 +1 216451 216650 CHH 0.99313 M 0.83441 +1 216501 216700 CHH 0.88467 M 0.79838 +1 216551 216750 CHH 0.52801 M 0.67985 +1 216601 216800 CHH 0.70857 I 0.59935 +1 216651 216850 CHH 0.69222 M 0.73401 +1 216701 216900 CHH 0.98849 M 0.83287 +1 216751 216950 CHH 0.99376 M 0.83462 +1 216801 217000 CHH 0.99623 M 0.83544 +1 216851 217050 CHH 0.99623 M 0.83544 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0.99992 U 0.17245 +1 218251 218450 CHH 0.99995 U 0.17244 +1 218301 218500 CHH 0.99999 U 0.17242 +1 218401 218600 CHH 0.99531 U 0.17398 +1 218451 218650 CHH 0.99731 U 0.17332 +1 218501 218700 CHH 0.99999 M 0.83668 +1 218551 218745 CHH 0.99999 M 0.83669 diff --git a/inst/extdata/grid_population/methimpute_p3_CG.txt b/inst/extdata/grid_population/methimpute_p3_CG.txt new file mode 100644 index 0000000..74ddb56 --- /dev/null +++ b/inst/extdata/grid_population/methimpute_p3_CG.txt @@ -0,0 +1,4248 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CG 0.99984 I 0.50279 +1 51 250 CG 0.6595 I 0.49738 +1 101 300 CG 0.6595 I 0.49738 +1 151 350 CG 0.33333 U 0.50273 +1 201 400 CG 0.33333 U 0.50273 +1 251 450 CG 0.33333 U 0.50273 +1 301 500 CG 0.62201 U 0.25409 +1 351 550 CG 0.65248 I 0.3718 +1 401 600 CG 0.65248 I 0.3718 +1 451 650 CG 0.89726 M 0.88914 +1 501 700 CG 0.98489 M 0.92687 +1 551 750 CG 0.99619 M 0.93174 +1 601 800 CG 0.99619 M 0.93174 +1 651 850 CG 0.62201 U 0.25409 +1 701 900 CG 0.62201 U 0.25409 +1 751 950 CG 0.65248 I 0.3718 +1 801 1000 CG 0.65248 I 0.3718 +1 851 1050 CG 0.6595 I 0.49738 +1 901 1100 CG 0.42948 I 0.50308 +1 1151 1350 CG 0.99999 M 0.93338 +1 1201 1400 CG 0.99999 M 0.93338 +1 1251 1450 CG 0.99999 M 0.93338 +1 1301 1500 CG 0.99999 M 0.93338 +1 1351 1550 CG 0.33333 U 0.50273 +1 1401 1600 CG 0.33333 U 0.50273 +1 1451 1650 CG 0.86451 M 0.87486 +1 1501 1700 CG 0.86451 M 0.87486 +1 1551 1750 CG 0.86451 M 0.87486 +1 1601 1800 CG 0.86451 M 0.87486 +1 1651 1850 CG 0.33333 U 0.50273 +1 1701 1900 CG 0.33333 U 0.50273 +1 1751 1950 CG 0.5368 I 0.69966 +1 1801 2000 CG 0.5368 I 0.69966 +1 1851 2050 CG 0.5368 I 0.69966 +1 1901 2100 CG 0.5368 I 0.69966 +1 1951 2150 CG 0.33333 U 0.50273 +1 2001 2200 CG 0.94978 M 0.91175 +1 2051 2250 CG 0.94978 M 0.91175 +1 2101 2300 CG 0.94978 M 0.91175 +1 2151 2350 CG 0.94978 M 0.91175 +1 2201 2400 CG 0.33333 U 0.50273 +1 2251 2450 CG 0.33333 U 0.50273 +1 2301 2500 CG 0.33333 U 0.50273 +1 2351 2550 CG 0.33333 U 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0.50398 +1 217451 217650 CHG 0.99929 I 0.50383 +1 217501 217700 CHG 0.72674 M 0.82244 +1 217551 217750 CHG 0.72674 M 0.82244 +1 217601 217800 CHG 0.56629 I 0.69199 +1 217651 217850 CHG 0.86687 M 0.88369 +1 217701 217900 CHG 0.33333 U 0.50414 +1 217751 217950 CHG 0.33333 U 0.50414 +1 217801 218000 CHG 0.33333 U 0.50414 +1 217851 218050 CHG 0.33333 U 0.50414 +1 217901 218100 CHG 0.33333 U 0.50414 +1 217951 218150 CHG 0.33333 U 0.50414 +1 218001 218200 CHG 0.33333 U 0.50414 +1 218051 218250 CHG 0.33333 U 0.50414 +1 218101 218300 CHG 0.33333 U 0.50414 +1 218151 218350 CHG 0.99996 U 0.06617 +1 218201 218400 CHG 0.99996 U 0.06617 +1 218251 218450 CHG 0.99996 U 0.06617 +1 218301 218500 CHG 0.99969 U 0.06629 +1 218351 218550 CHG 0.62292 M 0.75782 +1 218401 218600 CHG 0.77442 M 0.84166 +1 218451 218650 CHG 0.77442 M 0.84166 +1 218501 218700 CHG 0.62292 M 0.75782 +1 218551 218745 CHG 0.62292 M 0.75782 diff --git a/inst/extdata/grid_population/methimpute_p3_CHH.txt b/inst/extdata/grid_population/methimpute_p3_CHH.txt new file mode 100644 index 0000000..3ce199e --- /dev/null +++ b/inst/extdata/grid_population/methimpute_p3_CHH.txt @@ -0,0 +1,3964 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CHH 1 U 0.17091 +1 51 250 CHH 0.9407 U 0.19015 +1 101 300 CHH 0.81644 I 0.43581 +1 151 350 CHH 0.59145 M 0.68726 +1 201 400 CHH 0.53337 I 0.64674 +1 251 450 CHH 0.99999 M 0.81981 +1 301 500 CHH 0.99999 M 0.81981 +1 351 550 CHH 0.99998 M 0.81981 +1 401 600 CHH 0.99994 M 0.81979 +1 451 650 CHH 0.97846 I 0.50235 +1 501 700 CHH 0.95408 I 0.50624 +1 551 750 CHH 0.60206 M 0.69064 +1 601 800 CHH 0.99999 M 0.81981 +1 651 850 CHH 1 M 0.81981 +1 701 900 CHH 1 M 0.81981 +1 751 950 CHH 1 M 0.81981 +1 801 1000 CHH 0.99999 I 0.49536 +1 851 1050 CHH 0.99437 U 0.17274 +1 901 1100 CHH 0.99999 U 0.17091 +1 951 1150 CHH 0.99999 U 0.17091 +1 1001 1200 CHH 0.56947 U 0.31106 +1 1051 1250 CHH 0.6833 I 0.39507 +1 1151 1350 CHH 0.89134 I 0.47499 +1 1201 1400 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b/inst/extdata/grid_population/methimpute_p4_CHH.txt new file mode 100644 index 0000000..7e9f88b --- /dev/null +++ b/inst/extdata/grid_population/methimpute_p4_CHH.txt @@ -0,0 +1,3964 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CHH 0.99999 M 0.8309 +1 51 250 CHH 0.99999 M 0.8309 +1 101 300 CHH 0.99999 M 0.8309 +1 151 350 CHH 0.99999 M 0.8309 +1 201 400 CHH 0.99999 M 0.8309 +1 251 450 CHH 0.99999 M 0.8309 +1 301 500 CHH 0.99999 M 0.8309 +1 351 550 CHH 0.99999 M 0.8309 +1 401 600 CHH 0.99898 M 0.83055 +1 451 650 CHH 0.99429 I 0.49608 +1 501 700 CHH 0.87333 I 0.53681 +1 551 750 CHH 0.99955 I 0.49401 +1 601 800 CHH 0.95802 U 0.17155 +1 651 850 CHH 0.99817 I 0.49354 +1 701 900 CHH 0.51659 U 0.3202 +1 751 950 CHH 0.99999 U 0.15742 +1 801 1000 CHH 0.99985 U 0.15747 +1 851 1050 CHH 0.99999 U 0.15742 +1 901 1100 CHH 0.99999 I 0.49416 +1 951 1150 CHH 0.99999 I 0.49416 +1 1001 1200 CHH 0.99999 I 0.49416 +1 1051 1250 CHH 0.60865 M 0.69912 +1 1151 1350 CHH 0.99999 M 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218551 218745 CHH 0.99999 M 0.8309 diff --git a/inst/extdata/grid_replicate/Arabidopsis_Win200_Step50_CG.Rdata b/inst/extdata/grid_replicate/Arabidopsis_Win200_Step50_CG.Rdata new file mode 100644 index 0000000..acc1c50 --- /dev/null +++ b/inst/extdata/grid_replicate/Arabidopsis_Win200_Step50_CG.Rdata @@ -0,0 +1,2509 @@ +structure(list(chr = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, +1L, 1L, 1L, 1L, 1L, 1L, 1L, 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0.76587 U 0.15819 +1 101 300 CG 0.76587 U 0.15819 +1 151 350 CG 0.6289 M 0.73853 +1 201 400 CG 0.6289 M 0.73853 +1 251 450 CG 0.6289 M 0.73853 +1 301 500 CG 0.6289 M 0.73853 +1 351 550 CG 0.33333 U 0.48454 +1 401 600 CG 0.33333 U 0.48454 +1 451 650 CG 0.6289 M 0.73853 +1 501 700 CG 0.77849 M 0.81782 +1 551 750 CG 0.77849 M 0.81782 +1 601 800 CG 0.84641 U 0.12087 +1 651 850 CG 0.97985 U 0.06354 +1 701 900 CG 0.99767 U 0.05588 +1 751 950 CG 0.99962 U 0.05505 +1 801 1000 CG 0.85986 U 0.11537 +1 851 1050 CG 0.85986 U 0.11537 +1 901 1100 CG 0.85986 U 0.11537 +1 1151 1350 CG 0.44734 M 0.50804 +1 1201 1400 CG 0.33333 U 0.48454 +1 1251 1450 CG 0.61118 U 0.24578 +1 1301 1500 CG 0.61118 U 0.24578 +1 1351 1550 CG 0.76587 U 0.15819 +1 1401 1600 CG 0.76587 U 0.15819 +1 1451 1650 CG 0.85986 U 0.11537 +1 1501 1700 CG 0.85986 U 0.11537 +1 1551 1750 CG 0.76587 U 0.15819 +1 1601 1800 CG 0.76587 U 0.15819 +1 1651 1850 CG 0.33333 U 0.48454 +1 1701 1900 CG 0.33333 U 0.48454 +1 1751 1950 CG 0.33333 U 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+1 218501 218700 CHG 0.76322 U 0.17229 +1 218551 218745 CHG 0.76322 U 0.17229 diff --git a/inst/extdata/grid_replicate/methimpute_p1_CHH.txt b/inst/extdata/grid_replicate/methimpute_p1_CHH.txt new file mode 100644 index 0000000..a5f091b --- /dev/null +++ b/inst/extdata/grid_replicate/methimpute_p1_CHH.txt @@ -0,0 +1,3964 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CHH 0.99999 I 0.49604 +1 51 250 CHH 0.99999 I 0.49604 +1 101 300 CHH 0.99996 I 0.49605 +1 151 350 CHH 0.99961 M 0.83576 +1 201 400 CHH 0.99999 M 0.83589 +1 251 450 CHH 0.99966 M 0.83578 +1 301 500 CHH 0.99117 M 0.83289 +1 351 550 CHH 0.99887 I 0.49642 +1 401 600 CHH 0.99999 I 0.49604 +1 451 650 CHH 0.99999 I 0.49604 +1 501 700 CHH 0.99999 I 0.49604 +1 551 750 CHH 0.99671 M 0.83478 +1 601 800 CHH 0.99999 M 0.83589 +1 651 850 CHH 0.99999 M 0.83589 +1 701 900 CHH 0.99999 M 0.83589 +1 751 950 CHH 0.99999 M 0.83589 +1 801 1000 CHH 0.8629 I 0.46676 +1 851 1050 CHH 0.98445 M 0.83061 +1 901 1100 CHH 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a/inst/extdata/grid_replicate/methimpute_p2_CHG.txt b/inst/extdata/grid_replicate/methimpute_p2_CHG.txt new file mode 100644 index 0000000..16b9dfa --- /dev/null +++ b/inst/extdata/grid_replicate/methimpute_p2_CHG.txt @@ -0,0 +1,3964 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CHG 0.97903 M 0.93101 +1 51 250 CHG 0.62294 M 0.75625 +1 101 300 CHG 0.62294 M 0.75625 +1 401 600 CHG 0.33935 U 0.49653 +1 451 650 CHG 0.33333 U 0.50308 +1 501 700 CHG 0.33333 U 0.50308 +1 551 750 CHG 0.33333 U 0.50308 +1 651 850 CHG 0.55865 I 0.69392 +1 701 900 CHG 0.55865 I 0.69392 +1 751 950 CHG 0.99999 M 0.94017 +1 801 1000 CHG 0.99999 M 0.94017 +1 851 1050 CHG 0.99999 M 0.94017 +1 901 1100 CHG 0.99999 M 0.94017 +1 1001 1200 CHG 0.33333 U 0.50308 +1 1051 1250 CHG 0.33333 U 0.50308 +1 1101 1300 CHG 0.33333 U 0.50308 +1 1151 1350 CHG 0.97782 U 0.07568 +1 1201 1400 CHG 0.97782 U 0.07568 +1 1251 1450 CHG 0.9945 I 0.50548 +1 1301 1500 CHG 0.9945 I 0.50548 +1 1401 1600 CHG 0.99944 M 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0.67955 I 0.49667 +1 217801 218000 CHG 0.6709 I 0.37512 +1 217851 218050 CHG 0.62653 U 0.24677 +1 217901 218100 CHG 0.62653 U 0.24677 +1 217951 218150 CHG 0.67955 I 0.49667 +1 218001 218200 CHG 0.62294 M 0.75625 +1 218051 218250 CHG 0.62294 M 0.75625 +1 218101 218300 CHG 0.62294 M 0.75625 +1 218151 218350 CHG 0.7769 U 0.16489 +1 218201 218400 CHG 0.7769 U 0.16489 +1 218251 218450 CHG 0.7769 U 0.16489 +1 218301 218500 CHG 0.86892 U 0.12338 +1 218351 218550 CHG 0.62653 U 0.24677 +1 218401 218600 CHG 0.62653 U 0.24677 +1 218451 218650 CHG 0.62653 U 0.24677 +1 218501 218700 CHG 0.33333 U 0.50308 +1 218551 218745 CHG 0.33333 U 0.50308 diff --git a/inst/extdata/grid_replicate/methimpute_p2_CHH.txt b/inst/extdata/grid_replicate/methimpute_p2_CHH.txt new file mode 100644 index 0000000..5584e24 --- /dev/null +++ b/inst/extdata/grid_replicate/methimpute_p2_CHH.txt @@ -0,0 +1,3964 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CHH 1 I 0.50456 +1 51 250 CHH 0.97749 U 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CHH 0.70904 M 0.7379 +1 210901 211100 CHH 0.99999 M 0.83668 +1 210951 211150 CHH 0.99997 M 0.83668 +1 211001 211200 CHH 0.99999 I 0.50456 +1 211051 211250 CHH 0.99999 I 0.50456 +1 211101 211300 CHH 0.99998 I 0.50455 +1 211151 211350 CHH 0.99975 I 0.50448 +1 211201 211400 CHH 0.99999 I 0.50456 +1 211251 211450 CHH 0.99999 I 0.50456 +1 211301 211500 CHH 0.99999 I 0.50456 +1 211351 211550 CHH 0.88197 M 0.79749 +1 211401 211600 CHH 0.99999 M 0.83669 +1 211451 211650 CHH 0.99998 M 0.83668 +1 211501 211700 CHH 0.99989 M 0.83665 +1 211551 211750 CHH 0.58021 M 0.69726 +1 211601 211800 CHH 0.58021 M 0.69726 +1 211651 211850 CHH 0.92711 M 0.81248 +1 211701 211900 CHH 0.60393 M 0.70514 +1 211751 211950 CHH 0.99793 M 0.836 +1 211801 212000 CHH 0.99772 M 0.83593 +1 211851 212050 CHH 0.99924 M 0.83644 +1 211901 212100 CHH 0.99997 M 0.83668 +1 211951 212150 CHH 0.80396 M 0.77108 +1 212001 212200 CHH 0.76571 I 0.43168 +1 212051 212250 CHH 0.80156 U 0.23834 +1 212101 212300 CHH 0.79391 U 0.24087 +1 212151 212350 CHH 0.94957 U 0.18917 +1 212201 212400 CHH 0.59105 U 0.30851 +1 212251 212450 CHH 0.60041 U 0.30654 +1 212301 212500 CHH 0.88105 U 0.21201 +1 212351 212550 CHH 0.9963 U 0.17365 +1 212401 212600 CHH 0.99989 U 0.17246 +1 212451 212650 CHH 0.99989 U 0.17246 +1 212501 212700 CHH 0.99999 U 0.17242 +1 212551 212750 CHH 0.99999 U 0.17242 +1 212601 212800 CHH 0.64995 I 0.38829 +1 212651 212850 CHH 0.64995 I 0.38829 +1 212701 212900 CHH 0.93933 M 0.81654 +1 212751 212950 CHH 0.99998 M 0.83668 +1 212801 213000 CHH 0.99535 M 0.83514 +1 212851 213050 CHH 0.99944 M 0.8365 +1 212901 213100 CHH 0.92019 M 0.81018 +1 212951 213150 CHH 0.96681 I 0.50289 +1 213001 213200 CHH 0.97 I 0.51017 +1 213051 213250 CHH 0.9949 M 0.835 +1 213251 213450 CHH 0.66601 I 0.43329 +1 213301 213500 CHH 0.69022 I 0.49316 +1 213551 213750 CHH 0.99999 I 0.50456 +1 213601 213800 CHH 0.99999 I 0.50456 +1 214001 214200 CHH 0.99999 M 0.83669 +1 214051 214250 CHH 0.99999 M 0.83669 +1 214101 214300 CHH 0.99997 M 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217200 CHH 0.99999 U 0.17242 +1 217051 217250 CHH 0.99999 U 0.17242 +1 217101 217300 CHH 0.81069 I 0.44168 +1 217151 217350 CHH 0.96773 U 0.18314 +1 217201 217400 CHH 0.57074 I 0.64431 +1 217251 217450 CHH 0.77244 M 0.76109 +1 217301 217500 CHH 0.99972 M 0.8366 +1 217351 217550 CHH 0.99954 M 0.83654 +1 217401 217600 CHH 0.99995 M 0.83667 +1 217451 217650 CHH 0.99313 M 0.83441 +1 217501 217700 CHH 0.62031 I 0.63054 +1 217551 217750 CHH 0.73005 I 0.59381 +1 217601 217800 CHH 0.96942 M 0.82653 +1 217651 217850 CHH 0.99999 M 0.83669 +1 217751 217950 CHH 0.99999 M 0.83669 +1 217801 218000 CHH 0.99999 I 0.50456 +1 217851 218050 CHH 0.81472 U 0.23396 +1 217901 218100 CHH 0.99999 I 0.50455 +1 217951 218150 CHH 0.99973 I 0.50447 +1 218001 218200 CHH 0.99658 M 0.83555 +1 218051 218250 CHH 0.99434 M 0.83481 +1 218101 218300 CHH 0.55191 M 0.68749 +1 218151 218350 CHH 0.55191 M 0.68749 +1 218201 218400 CHH 0.99992 U 0.17245 +1 218251 218450 CHH 0.99995 U 0.17244 +1 218301 218500 CHH 0.99999 U 0.17242 +1 218401 218600 CHH 0.99531 U 0.17398 +1 218451 218650 CHH 0.99731 U 0.17332 +1 218501 218700 CHH 0.99999 M 0.83668 +1 218551 218745 CHH 0.99999 M 0.83669 diff --git a/inst/extdata/grid_replicate/methimpute_p3_CG.txt b/inst/extdata/grid_replicate/methimpute_p3_CG.txt new file mode 100644 index 0000000..74ddb56 --- /dev/null +++ b/inst/extdata/grid_replicate/methimpute_p3_CG.txt @@ -0,0 +1,4248 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CG 0.99984 I 0.50279 +1 51 250 CG 0.6595 I 0.49738 +1 101 300 CG 0.6595 I 0.49738 +1 151 350 CG 0.33333 U 0.50273 +1 201 400 CG 0.33333 U 0.50273 +1 251 450 CG 0.33333 U 0.50273 +1 301 500 CG 0.62201 U 0.25409 +1 351 550 CG 0.65248 I 0.3718 +1 401 600 CG 0.65248 I 0.3718 +1 451 650 CG 0.89726 M 0.88914 +1 501 700 CG 0.98489 M 0.92687 +1 551 750 CG 0.99619 M 0.93174 +1 601 800 CG 0.99619 M 0.93174 +1 651 850 CG 0.62201 U 0.25409 +1 701 900 CG 0.62201 U 0.25409 +1 751 950 CG 0.65248 I 0.3718 +1 801 1000 CG 0.65248 I 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218650 CG 0.77379 U 0.17121 +1 218501 218700 CG 0.92378 U 0.10491 +1 218551 218745 CG 0.92378 U 0.10491 diff --git a/inst/extdata/grid_replicate/methimpute_p3_CHG.txt b/inst/extdata/grid_replicate/methimpute_p3_CHG.txt new file mode 100644 index 0000000..4ec6465 --- /dev/null +++ b/inst/extdata/grid_replicate/methimpute_p3_CHG.txt @@ -0,0 +1,3964 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CHG 0.97683 U 0.0763 +1 51 250 CHG 0.33333 U 0.50414 +1 101 300 CHG 0.33333 U 0.50414 +1 401 600 CHG 0.36299 U 0.47456 +1 451 650 CHG 0.33333 U 0.50414 +1 501 700 CHG 0.33333 U 0.50414 +1 551 750 CHG 0.33333 U 0.50414 +1 651 850 CHG 0.33333 U 0.50414 +1 701 900 CHG 0.33333 U 0.50414 +1 751 950 CHG 0.33333 U 0.50414 +1 801 1000 CHG 0.33333 U 0.50414 +1 851 1050 CHG 0.33333 U 0.50414 +1 901 1100 CHG 0.33333 U 0.50414 +1 1001 1200 CHG 0.33333 U 0.50414 +1 1051 1250 CHG 0.99383 M 0.93943 +1 1101 1300 CHG 0.99383 M 0.93943 +1 1151 1350 CHG 0.99383 M 0.93943 +1 1201 1400 CHG 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CHG 0.67073 I 0.37488 +1 214851 215050 CHG 0.902 I 0.4988 +1 214901 215100 CHG 0.77442 M 0.84166 +1 214951 215150 CHG 0.77442 M 0.84166 +1 215001 215200 CHG 0.77442 M 0.84166 +1 215151 215350 CHG 0.62776 U 0.24622 +1 215201 215400 CHG 0.62776 U 0.24622 +1 215251 215450 CHG 0.62776 U 0.24622 +1 215301 215500 CHG 0.67073 I 0.37488 +1 215351 215550 CHG 0.68248 I 0.49545 +1 215401 215600 CHG 0.68248 I 0.49545 +1 215501 215700 CHG 0.99995 M 0.94211 +1 215551 215750 CHG 0.99995 M 0.94211 +1 215601 215800 CHG 0.99995 M 0.94211 +1 215651 215850 CHG 0.99995 M 0.94211 +1 215701 215900 CHG 0.62776 U 0.24622 +1 215751 215950 CHG 0.62776 U 0.24622 +1 215801 216000 CHG 0.77773 U 0.16481 +1 215851 216050 CHG 0.77773 U 0.16481 +1 215901 216100 CHG 0.62776 U 0.24622 +1 215951 216150 CHG 0.99988 M 0.94208 +1 216001 216200 CHG 0.99998 M 0.94212 +1 216051 216250 CHG 0.99998 M 0.94212 +1 216101 216300 CHG 0.99998 M 0.94212 +1 216151 216350 CHG 0.33333 U 0.50414 +1 216201 216400 CHG 0.33333 U 0.50414 +1 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0.82244 +1 217551 217750 CHG 0.72674 M 0.82244 +1 217601 217800 CHG 0.56629 I 0.69199 +1 217651 217850 CHG 0.86687 M 0.88369 +1 217701 217900 CHG 0.33333 U 0.50414 +1 217751 217950 CHG 0.33333 U 0.50414 +1 217801 218000 CHG 0.33333 U 0.50414 +1 217851 218050 CHG 0.33333 U 0.50414 +1 217901 218100 CHG 0.33333 U 0.50414 +1 217951 218150 CHG 0.33333 U 0.50414 +1 218001 218200 CHG 0.33333 U 0.50414 +1 218051 218250 CHG 0.33333 U 0.50414 +1 218101 218300 CHG 0.33333 U 0.50414 +1 218151 218350 CHG 0.99996 U 0.06617 +1 218201 218400 CHG 0.99996 U 0.06617 +1 218251 218450 CHG 0.99996 U 0.06617 +1 218301 218500 CHG 0.99969 U 0.06629 +1 218351 218550 CHG 0.62292 M 0.75782 +1 218401 218600 CHG 0.77442 M 0.84166 +1 218451 218650 CHG 0.77442 M 0.84166 +1 218501 218700 CHG 0.62292 M 0.75782 +1 218551 218745 CHG 0.62292 M 0.75782 diff --git a/inst/extdata/grid_replicate/methimpute_p3_CHH.txt b/inst/extdata/grid_replicate/methimpute_p3_CHH.txt new file mode 100644 index 0000000..3ce199e --- /dev/null +++ b/inst/extdata/grid_replicate/methimpute_p3_CHH.txt @@ -0,0 +1,3964 @@ +seqnames start end context posteriorMax status rc.meth.lvl +1 1 200 CHH 1 U 0.17091 +1 51 250 CHH 0.9407 U 0.19015 +1 101 300 CHH 0.81644 I 0.43581 +1 151 350 CHH 0.59145 M 0.68726 +1 201 400 CHH 0.53337 I 0.64674 +1 251 450 CHH 0.99999 M 0.81981 +1 301 500 CHH 0.99999 M 0.81981 +1 351 550 CHH 0.99998 M 0.81981 +1 401 600 CHH 0.99994 M 0.81979 +1 451 650 CHH 0.97846 I 0.50235 +1 501 700 CHH 0.95408 I 0.50624 +1 551 750 CHH 0.60206 M 0.69064 +1 601 800 CHH 0.99999 M 0.81981 +1 651 850 CHH 1 M 0.81981 +1 701 900 CHH 1 M 0.81981 +1 751 950 CHH 1 M 0.81981 +1 801 1000 CHH 0.99999 I 0.49536 +1 851 1050 CHH 0.99437 U 0.17274 +1 901 1100 CHH 0.99999 U 0.17091 +1 951 1150 CHH 0.99999 U 0.17091 +1 1001 1200 CHH 0.56947 U 0.31106 +1 1051 1250 CHH 0.6833 I 0.39507 +1 1151 1350 CHH 0.89134 I 0.47499 +1 1201 1400 CHH 0.92957 I 0.4982 +1 1251 1450 CHH 0.87762 I 0.52357 +1 1301 1500 CHH 0.89134 I 0.47499 +1 1351 1550 CHH 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replicate toyData/methimpute_p1.txt methylomeA rep1 toyData/methimpute_p2.txt methylomeB rep1 toyData/methimpute_p3.txt methylomeC rep1 -toyData/methimpute_p4.txt methylomeD rep1 +toyData/methimpute_p4.txt methylomeD rep1 \ No newline at end of file diff --git a/inst/extdata/matrix_CT_replicate/CG_WT_mutant1_StateCalls.txt b/inst/extdata/matrix_CT_replicate/CG_WT_mutant1_StateCalls.txt new file mode 100644 index 0000000..3eeba7f --- /dev/null +++ b/inst/extdata/matrix_CT_replicate/CG_WT_mutant1_StateCalls.txt @@ -0,0 +1,4248 @@ +seqnames start end WT_rep1 WT_rep2 mutant1_rep1 mutant1_rep2 +1 1 200 0 1 1 1 +1 51 250 0 1 1 1 +1 101 300 0 1 1 1 +1 151 350 1 1 0 0 +1 201 400 1 0 0 0 +1 251 450 1 0 0 0 +1 301 500 1 0 0 0 +1 351 550 0 0 1 1 +1 401 600 0 0 1 1 +1 451 650 1 0 1 1 +1 501 700 1 0 1 1 +1 551 750 1 0 1 0 +1 601 800 0 1 1 0 +1 651 850 0 0 0 1 +1 701 900 0 0 0 1 +1 751 950 0 1 1 1 +1 801 1000 0 1 1 1 +1 851 1050 0 1 1 0 +1 901 1100 0 1 1 0 +1 1151 1350 1 1 1 1 +1 1201 1400 0 0 1 0 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a/inst/extdata/toyData/TAIR10.gene.chr1.gff3 b/inst/extdata/toyData/TAIR10.gene.chr1.gff3 deleted file mode 100644 index df470a2..0000000 --- a/inst/extdata/toyData/TAIR10.gene.chr1.gff3 +++ /dev/null @@ -1,3003 +0,0 @@ -##gff-version 3 -##source-version rtracklayer 1.50.0 -##date 2023-07-31 -1 The Arabidopsis Information Resource chromosome 1 30427671 . . . ID=chromosome:1;Alias=CP002684.1,Chr1,NC_003070.9; -1 araport11 gene 3631 5899 . + . ID=gene:AT1G01010;Name=NAC001;biotype=protein_coding;description=NAC domain-containing protein 1 [Source:UniProtKB/Swiss-Prot%3bAcc:Q0WV96];gene_id=AT1G01010;logic_name=araport11; -1 araport11 mRNA 3631 5899 . + . ID=transcript:AT1G01010.1;biotype=protein_coding;Parent=gene:AT1G01010;transcript_id=AT1G01010.1; -1 araport11 five_prime_UTR 3631 3759 . + . Parent=transcript:AT1G01010.1; -1 araport11 exon 3631 3913 . + . Name=AT1G01010.1.exon1;Parent=transcript:AT1G01010.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01010.1.exon1;rank=1; -1 araport11 CDS 3760 3913 . + 0 ID=CDS:AT1G01010.1;Parent=transcript:AT1G01010.1;protein_id=AT1G01010.1 -1 araport11 exon 3996 4276 . + . Name=AT1G01010.1.exon2;Parent=transcript:AT1G01010.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01010.1.exon2;rank=2; -1 araport11 CDS 3996 4276 . + 2 ID=CDS:AT1G01010.1;Parent=transcript:AT1G01010.1;protein_id=AT1G01010.1 -1 araport11 exon 4486 4605 . + . Name=AT1G01010.1.exon3;Parent=transcript:AT1G01010.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01010.1.exon3;rank=3; -1 araport11 CDS 4486 4605 . + 0 ID=CDS:AT1G01010.1;Parent=transcript:AT1G01010.1;protein_id=AT1G01010.1 -1 araport11 exon 4706 5095 . + . Name=AT1G01010.1.exon4;Parent=transcript:AT1G01010.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01010.1.exon4;rank=4; -1 araport11 CDS 4706 5095 . + 0 ID=CDS:AT1G01010.1;Parent=transcript:AT1G01010.1;protein_id=AT1G01010.1 -1 araport11 exon 5174 5326 . + . Name=AT1G01010.1.exon5;Parent=transcript:AT1G01010.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01010.1.exon5;rank=5; -1 araport11 CDS 5174 5326 . + 0 ID=CDS:AT1G01010.1;Parent=transcript:AT1G01010.1;protein_id=AT1G01010.1 -1 araport11 CDS 5439 5630 . + 0 ID=CDS:AT1G01010.1;Parent=transcript:AT1G01010.1;protein_id=AT1G01010.1 -1 araport11 exon 5439 5899 . + . Name=AT1G01010.1.exon6;Parent=transcript:AT1G01010.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01010.1.exon6;rank=6; -1 araport11 three_prime_UTR 5631 5899 . + . Parent=transcript:AT1G01010.1; -1 araport11 gene 6788 9130 . - . ID=gene:AT1G01020;Name=ARV1;biotype=protein_coding;description=ARV1 family protein [Source:UniProtKB/TrEMBL%3bAcc:Q5MK24];gene_id=AT1G01020;logic_name=araport11; -1 araport11 mRNA 6788 8737 . - . ID=transcript:AT1G01020.6;biotype=protein_coding;Parent=gene:AT1G01020;transcript_id=AT1G01020.6; -1 araport11 exon 6788 7069 . - . Name=AT1G01020.2.exon8;Parent=transcript:AT1G01020.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01020.2.exon8;rank=6; -1 araport11 three_prime_UTR 6788 7069 . - . Parent=transcript:AT1G01020.6; -1 araport11 three_prime_UTR 7157 7314 . - . Parent=transcript:AT1G01020.6; -1 araport11 exon 7157 7450 . - . Name=AT1G01020.2.exon7;Parent=transcript:AT1G01020.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01020.2.exon7;rank=5; -1 araport11 CDS 7315 7450 . - 1 ID=CDS:AT1G01020.6;Parent=transcript:AT1G01020.6;protein_id=AT1G01020.6 -1 araport11 exon 7564 7649 . - . Name=AT1G01020.1.exon6;Parent=transcript:AT1G01020.6;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01020.1.exon6;rank=4; -1 araport11 CDS 7564 7649 . - 0 ID=CDS:AT1G01020.6;Parent=transcript:AT1G01020.6;protein_id=AT1G01020.6 -1 araport11 exon 8236 8325 . - . Name=AT1G01020.1.exon3;Parent=transcript:AT1G01020.6;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01020.1.exon3;rank=3; -1 araport11 CDS 8236 8325 . - 0 ID=CDS:AT1G01020.6;Parent=transcript:AT1G01020.6;protein_id=AT1G01020.6 -1 araport11 CDS 8417 8419 . - 0 ID=CDS:AT1G01020.6;Parent=transcript:AT1G01020.6;protein_id=AT1G01020.6 -1 araport11 exon 8417 8464 . - . Name=AT1G01020.5.exon2;Parent=transcript:AT1G01020.6;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01020.5.exon2;rank=2; -1 araport11 five_prime_UTR 8420 8464 . - . Parent=transcript:AT1G01020.6; -1 araport11 exon 8594 8737 . - . Name=AT1G01020.6.exon1;Parent=transcript:AT1G01020.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01020.6.exon1;rank=1; -1 araport11 five_prime_UTR 8594 8737 . - . Parent=transcript:AT1G01020.6; -1 araport11 mRNA 6788 8737 . - . ID=transcript:AT1G01020.2;biotype=protein_coding;Parent=gene:AT1G01020;transcript_id=AT1G01020.2; -1 araport11 exon 6788 7069 . - . Name=AT1G01020.2.exon8;Parent=transcript:AT1G01020.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01020.2.exon8;rank=8; -1 araport11 three_prime_UTR 6788 7069 . - . Parent=transcript:AT1G01020.2; -1 araport11 three_prime_UTR 7157 7314 . - . Parent=transcript:AT1G01020.2; -1 araport11 exon 7157 7450 . - . Name=AT1G01020.2.exon7;Parent=transcript:AT1G01020.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01020.2.exon7;rank=7; -1 araport11 CDS 7315 7450 . - 1 ID=CDS:AT1G01020.2;Parent=transcript:AT1G01020.2;protein_id=AT1G01020.2 -1 araport11 exon 7564 7649 . - . Name=AT1G01020.1.exon6;Parent=transcript:AT1G01020.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01020.1.exon6;rank=6; -1 araport11 CDS 7564 7649 . - 0 ID=CDS:AT1G01020.2;Parent=transcript:AT1G01020.2;protein_id=AT1G01020.2 -1 araport11 exon 7762 7835 . - . Name=AT1G01020.1.exon5;Parent=transcript:AT1G01020.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01020.1.exon5;rank=5; -1 araport11 CDS 7762 7835 . - 2 ID=CDS:AT1G01020.2;Parent=transcript:AT1G01020.2;protein_id=AT1G01020.2 -1 araport11 exon 7942 7987 . - . Name=AT1G01020.1.exon4;Parent=transcript:AT1G01020.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon4;rank=4; -1 araport11 CDS 7942 7987 . - 0 ID=CDS:AT1G01020.2;Parent=transcript:AT1G01020.2;protein_id=AT1G01020.2 -1 araport11 exon 8236 8325 . - . Name=AT1G01020.1.exon3;Parent=transcript:AT1G01020.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01020.1.exon3;rank=3; -1 araport11 CDS 8236 8325 . - 0 ID=CDS:AT1G01020.2;Parent=transcript:AT1G01020.2;protein_id=AT1G01020.2 -1 araport11 exon 8417 8464 . - . Name=AT1G01020.1.exon2;Parent=transcript:AT1G01020.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01020.1.exon2;rank=2; -1 araport11 CDS 8417 8464 . - 0 ID=CDS:AT1G01020.2;Parent=transcript:AT1G01020.2;protein_id=AT1G01020.2 -1 araport11 CDS 8571 8666 . - 0 ID=CDS:AT1G01020.2;Parent=transcript:AT1G01020.2;protein_id=AT1G01020.2 -1 araport11 exon 8571 8737 . - . Name=AT1G01020.2.exon1;Parent=transcript:AT1G01020.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01020.2.exon1;rank=1; -1 araport11 five_prime_UTR 8667 8737 . - . Parent=transcript:AT1G01020.2; -1 araport11 mRNA 6788 9130 . - . ID=transcript:AT1G01020.3;biotype=protein_coding;Parent=gene:AT1G01020;transcript_id=AT1G01020.3; -1 araport11 three_prime_UTR 6788 6914 . - . Parent=transcript:AT1G01020.3; -1 araport11 exon 6788 7069 . - . Name=AT1G01020.1.exon9;Parent=transcript:AT1G01020.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01020.1.exon9;rank=8; -1 araport11 CDS 6915 7069 . - 2 ID=CDS:AT1G01020.3;Parent=transcript:AT1G01020.3;protein_id=AT1G01020.3 -1 araport11 exon 7157 7232 . - . Name=AT1G01020.1.exon8;Parent=transcript:AT1G01020.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon8;rank=7; -1 araport11 CDS 7157 7232 . - 0 ID=CDS:AT1G01020.3;Parent=transcript:AT1G01020.3;protein_id=AT1G01020.3 -1 araport11 exon 7384 7450 . - . Name=AT1G01020.1.exon7;Parent=transcript:AT1G01020.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01020.1.exon7;rank=6; -1 araport11 CDS 7384 7450 . - 1 ID=CDS:AT1G01020.3;Parent=transcript:AT1G01020.3;protein_id=AT1G01020.3 -1 araport11 exon 7564 7649 . - . Name=AT1G01020.1.exon6;Parent=transcript:AT1G01020.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01020.1.exon6;rank=5; -1 araport11 CDS 7564 7649 . - 0 ID=CDS:AT1G01020.3;Parent=transcript:AT1G01020.3;protein_id=AT1G01020.3 -1 araport11 exon 7762 7835 . - . Name=AT1G01020.1.exon5;Parent=transcript:AT1G01020.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01020.1.exon5;rank=4; -1 araport11 CDS 7762 7835 . - 2 ID=CDS:AT1G01020.3;Parent=transcript:AT1G01020.3;protein_id=AT1G01020.3 -1 araport11 exon 7942 7987 . - . Name=AT1G01020.1.exon4;Parent=transcript:AT1G01020.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon4;rank=3; -1 araport11 CDS 7942 7987 . - 0 ID=CDS:AT1G01020.3;Parent=transcript:AT1G01020.3;protein_id=AT1G01020.3 -1 araport11 CDS 8236 8442 . - 0 ID=CDS:AT1G01020.3;Parent=transcript:AT1G01020.3;protein_id=AT1G01020.3 -1 araport11 exon 8236 8464 . - . Name=AT1G01020.4.exon2;Parent=transcript:AT1G01020.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01020.4.exon2;rank=2; -1 araport11 five_prime_UTR 8443 8464 . - . Parent=transcript:AT1G01020.3; -1 araport11 exon 8571 9130 . - . Name=AT1G01020.3.exon1;Parent=transcript:AT1G01020.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01020.3.exon1;rank=1; -1 araport11 five_prime_UTR 8571 9130 . - . Parent=transcript:AT1G01020.3; -1 araport11 mRNA 6788 9130 . - . ID=transcript:AT1G01020.5;biotype=protein_coding;Parent=gene:AT1G01020;transcript_id=AT1G01020.5; -1 araport11 three_prime_UTR 6788 6914 . - . Parent=transcript:AT1G01020.5; -1 araport11 exon 6788 7069 . - . Name=AT1G01020.1.exon9;Parent=transcript:AT1G01020.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01020.1.exon9;rank=9; -1 araport11 CDS 6915 7069 . - 2 ID=CDS:AT1G01020.5;Parent=transcript:AT1G01020.5;protein_id=AT1G01020.5 -1 araport11 exon 7157 7232 . - . Name=AT1G01020.1.exon8;Parent=transcript:AT1G01020.5;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon8;rank=8; -1 araport11 CDS 7157 7232 . - 0 ID=CDS:AT1G01020.5;Parent=transcript:AT1G01020.5;protein_id=AT1G01020.5 -1 araport11 exon 7384 7450 . - . Name=AT1G01020.1.exon7;Parent=transcript:AT1G01020.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01020.1.exon7;rank=7; -1 araport11 CDS 7384 7450 . - 1 ID=CDS:AT1G01020.5;Parent=transcript:AT1G01020.5;protein_id=AT1G01020.5 -1 araport11 exon 7564 7649 . - . Name=AT1G01020.1.exon6;Parent=transcript:AT1G01020.5;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01020.1.exon6;rank=6; -1 araport11 CDS 7564 7649 . - 0 ID=CDS:AT1G01020.5;Parent=transcript:AT1G01020.5;protein_id=AT1G01020.5 -1 araport11 exon 7762 7835 . - . Name=AT1G01020.1.exon5;Parent=transcript:AT1G01020.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01020.1.exon5;rank=5; -1 araport11 CDS 7762 7835 . - 2 ID=CDS:AT1G01020.5;Parent=transcript:AT1G01020.5;protein_id=AT1G01020.5 -1 araport11 exon 7942 7987 . - . Name=AT1G01020.1.exon4;Parent=transcript:AT1G01020.5;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon4;rank=4; -1 araport11 CDS 7942 7987 . - 0 ID=CDS:AT1G01020.5;Parent=transcript:AT1G01020.5;protein_id=AT1G01020.5 -1 araport11 exon 8236 8325 . - . Name=AT1G01020.1.exon3;Parent=transcript:AT1G01020.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01020.1.exon3;rank=3; -1 araport11 CDS 8236 8325 . - 0 ID=CDS:AT1G01020.5;Parent=transcript:AT1G01020.5;protein_id=AT1G01020.5 -1 araport11 CDS 8417 8419 . - 0 ID=CDS:AT1G01020.5;Parent=transcript:AT1G01020.5;protein_id=AT1G01020.5 -1 araport11 exon 8417 8464 . - . Name=AT1G01020.5.exon2;Parent=transcript:AT1G01020.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01020.5.exon2;rank=2; -1 araport11 five_prime_UTR 8420 8464 . - . Parent=transcript:AT1G01020.5; -1 araport11 exon 8594 9130 . - . Name=AT1G01020.4.exon1;Parent=transcript:AT1G01020.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01020.4.exon1;rank=1; -1 araport11 five_prime_UTR 8594 9130 . - . Parent=transcript:AT1G01020.5; -1 araport11 mRNA 6788 9130 . - . ID=transcript:AT1G01020.4;biotype=protein_coding;Parent=gene:AT1G01020;transcript_id=AT1G01020.4; -1 araport11 three_prime_UTR 6788 6914 . - . Parent=transcript:AT1G01020.4; -1 araport11 exon 6788 7069 . - . Name=AT1G01020.1.exon9;Parent=transcript:AT1G01020.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01020.1.exon9;rank=8; -1 araport11 CDS 6915 7069 . - 2 ID=CDS:AT1G01020.4;Parent=transcript:AT1G01020.4;protein_id=AT1G01020.4 -1 araport11 exon 7157 7232 . - . Name=AT1G01020.1.exon8;Parent=transcript:AT1G01020.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon8;rank=7; -1 araport11 CDS 7157 7232 . - 0 ID=CDS:AT1G01020.4;Parent=transcript:AT1G01020.4;protein_id=AT1G01020.4 -1 araport11 exon 7384 7450 . - . Name=AT1G01020.1.exon7;Parent=transcript:AT1G01020.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01020.1.exon7;rank=6; -1 araport11 CDS 7384 7450 . - 1 ID=CDS:AT1G01020.4;Parent=transcript:AT1G01020.4;protein_id=AT1G01020.4 -1 araport11 exon 7564 7649 . - . Name=AT1G01020.1.exon6;Parent=transcript:AT1G01020.4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01020.1.exon6;rank=5; -1 araport11 CDS 7564 7649 . - 0 ID=CDS:AT1G01020.4;Parent=transcript:AT1G01020.4;protein_id=AT1G01020.4 -1 araport11 exon 7762 7835 . - . Name=AT1G01020.1.exon5;Parent=transcript:AT1G01020.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01020.1.exon5;rank=4; -1 araport11 CDS 7762 7835 . - 2 ID=CDS:AT1G01020.4;Parent=transcript:AT1G01020.4;protein_id=AT1G01020.4 -1 araport11 exon 7942 7987 . - . Name=AT1G01020.1.exon4;Parent=transcript:AT1G01020.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon4;rank=3; -1 araport11 CDS 7942 7987 . - 0 ID=CDS:AT1G01020.4;Parent=transcript:AT1G01020.4;protein_id=AT1G01020.4 -1 araport11 CDS 8236 8442 . - 0 ID=CDS:AT1G01020.4;Parent=transcript:AT1G01020.4;protein_id=AT1G01020.4 -1 araport11 exon 8236 8464 . - . Name=AT1G01020.4.exon2;Parent=transcript:AT1G01020.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01020.4.exon2;rank=2; -1 araport11 five_prime_UTR 8443 8464 . - . Parent=transcript:AT1G01020.4; -1 araport11 exon 8594 9130 . - . Name=AT1G01020.4.exon1;Parent=transcript:AT1G01020.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01020.4.exon1;rank=1; -1 araport11 five_prime_UTR 8594 9130 . - . Parent=transcript:AT1G01020.4; -1 araport11 mRNA 6788 9130 . - . ID=transcript:AT1G01020.1;biotype=protein_coding;Parent=gene:AT1G01020;transcript_id=AT1G01020.1; -1 araport11 three_prime_UTR 6788 6914 . - . Parent=transcript:AT1G01020.1; -1 araport11 exon 6788 7069 . - . Name=AT1G01020.1.exon9;Parent=transcript:AT1G01020.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01020.1.exon9;rank=9; -1 araport11 CDS 6915 7069 . - 2 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 exon 7157 7232 . - . Name=AT1G01020.1.exon8;Parent=transcript:AT1G01020.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon8;rank=8; -1 araport11 CDS 7157 7232 . - 0 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 exon 7384 7450 . - . Name=AT1G01020.1.exon7;Parent=transcript:AT1G01020.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01020.1.exon7;rank=7; -1 araport11 CDS 7384 7450 . - 1 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 exon 7564 7649 . - . Name=AT1G01020.1.exon6;Parent=transcript:AT1G01020.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01020.1.exon6;rank=6; -1 araport11 CDS 7564 7649 . - 0 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 exon 7762 7835 . - . Name=AT1G01020.1.exon5;Parent=transcript:AT1G01020.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01020.1.exon5;rank=5; -1 araport11 CDS 7762 7835 . - 2 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 exon 7942 7987 . - . Name=AT1G01020.1.exon4;Parent=transcript:AT1G01020.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01020.1.exon4;rank=4; -1 araport11 CDS 7942 7987 . - 0 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 exon 8236 8325 . - . Name=AT1G01020.1.exon3;Parent=transcript:AT1G01020.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01020.1.exon3;rank=3; -1 araport11 CDS 8236 8325 . - 0 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 exon 8417 8464 . - . Name=AT1G01020.1.exon2;Parent=transcript:AT1G01020.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01020.1.exon2;rank=2; -1 araport11 CDS 8417 8464 . - 0 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 CDS 8571 8666 . - 0 ID=CDS:AT1G01020.1;Parent=transcript:AT1G01020.1;protein_id=AT1G01020.1 -1 araport11 exon 8571 9130 . - . Name=AT1G01020.1.exon1;Parent=transcript:AT1G01020.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01020.1.exon1;rank=1; -1 araport11 five_prime_UTR 8667 9130 . - . Parent=transcript:AT1G01020.1; -1 araport11 ncRNA_gene 11101 11372 . + . ID=gene:AT1G03987;biotype=lncRNA;gene_id=AT1G03987;logic_name=araport11; -1 araport11 lnc_RNA 11101 11372 . + . ID=transcript:AT1G03987.1;biotype=lncRNA;Parent=gene:AT1G03987;transcript_id=AT1G03987.1; -1 araport11 exon 11101 11372 . + . Name=AT1G03987.1.exon1;Parent=transcript:AT1G03987.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G03987.1.exon1;rank=1; -1 araport11 gene 11649 13714 . - . ID=gene:AT1G01030;Name=NGA3;biotype=protein_coding;description=B3 domain-containing transcription factor NGA3 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9MAN1];gene_id=AT1G01030;logic_name=araport11; -1 araport11 mRNA 11649 13714 . - . ID=transcript:AT1G01030.1;biotype=protein_coding;Parent=gene:AT1G01030;transcript_id=AT1G01030.1; -1 araport11 three_prime_UTR 11649 11863 . - . Parent=transcript:AT1G01030.1; -1 araport11 exon 11649 13173 . - . Name=AT1G01030.1.exon2;Parent=transcript:AT1G01030.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01030.1.exon2;rank=2; -1 araport11 CDS 11864 12940 . - 0 ID=CDS:AT1G01030.1;Parent=transcript:AT1G01030.1;protein_id=AT1G01030.1 -1 araport11 five_prime_UTR 12941 13173 . - . Parent=transcript:AT1G01030.1; -1 araport11 exon 13335 13714 . - . Name=AT1G01030.2.exon1;Parent=transcript:AT1G01030.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01030.2.exon1;rank=1; -1 araport11 five_prime_UTR 13335 13714 . - . Parent=transcript:AT1G01030.1; -1 araport11 mRNA 11649 13714 . - . ID=transcript:AT1G01030.2;biotype=protein_coding;Parent=gene:AT1G01030;transcript_id=AT1G01030.2; -1 araport11 three_prime_UTR 11649 11863 . - . Parent=transcript:AT1G01030.2; -1 araport11 exon 11649 12354 . - . Name=AT1G01030.2.exon3;Parent=transcript:AT1G01030.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01030.2.exon3;rank=3; -1 araport11 CDS 11864 12354 . - 2 ID=CDS:AT1G01030.2;Parent=transcript:AT1G01030.2;protein_id=AT1G01030.2 -1 araport11 CDS 12424 12940 . - 0 ID=CDS:AT1G01030.2;Parent=transcript:AT1G01030.2;protein_id=AT1G01030.2 -1 araport11 exon 12424 13173 . - . Name=AT1G01030.2.exon2;Parent=transcript:AT1G01030.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01030.2.exon2;rank=2; -1 araport11 five_prime_UTR 12941 13173 . - . Parent=transcript:AT1G01030.2; -1 araport11 exon 13335 13714 . - . Name=AT1G01030.2.exon1;Parent=transcript:AT1G01030.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01030.2.exon1;rank=1; -1 araport11 five_prime_UTR 13335 13714 . - . Parent=transcript:AT1G01030.2; -1 araport11 gene 23121 31227 . + . ID=gene:AT1G01040;Name=DCL1;biotype=protein_coding;description=Dicer-like 1 [Source:UniProtKB/TrEMBL%3bAcc:F4HQG6];gene_id=AT1G01040;logic_name=araport11; -1 araport11 mRNA 23121 31227 . + . ID=transcript:AT1G01040.1;biotype=protein_coding;Parent=gene:AT1G01040;transcript_id=AT1G01040.1; -1 araport11 five_prime_UTR 23121 23518 . + . Parent=transcript:AT1G01040.1; -1 araport11 exon 23121 24451 . + . Name=AT1G01040.1.exon1;Parent=transcript:AT1G01040.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01040.1.exon1;rank=1; -1 araport11 CDS 23519 24451 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 24542 24655 . + . Name=AT1G01040.1.exon2;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon2;rank=2; -1 araport11 CDS 24542 24655 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 24752 24962 . + . Name=AT1G01040.1.exon3;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01040.1.exon3;rank=3; -1 araport11 CDS 24752 24962 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 25041 25435 . + . Name=AT1G01040.1.exon4;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01040.1.exon4;rank=4; -1 araport11 CDS 25041 25435 . + 2 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 25524 25743 . + . Name=AT1G01040.1.exon5;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01040.1.exon5;rank=5; -1 araport11 CDS 25524 25743 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 25825 25997 . + . Name=AT1G01040.1.exon6;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01040.1.exon6;rank=6; -1 araport11 CDS 25825 25997 . + 2 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 26081 26203 . + . Name=AT1G01040.1.exon7;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon7;rank=7; -1 araport11 CDS 26081 26203 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 26292 26452 . + . Name=AT1G01040.1.exon8;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01040.1.exon8;rank=8; -1 araport11 CDS 26292 26452 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 26543 26776 . + . Name=AT1G01040.1.exon9;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01040.1.exon9;rank=9; -1 araport11 CDS 26543 26776 . + 1 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 26862 27012 . + . Name=AT1G01040.1.exon10;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01040.1.exon10;rank=10; -1 araport11 CDS 26862 27012 . + 1 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 27099 27281 . + . Name=AT1G01040.1.exon11;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon11;rank=11; -1 araport11 CDS 27099 27281 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 27372 27533 . + . Name=AT1G01040.1.exon12;Parent=transcript:AT1G01040.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon12;rank=12; -1 araport11 CDS 27372 27533 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 27618 27713 . + . Name=AT1G01040.1.exon13;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon13;rank=13; -1 araport11 CDS 27618 27713 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 27803 28431 . + . Name=AT1G01040.1.exon14;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01040.1.exon14;rank=14; -1 araport11 CDS 27803 28431 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 28708 28805 . + . Name=AT1G01040.1.exon15;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01040.1.exon15;rank=15; -1 araport11 CDS 28708 28805 . + 1 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 28890 29080 . + . Name=AT1G01040.1.exon16;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01040.1.exon16;rank=16; -1 araport11 CDS 28890 29080 . + 2 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 29160 30065 . + . Name=AT1G01040.1.exon17;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon17;rank=17; -1 araport11 CDS 29160 30065 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 30147 30311 . + . Name=AT1G01040.1.exon18;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon18;rank=18; -1 araport11 CDS 30147 30311 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 30410 30816 . + . Name=AT1G01040.1.exon19;Parent=transcript:AT1G01040.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01040.1.exon19;rank=19; -1 araport11 CDS 30410 30816 . + 0 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 CDS 30902 31079 . + 1 ID=CDS:AT1G01040.1;Parent=transcript:AT1G01040.1;protein_id=AT1G01040.1 -1 araport11 exon 30902 31227 . + . Name=AT1G01040.1.exon20;Parent=transcript:AT1G01040.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01040.1.exon20;rank=20; -1 araport11 three_prime_UTR 31080 31227 . + . Parent=transcript:AT1G01040.1; -1 araport11 mRNA 23416 31120 . + . ID=transcript:AT1G01040.2;biotype=protein_coding;Parent=gene:AT1G01040;transcript_id=AT1G01040.2; -1 araport11 five_prime_UTR 23416 23518 . + . Parent=transcript:AT1G01040.2; -1 araport11 exon 23416 24451 . + . Name=AT1G01040.2.exon1;Parent=transcript:AT1G01040.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01040.2.exon1;rank=1; -1 araport11 CDS 23519 24451 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 24542 24655 . + . Name=AT1G01040.1.exon2;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon2;rank=2; -1 araport11 CDS 24542 24655 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 24752 24962 . + . Name=AT1G01040.1.exon3;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01040.1.exon3;rank=3; -1 araport11 CDS 24752 24962 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 25041 25435 . + . Name=AT1G01040.1.exon4;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01040.1.exon4;rank=4; -1 araport11 CDS 25041 25435 . + 2 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 25524 25743 . + . Name=AT1G01040.1.exon5;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01040.1.exon5;rank=5; -1 araport11 CDS 25524 25743 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 25825 25997 . + . Name=AT1G01040.1.exon6;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01040.1.exon6;rank=6; -1 araport11 CDS 25825 25997 . + 2 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 26081 26203 . + . Name=AT1G01040.1.exon7;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon7;rank=7; -1 araport11 CDS 26081 26203 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 26292 26452 . + . Name=AT1G01040.1.exon8;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01040.1.exon8;rank=8; -1 araport11 CDS 26292 26452 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 26543 26776 . + . Name=AT1G01040.1.exon9;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01040.1.exon9;rank=9; -1 araport11 CDS 26543 26776 . + 1 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 26862 27012 . + . Name=AT1G01040.1.exon10;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01040.1.exon10;rank=10; -1 araport11 CDS 26862 27012 . + 1 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 27099 27281 . + . Name=AT1G01040.1.exon11;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon11;rank=11; -1 araport11 CDS 27099 27281 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 27372 27536 . + . Name=AT1G01040.2.exon12;Parent=transcript:AT1G01040.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.2.exon12;rank=12; -1 araport11 CDS 27372 27536 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 27618 27713 . + . Name=AT1G01040.1.exon13;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon13;rank=13; -1 araport11 CDS 27618 27713 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 27803 28431 . + . Name=AT1G01040.1.exon14;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01040.1.exon14;rank=14; -1 araport11 CDS 27803 28431 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 28708 28805 . + . Name=AT1G01040.1.exon15;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01040.1.exon15;rank=15; -1 araport11 CDS 28708 28805 . + 1 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 28890 29080 . + . Name=AT1G01040.1.exon16;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01040.1.exon16;rank=16; -1 araport11 CDS 28890 29080 . + 2 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 29160 30065 . + . Name=AT1G01040.1.exon17;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon17;rank=17; -1 araport11 CDS 29160 30065 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 30147 30311 . + . Name=AT1G01040.1.exon18;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01040.1.exon18;rank=18; -1 araport11 CDS 30147 30311 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 30410 30816 . + . Name=AT1G01040.1.exon19;Parent=transcript:AT1G01040.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01040.1.exon19;rank=19; -1 araport11 CDS 30410 30816 . + 0 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 CDS 30902 31079 . + 1 ID=CDS:AT1G01040.2;Parent=transcript:AT1G01040.2;protein_id=AT1G01040.2 -1 araport11 exon 30902 31120 . + . Name=AT1G01040.2.exon20;Parent=transcript:AT1G01040.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01040.2.exon20;rank=20; -1 araport11 three_prime_UTR 31080 31120 . + . Parent=transcript:AT1G01040.2; -1 araport11 ncRNA_gene 23312 24099 . - . ID=gene:AT1G03993;biotype=lncRNA;gene_id=AT1G03993;logic_name=araport11; -1 araport11 lnc_RNA 23312 24099 . - . ID=transcript:AT1G03993.1;biotype=lncRNA;Parent=gene:AT1G03993;transcript_id=AT1G03993.1; -1 araport11 exon 23312 24099 . - . Name=AT1G03993.1.exon1;Parent=transcript:AT1G03993.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G03993.1.exon1;rank=1; -1 araport11 ncRNA_gene 28500 28706 . + . ID=gene:AT1G01046;Name=MIR838A;biotype=miRNA;description=MIR838a%3b miRNA [Source:TAIR%3bAcc:AT1G01046];gene_id=AT1G01046;logic_name=araport11; -1 araport11 miRNA 28500 28706 . + . ID=transcript:at1g01046;biotype=miRNA;Parent=gene:AT1G01046;transcript_id=at1g01046; -1 araport11 exon 28500 28706 . + . Name=at1g01046.exon;Parent=transcript:at1g01046;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=at1g01046.exon;rank=1; -1 araport11 gene 31170 33171 . - . ID=gene:AT1G01050;Name=PPA1;biotype=protein_coding;description=Soluble inorganic pyrophosphatase 1 [Source:UniProtKB/Swiss-Prot%3bAcc:Q93V56];gene_id=AT1G01050;logic_name=araport11; -1 araport11 mRNA 31170 33171 . - . ID=transcript:AT1G01050.1;biotype=protein_coding;Parent=gene:AT1G01050;transcript_id=AT1G01050.1; -1 araport11 three_prime_UTR 31170 31381 . - . Parent=transcript:AT1G01050.1; -1 araport11 exon 31170 31424 . - . Name=AT1G01050.1.exon9;Parent=transcript:AT1G01050.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01050.1.exon9;rank=9; -1 araport11 CDS 31382 31424 . - 1 ID=CDS:AT1G01050.1;Parent=transcript:AT1G01050.1;protein_id=AT1G01050.1 -1 araport11 exon 31521 31602 . - . Name=AT1G01050.2.exon8;Parent=transcript:AT1G01050.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01050.2.exon8;rank=8; -1 araport11 CDS 31521 31602 . - 2 ID=CDS:AT1G01050.1;Parent=transcript:AT1G01050.1;protein_id=AT1G01050.1 -1 araport11 exon 31693 31813 . - . Name=AT1G01050.2.exon7;Parent=transcript:AT1G01050.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01050.2.exon7;rank=7; -1 araport11 CDS 31693 31813 . - 0 ID=CDS:AT1G01050.1;Parent=transcript:AT1G01050.1;protein_id=AT1G01050.1 -1 araport11 exon 31933 31998 . - . Name=AT1G01050.2.exon6;Parent=transcript:AT1G01050.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01050.2.exon6;rank=6; -1 araport11 CDS 31933 31998 . - 0 ID=CDS:AT1G01050.1;Parent=transcript:AT1G01050.1;protein_id=AT1G01050.1 -1 araport11 exon 32088 32195 . - . Name=AT1G01050.2.exon5;Parent=transcript:AT1G01050.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01050.2.exon5;rank=5; -1 araport11 CDS 32088 32195 . - 0 ID=CDS:AT1G01050.1;Parent=transcript:AT1G01050.1;protein_id=AT1G01050.1 -1 araport11 exon 32282 32347 . - . Name=AT1G01050.2.exon4;Parent=transcript:AT1G01050.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01050.2.exon4;rank=4; -1 araport11 CDS 32282 32347 . - 0 ID=CDS:AT1G01050.1;Parent=transcript:AT1G01050.1;protein_id=AT1G01050.1 -1 araport11 exon 32431 32459 . - . Name=AT1G01050.2.exon3;Parent=transcript:AT1G01050.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01050.2.exon3;rank=3; -1 araport11 CDS 32431 32459 . - 2 ID=CDS:AT1G01050.1;Parent=transcript:AT1G01050.1;protein_id=AT1G01050.1 -1 araport11 exon 32547 32670 . - . Name=AT1G01050.2.exon2;Parent=transcript:AT1G01050.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01050.2.exon2;rank=2; -1 araport11 CDS 32547 32670 . - 0 ID=CDS:AT1G01050.1;Parent=transcript:AT1G01050.1;protein_id=AT1G01050.1 -1 araport11 exon 33029 33171 . - . Name=AT1G01050.1.exon1;Parent=transcript:AT1G01050.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01050.1.exon1;rank=1; -1 araport11 five_prime_UTR 33029 33171 . - . Parent=transcript:AT1G01050.1; -1 araport11 mRNA 31382 33009 . - . ID=transcript:AT1G01050.2;biotype=protein_coding;Parent=gene:AT1G01050;transcript_id=AT1G01050.2; -1 araport11 exon 31382 31424 . - . Name=AT1G01050.2.exon9;Parent=transcript:AT1G01050.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01050.2.exon9;rank=9; -1 araport11 CDS 31382 31424 . - 1 ID=CDS:AT1G01050.2;Parent=transcript:AT1G01050.2;protein_id=AT1G01050.2 -1 araport11 exon 31521 31602 . - . Name=AT1G01050.2.exon8;Parent=transcript:AT1G01050.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01050.2.exon8;rank=8; -1 araport11 CDS 31521 31602 . - 2 ID=CDS:AT1G01050.2;Parent=transcript:AT1G01050.2;protein_id=AT1G01050.2 -1 araport11 exon 31693 31813 . - . Name=AT1G01050.2.exon7;Parent=transcript:AT1G01050.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01050.2.exon7;rank=7; -1 araport11 CDS 31693 31813 . - 0 ID=CDS:AT1G01050.2;Parent=transcript:AT1G01050.2;protein_id=AT1G01050.2 -1 araport11 exon 31933 31998 . - . Name=AT1G01050.2.exon6;Parent=transcript:AT1G01050.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01050.2.exon6;rank=6; -1 araport11 CDS 31933 31998 . - 0 ID=CDS:AT1G01050.2;Parent=transcript:AT1G01050.2;protein_id=AT1G01050.2 -1 araport11 exon 32088 32195 . - . Name=AT1G01050.2.exon5;Parent=transcript:AT1G01050.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01050.2.exon5;rank=5; -1 araport11 CDS 32088 32195 . - 0 ID=CDS:AT1G01050.2;Parent=transcript:AT1G01050.2;protein_id=AT1G01050.2 -1 araport11 exon 32282 32347 . - . Name=AT1G01050.2.exon4;Parent=transcript:AT1G01050.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01050.2.exon4;rank=4; -1 araport11 CDS 32282 32347 . - 0 ID=CDS:AT1G01050.2;Parent=transcript:AT1G01050.2;protein_id=AT1G01050.2 -1 araport11 exon 32431 32459 . - . Name=AT1G01050.2.exon3;Parent=transcript:AT1G01050.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01050.2.exon3;rank=3; -1 araport11 CDS 32431 32459 . - 2 ID=CDS:AT1G01050.2;Parent=transcript:AT1G01050.2;protein_id=AT1G01050.2 -1 araport11 exon 32547 32670 . - . Name=AT1G01050.2.exon2;Parent=transcript:AT1G01050.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01050.2.exon2;rank=2; -1 araport11 CDS 32547 32670 . - 0 ID=CDS:AT1G01050.2;Parent=transcript:AT1G01050.2;protein_id=AT1G01050.2 -1 araport11 exon 32839 33009 . - . Name=AT1G01050.2.exon1;Parent=transcript:AT1G01050.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01050.2.exon1;rank=1; -1 araport11 five_prime_UTR 32839 33009 . - . Parent=transcript:AT1G01050.2; -1 araport11 ncRNA_gene 32727 33009 . + . ID=gene:AT1G03997;biotype=lncRNA;gene_id=AT1G03997;logic_name=araport11; -1 araport11 lnc_RNA 32727 33009 . + . ID=transcript:AT1G03997.1;biotype=lncRNA;Parent=gene:AT1G03997;transcript_id=AT1G03997.1; -1 araport11 exon 32727 33009 . + . Name=AT1G03997.1.exon1;Parent=transcript:AT1G03997.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G03997.1.exon1;rank=1; -1 araport11 gene 33365 37871 . - . ID=gene:AT1G01060;Name=LHY;biotype=protein_coding;description=LHY1 [Source:UniProtKB/TrEMBL%3bAcc:A0A178W761];gene_id=AT1G01060;logic_name=araport11; -1 araport11 mRNA 33365 37871 . - . ID=transcript:AT1G01060.6;biotype=protein_coding;Parent=gene:AT1G01060;transcript_id=AT1G01060.6; -1 araport11 exon 33365 33589 . - . Name=AT1G01060.6.exon10;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.6.exon10;rank=10; -1 araport11 three_prime_UTR 33365 33589 . - . Parent=transcript:AT1G01060.6; -1 araport11 three_prime_UTR 33981 33991 . - . Parent=transcript:AT1G01060.6; -1 araport11 exon 33981 34327 . - . Name=AT1G01060.6.exon9;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01060.6.exon9;rank=9; -1 araport11 CDS 33992 34327 . - 0 ID=CDS:AT1G01060.6;Parent=transcript:AT1G01060.6;protein_id=AT1G01060.6 -1 araport11 exon 34401 35474 . - . Name=AT1G01060.5.exon8;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon8;rank=8; -1 araport11 CDS 34401 35474 . - 0 ID=CDS:AT1G01060.6;Parent=transcript:AT1G01060.6;protein_id=AT1G01060.6 -1 araport11 exon 35567 35647 . - . Name=AT1G01060.5.exon7;Parent=transcript:AT1G01060.6;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon7;rank=7; -1 araport11 CDS 35567 35647 . - 0 ID=CDS:AT1G01060.6;Parent=transcript:AT1G01060.6;protein_id=AT1G01060.6 -1 araport11 exon 35730 35999 . - . Name=AT1G01060.5.exon6;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon6;rank=6; -1 araport11 CDS 35730 35999 . - 0 ID=CDS:AT1G01060.6;Parent=transcript:AT1G01060.6;protein_id=AT1G01060.6 -1 araport11 exon 36090 36171 . - . Name=AT1G01060.5.exon5;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01060.5.exon5;rank=5; -1 araport11 CDS 36090 36171 . - 1 ID=CDS:AT1G01060.6;Parent=transcript:AT1G01060.6;protein_id=AT1G01060.6 -1 araport11 exon 36624 36685 . - . Name=AT1G01060.5.exon4;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01060.5.exon4;rank=4; -1 araport11 CDS 36624 36685 . - 0 ID=CDS:AT1G01060.6;Parent=transcript:AT1G01060.6;protein_id=AT1G01060.6 -1 araport11 CDS 36810 36836 . - 0 ID=CDS:AT1G01060.6;Parent=transcript:AT1G01060.6;protein_id=AT1G01060.6 -1 araport11 exon 36810 36921 . - . Name=AT1G01060.5.exon3;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01060.5.exon3;rank=3; -1 araport11 five_prime_UTR 36837 36921 . - . Parent=transcript:AT1G01060.6; -1 araport11 exon 37023 37203 . - . Name=AT1G01060.5.exon2;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.5.exon2;rank=2; -1 araport11 five_prime_UTR 37023 37203 . - . Parent=transcript:AT1G01060.6; -1 araport11 exon 37373 37871 . - . Name=AT1G01060.5.exon1;Parent=transcript:AT1G01060.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.5.exon1;rank=1; -1 araport11 five_prime_UTR 37373 37871 . - . Parent=transcript:AT1G01060.6; -1 araport11 mRNA 33379 37757 . - . ID=transcript:AT1G01060.3;biotype=protein_coding;Parent=gene:AT1G01060;transcript_id=AT1G01060.3; -1 araport11 exon 33379 33589 . - . Name=AT1G01060.3.exon10;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.3.exon10;rank=10; -1 araport11 three_prime_UTR 33379 33589 . - . Parent=transcript:AT1G01060.3; -1 araport11 three_prime_UTR 33981 33991 . - . Parent=transcript:AT1G01060.3; -1 araport11 exon 33981 34327 . - . Name=AT1G01060.6.exon9;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01060.6.exon9;rank=9; -1 araport11 CDS 33992 34327 . - 0 ID=CDS:AT1G01060.3;Parent=transcript:AT1G01060.3;protein_id=AT1G01060.3 -1 araport11 exon 34401 35474 . - . Name=AT1G01060.5.exon8;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon8;rank=8; -1 araport11 CDS 34401 35474 . - 0 ID=CDS:AT1G01060.3;Parent=transcript:AT1G01060.3;protein_id=AT1G01060.3 -1 araport11 exon 35567 35647 . - . Name=AT1G01060.5.exon7;Parent=transcript:AT1G01060.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon7;rank=7; -1 araport11 CDS 35567 35647 . - 0 ID=CDS:AT1G01060.3;Parent=transcript:AT1G01060.3;protein_id=AT1G01060.3 -1 araport11 exon 35730 35963 . - . Name=AT1G01060.7.exon5;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.7.exon5;rank=6; -1 araport11 CDS 35730 35963 . - 0 ID=CDS:AT1G01060.3;Parent=transcript:AT1G01060.3;protein_id=AT1G01060.3 -1 araport11 exon 36624 36685 . - . Name=AT1G01060.7.exon4;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01060.7.exon4;rank=5; -1 araport11 CDS 36624 36685 . - 2 ID=CDS:AT1G01060.3;Parent=transcript:AT1G01060.3;protein_id=AT1G01060.3 -1 araport11 exon 36810 36921 . - . Name=AT1G01060.7.exon3;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01060.7.exon3;rank=4; -1 araport11 CDS 36810 36921 . - 0 ID=CDS:AT1G01060.3;Parent=transcript:AT1G01060.3;protein_id=AT1G01060.3 -1 araport11 CDS 37023 37061 . - 0 ID=CDS:AT1G01060.3;Parent=transcript:AT1G01060.3;protein_id=AT1G01060.3 -1 araport11 exon 37023 37203 . - . Name=AT1G01060.1.exon3;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01060.1.exon3;rank=3; -1 araport11 five_prime_UTR 37062 37203 . - . Parent=transcript:AT1G01060.3; -1 araport11 exon 37373 37398 . - . Name=AT1G01060.1.exon2;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.1.exon2;rank=2; -1 araport11 five_prime_UTR 37373 37398 . - . Parent=transcript:AT1G01060.3; -1 araport11 exon 37569 37757 . - . Name=AT1G01060.3.exon1;Parent=transcript:AT1G01060.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.3.exon1;rank=1; -1 araport11 five_prime_UTR 37569 37757 . - . Parent=transcript:AT1G01060.3; -1 araport11 mRNA 33662 37840 . - . ID=transcript:AT1G01060.1;biotype=protein_coding;Parent=gene:AT1G01060;transcript_id=AT1G01060.1; -1 araport11 three_prime_UTR 33662 33991 . - . Parent=transcript:AT1G01060.1; -1 araport11 exon 33662 34327 . - . Name=AT1G01060.7.exon8;Parent=transcript:AT1G01060.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01060.7.exon8;rank=9; -1 araport11 CDS 33992 34327 . - 0 ID=CDS:AT1G01060.1;Parent=transcript:AT1G01060.1;protein_id=AT1G01060.1 -1 araport11 exon 34401 35474 . - . Name=AT1G01060.5.exon8;Parent=transcript:AT1G01060.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon8;rank=8; -1 araport11 CDS 34401 35474 . - 0 ID=CDS:AT1G01060.1;Parent=transcript:AT1G01060.1;protein_id=AT1G01060.1 -1 araport11 exon 35567 35647 . - . Name=AT1G01060.5.exon7;Parent=transcript:AT1G01060.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon7;rank=7; -1 araport11 CDS 35567 35647 . - 0 ID=CDS:AT1G01060.1;Parent=transcript:AT1G01060.1;protein_id=AT1G01060.1 -1 araport11 exon 35730 35963 . - . Name=AT1G01060.7.exon5;Parent=transcript:AT1G01060.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.7.exon5;rank=6; -1 araport11 CDS 35730 35963 . - 0 ID=CDS:AT1G01060.1;Parent=transcript:AT1G01060.1;protein_id=AT1G01060.1 -1 araport11 exon 36624 36685 . - . Name=AT1G01060.7.exon4;Parent=transcript:AT1G01060.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01060.7.exon4;rank=5; -1 araport11 CDS 36624 36685 . - 2 ID=CDS:AT1G01060.1;Parent=transcript:AT1G01060.1;protein_id=AT1G01060.1 -1 araport11 exon 36810 36921 . - . Name=AT1G01060.7.exon3;Parent=transcript:AT1G01060.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01060.7.exon3;rank=4; -1 araport11 CDS 36810 36921 . - 0 ID=CDS:AT1G01060.1;Parent=transcript:AT1G01060.1;protein_id=AT1G01060.1 -1 araport11 CDS 37023 37061 . - 0 ID=CDS:AT1G01060.1;Parent=transcript:AT1G01060.1;protein_id=AT1G01060.1 -1 araport11 exon 37023 37203 . - . Name=AT1G01060.1.exon3;Parent=transcript:AT1G01060.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01060.1.exon3;rank=3; -1 araport11 five_prime_UTR 37062 37203 . - . Parent=transcript:AT1G01060.1; -1 araport11 exon 37373 37398 . - . Name=AT1G01060.1.exon2;Parent=transcript:AT1G01060.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.1.exon2;rank=2; -1 araport11 five_prime_UTR 37373 37398 . - . Parent=transcript:AT1G01060.1; -1 araport11 exon 37569 37840 . - . Name=AT1G01060.1.exon1;Parent=transcript:AT1G01060.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.1.exon1;rank=1; -1 araport11 five_prime_UTR 37569 37840 . - . Parent=transcript:AT1G01060.1; -1 araport11 mRNA 33662 37871 . - . ID=transcript:AT1G01060.7;biotype=protein_coding;Parent=gene:AT1G01060;transcript_id=AT1G01060.7; -1 araport11 three_prime_UTR 33662 33991 . - . Parent=transcript:AT1G01060.7; -1 araport11 exon 33662 34327 . - . Name=AT1G01060.7.exon8;Parent=transcript:AT1G01060.7;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01060.7.exon8;rank=8; -1 araport11 CDS 33992 34327 . - 0 ID=CDS:AT1G01060.7;Parent=transcript:AT1G01060.7;protein_id=AT1G01060.7 -1 araport11 exon 34401 35474 . - . Name=AT1G01060.5.exon8;Parent=transcript:AT1G01060.7;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon8;rank=7; -1 araport11 CDS 34401 35474 . - 0 ID=CDS:AT1G01060.7;Parent=transcript:AT1G01060.7;protein_id=AT1G01060.7 -1 araport11 exon 35567 35647 . - . Name=AT1G01060.5.exon7;Parent=transcript:AT1G01060.7;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon7;rank=6; -1 araport11 CDS 35567 35647 . - 0 ID=CDS:AT1G01060.7;Parent=transcript:AT1G01060.7;protein_id=AT1G01060.7 -1 araport11 exon 35730 35963 . - . Name=AT1G01060.7.exon5;Parent=transcript:AT1G01060.7;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.7.exon5;rank=5; -1 araport11 CDS 35730 35963 . - 0 ID=CDS:AT1G01060.7;Parent=transcript:AT1G01060.7;protein_id=AT1G01060.7 -1 araport11 exon 36624 36685 . - . Name=AT1G01060.7.exon4;Parent=transcript:AT1G01060.7;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01060.7.exon4;rank=4; -1 araport11 CDS 36624 36685 . - 2 ID=CDS:AT1G01060.7;Parent=transcript:AT1G01060.7;protein_id=AT1G01060.7 -1 araport11 exon 36810 36921 . - . Name=AT1G01060.7.exon3;Parent=transcript:AT1G01060.7;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01060.7.exon3;rank=3; -1 araport11 CDS 36810 36921 . - 0 ID=CDS:AT1G01060.7;Parent=transcript:AT1G01060.7;protein_id=AT1G01060.7 -1 araport11 CDS 37023 37061 . - 0 ID=CDS:AT1G01060.7;Parent=transcript:AT1G01060.7;protein_id=AT1G01060.7 -1 araport11 exon 37023 37398 . - . Name=AT1G01060.7.exon2;Parent=transcript:AT1G01060.7;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01060.7.exon2;rank=2; -1 araport11 five_prime_UTR 37062 37398 . - . Parent=transcript:AT1G01060.7; -1 araport11 exon 37569 37871 . - . Name=AT1G01060.7.exon1;Parent=transcript:AT1G01060.7;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.7.exon1;rank=1; -1 araport11 five_prime_UTR 37569 37871 . - . Parent=transcript:AT1G01060.7; -1 araport11 mRNA 33666 37780 . - . ID=transcript:AT1G01060.4;biotype=protein_coding;Parent=gene:AT1G01060;transcript_id=AT1G01060.4; -1 araport11 three_prime_UTR 33666 33991 . - . Parent=transcript:AT1G01060.4; -1 araport11 exon 33666 34327 . - . Name=AT1G01060.2.exon8;Parent=transcript:AT1G01060.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01060.2.exon8;rank=9; -1 araport11 CDS 33992 34327 . - 0 ID=CDS:AT1G01060.4;Parent=transcript:AT1G01060.4;protein_id=AT1G01060.4 -1 araport11 exon 34401 35471 . - . Name=AT1G01060.4.exon8;Parent=transcript:AT1G01060.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.4.exon8;rank=8; -1 araport11 CDS 34401 35471 . - 0 ID=CDS:AT1G01060.4;Parent=transcript:AT1G01060.4;protein_id=AT1G01060.4 -1 araport11 exon 35567 35647 . - . Name=AT1G01060.5.exon7;Parent=transcript:AT1G01060.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon7;rank=7; -1 araport11 CDS 35567 35647 . - 0 ID=CDS:AT1G01060.4;Parent=transcript:AT1G01060.4;protein_id=AT1G01060.4 -1 araport11 exon 35730 35963 . - . Name=AT1G01060.7.exon5;Parent=transcript:AT1G01060.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.7.exon5;rank=6; -1 araport11 CDS 35730 35963 . - 0 ID=CDS:AT1G01060.4;Parent=transcript:AT1G01060.4;protein_id=AT1G01060.4 -1 araport11 exon 36624 36685 . - . Name=AT1G01060.7.exon4;Parent=transcript:AT1G01060.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01060.7.exon4;rank=5; -1 araport11 CDS 36624 36685 . - 2 ID=CDS:AT1G01060.4;Parent=transcript:AT1G01060.4;protein_id=AT1G01060.4 -1 araport11 exon 36810 36921 . - . Name=AT1G01060.7.exon3;Parent=transcript:AT1G01060.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01060.7.exon3;rank=4; -1 araport11 CDS 36810 36921 . - 0 ID=CDS:AT1G01060.4;Parent=transcript:AT1G01060.4;protein_id=AT1G01060.4 -1 araport11 CDS 37023 37061 . - 0 ID=CDS:AT1G01060.4;Parent=transcript:AT1G01060.4;protein_id=AT1G01060.4 -1 araport11 exon 37023 37203 . - . Name=AT1G01060.1.exon3;Parent=transcript:AT1G01060.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01060.1.exon3;rank=3; -1 araport11 five_prime_UTR 37062 37203 . - . Parent=transcript:AT1G01060.4; -1 araport11 exon 37373 37398 . - . Name=AT1G01060.1.exon2;Parent=transcript:AT1G01060.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.1.exon2;rank=2; -1 araport11 five_prime_UTR 37373 37398 . - . Parent=transcript:AT1G01060.4; -1 araport11 exon 37569 37780 . - . Name=AT1G01060.4.exon1;Parent=transcript:AT1G01060.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.4.exon1;rank=1; -1 araport11 five_prime_UTR 37569 37780 . - . Parent=transcript:AT1G01060.4; -1 araport11 mRNA 33666 37780 . - . ID=transcript:AT1G01060.2;biotype=protein_coding;Parent=gene:AT1G01060;transcript_id=AT1G01060.2; -1 araport11 three_prime_UTR 33666 33991 . - . Parent=transcript:AT1G01060.2; -1 araport11 exon 33666 34327 . - . Name=AT1G01060.2.exon8;Parent=transcript:AT1G01060.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01060.2.exon8;rank=8; -1 araport11 CDS 33992 34327 . - 0 ID=CDS:AT1G01060.2;Parent=transcript:AT1G01060.2;protein_id=AT1G01060.2 -1 araport11 exon 34401 35474 . - . Name=AT1G01060.5.exon8;Parent=transcript:AT1G01060.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon8;rank=7; -1 araport11 CDS 34401 35474 . - 0 ID=CDS:AT1G01060.2;Parent=transcript:AT1G01060.2;protein_id=AT1G01060.2 -1 araport11 exon 35567 35647 . - . Name=AT1G01060.5.exon7;Parent=transcript:AT1G01060.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon7;rank=6; -1 araport11 CDS 35567 35647 . - 0 ID=CDS:AT1G01060.2;Parent=transcript:AT1G01060.2;protein_id=AT1G01060.2 -1 araport11 exon 35730 35963 . - . Name=AT1G01060.7.exon5;Parent=transcript:AT1G01060.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.7.exon5;rank=5; -1 araport11 CDS 35730 35963 . - 0 ID=CDS:AT1G01060.2;Parent=transcript:AT1G01060.2;protein_id=AT1G01060.2 -1 araport11 exon 36624 36685 . - . Name=AT1G01060.7.exon4;Parent=transcript:AT1G01060.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01060.7.exon4;rank=4; -1 araport11 CDS 36624 36685 . - 2 ID=CDS:AT1G01060.2;Parent=transcript:AT1G01060.2;protein_id=AT1G01060.2 -1 araport11 exon 36810 36921 . - . Name=AT1G01060.7.exon3;Parent=transcript:AT1G01060.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01060.7.exon3;rank=3; -1 araport11 CDS 36810 36921 . - 0 ID=CDS:AT1G01060.2;Parent=transcript:AT1G01060.2;protein_id=AT1G01060.2 -1 araport11 CDS 37023 37061 . - 0 ID=CDS:AT1G01060.2;Parent=transcript:AT1G01060.2;protein_id=AT1G01060.2 -1 araport11 exon 37023 37203 . - . Name=AT1G01060.1.exon3;Parent=transcript:AT1G01060.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01060.1.exon3;rank=2; -1 araport11 five_prime_UTR 37062 37203 . - . Parent=transcript:AT1G01060.2; -1 araport11 exon 37373 37780 . - . Name=AT1G01060.2.exon1;Parent=transcript:AT1G01060.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.2.exon1;rank=1; -1 araport11 five_prime_UTR 37373 37780 . - . Parent=transcript:AT1G01060.2; -1 araport11 mRNA 33967 37230 . - . ID=transcript:AT1G01060.8;biotype=protein_coding;Parent=gene:AT1G01060;transcript_id=AT1G01060.8; -1 araport11 three_prime_UTR 33967 33991 . - . Parent=transcript:AT1G01060.8; -1 araport11 exon 33967 34327 . - . Name=AT1G01060.5.exon9;Parent=transcript:AT1G01060.8;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01060.5.exon9;rank=7; -1 araport11 CDS 33992 34327 . - 0 ID=CDS:AT1G01060.8;Parent=transcript:AT1G01060.8;protein_id=AT1G01060.8 -1 araport11 exon 34401 35474 . - . Name=AT1G01060.5.exon8;Parent=transcript:AT1G01060.8;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon8;rank=6; -1 araport11 CDS 34401 35474 . - 0 ID=CDS:AT1G01060.8;Parent=transcript:AT1G01060.8;protein_id=AT1G01060.8 -1 araport11 exon 35567 35647 . - . Name=AT1G01060.5.exon7;Parent=transcript:AT1G01060.8;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon7;rank=5; -1 araport11 CDS 35567 35647 . - 0 ID=CDS:AT1G01060.8;Parent=transcript:AT1G01060.8;protein_id=AT1G01060.8 -1 araport11 exon 35730 35963 . - . Name=AT1G01060.7.exon5;Parent=transcript:AT1G01060.8;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.7.exon5;rank=4; -1 araport11 CDS 35730 35963 . - 0 ID=CDS:AT1G01060.8;Parent=transcript:AT1G01060.8;protein_id=AT1G01060.8 -1 araport11 exon 36624 36685 . - . Name=AT1G01060.7.exon4;Parent=transcript:AT1G01060.8;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01060.7.exon4;rank=3; -1 araport11 CDS 36624 36685 . - 2 ID=CDS:AT1G01060.8;Parent=transcript:AT1G01060.8;protein_id=AT1G01060.8 -1 araport11 exon 36810 36921 . - . Name=AT1G01060.7.exon3;Parent=transcript:AT1G01060.8;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01060.7.exon3;rank=2; -1 araport11 CDS 36810 36921 . - 0 ID=CDS:AT1G01060.8;Parent=transcript:AT1G01060.8;protein_id=AT1G01060.8 -1 araport11 CDS 37023 37061 . - 0 ID=CDS:AT1G01060.8;Parent=transcript:AT1G01060.8;protein_id=AT1G01060.8 -1 araport11 exon 37023 37230 . - . Name=AT1G01060.8.exon1;Parent=transcript:AT1G01060.8;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01060.8.exon1;rank=1; -1 araport11 five_prime_UTR 37062 37230 . - . Parent=transcript:AT1G01060.8; -1 araport11 mRNA 33967 37871 . - . ID=transcript:AT1G01060.5;biotype=protein_coding;Parent=gene:AT1G01060;transcript_id=AT1G01060.5; -1 araport11 three_prime_UTR 33967 33991 . - . Parent=transcript:AT1G01060.5; -1 araport11 exon 33967 34327 . - . Name=AT1G01060.5.exon9;Parent=transcript:AT1G01060.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01060.5.exon9;rank=9; -1 araport11 CDS 33992 34327 . - 0 ID=CDS:AT1G01060.5;Parent=transcript:AT1G01060.5;protein_id=AT1G01060.5 -1 araport11 exon 34401 35474 . - . Name=AT1G01060.5.exon8;Parent=transcript:AT1G01060.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon8;rank=8; -1 araport11 CDS 34401 35474 . - 0 ID=CDS:AT1G01060.5;Parent=transcript:AT1G01060.5;protein_id=AT1G01060.5 -1 araport11 exon 35567 35647 . - . Name=AT1G01060.5.exon7;Parent=transcript:AT1G01060.5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon7;rank=7; -1 araport11 CDS 35567 35647 . - 0 ID=CDS:AT1G01060.5;Parent=transcript:AT1G01060.5;protein_id=AT1G01060.5 -1 araport11 exon 35730 35999 . - . Name=AT1G01060.5.exon6;Parent=transcript:AT1G01060.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01060.5.exon6;rank=6; -1 araport11 CDS 35730 35999 . - 0 ID=CDS:AT1G01060.5;Parent=transcript:AT1G01060.5;protein_id=AT1G01060.5 -1 araport11 exon 36090 36171 . - . Name=AT1G01060.5.exon5;Parent=transcript:AT1G01060.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01060.5.exon5;rank=5; -1 araport11 CDS 36090 36171 . - 1 ID=CDS:AT1G01060.5;Parent=transcript:AT1G01060.5;protein_id=AT1G01060.5 -1 araport11 exon 36624 36685 . - . Name=AT1G01060.5.exon4;Parent=transcript:AT1G01060.5;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01060.5.exon4;rank=4; -1 araport11 CDS 36624 36685 . - 0 ID=CDS:AT1G01060.5;Parent=transcript:AT1G01060.5;protein_id=AT1G01060.5 -1 araport11 CDS 36810 36836 . - 0 ID=CDS:AT1G01060.5;Parent=transcript:AT1G01060.5;protein_id=AT1G01060.5 -1 araport11 exon 36810 36921 . - . Name=AT1G01060.5.exon3;Parent=transcript:AT1G01060.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01060.5.exon3;rank=3; -1 araport11 five_prime_UTR 36837 36921 . - . Parent=transcript:AT1G01060.5; -1 araport11 exon 37023 37203 . - . Name=AT1G01060.5.exon2;Parent=transcript:AT1G01060.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.5.exon2;rank=2; -1 araport11 five_prime_UTR 37023 37203 . - . Parent=transcript:AT1G01060.5; -1 araport11 exon 37373 37871 . - . Name=AT1G01060.5.exon1;Parent=transcript:AT1G01060.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01060.5.exon1;rank=1; -1 araport11 five_prime_UTR 37373 37871 . - . Parent=transcript:AT1G01060.5; -1 araport11 gene 38444 41017 . - . ID=gene:AT1G01070;biotype=protein_coding;description=WAT1-related protein [Source:UniProtKB/TrEMBL%3bAcc:A0A178WFU3];gene_id=AT1G01070;logic_name=araport11; -1 araport11 mRNA 38444 41017 . - . ID=transcript:AT1G01070.1;biotype=protein_coding;Parent=gene:AT1G01070;transcript_id=AT1G01070.1; -1 araport11 three_prime_UTR 38444 38897 . - . Parent=transcript:AT1G01070.1; -1 araport11 exon 38444 39054 . - . Name=AT1G01070.1.exon6;Parent=transcript:AT1G01070.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01070.1.exon6;rank=6; -1 araport11 CDS 38898 39054 . - 1 ID=CDS:AT1G01070.1;Parent=transcript:AT1G01070.1;protein_id=AT1G01070.1 -1 araport11 exon 39136 39287 . - . Name=AT1G01070.2.exon4;Parent=transcript:AT1G01070.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01070.2.exon4;rank=5; -1 araport11 CDS 39136 39287 . - 0 ID=CDS:AT1G01070.1;Parent=transcript:AT1G01070.1;protein_id=AT1G01070.1 -1 araport11 exon 39409 39814 . - . Name=AT1G01070.2.exon3;Parent=transcript:AT1G01070.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01070.2.exon3;rank=4; -1 araport11 CDS 39409 39814 . - 1 ID=CDS:AT1G01070.1;Parent=transcript:AT1G01070.1;protein_id=AT1G01070.1 -1 araport11 exon 40213 40329 . - . Name=AT1G01070.2.exon2;Parent=transcript:AT1G01070.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01070.2.exon2;rank=3; -1 araport11 CDS 40213 40329 . - 1 ID=CDS:AT1G01070.1;Parent=transcript:AT1G01070.1;protein_id=AT1G01070.1 -1 araport11 exon 40473 40535 . - . Name=AT1G01070.1.exon2;Parent=transcript:AT1G01070.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01070.1.exon2;rank=2; -1 araport11 CDS 40473 40535 . - 1 ID=CDS:AT1G01070.1;Parent=transcript:AT1G01070.1;protein_id=AT1G01070.1 -1 araport11 CDS 40675 40877 . - 0 ID=CDS:AT1G01070.1;Parent=transcript:AT1G01070.1;protein_id=AT1G01070.1 -1 araport11 exon 40675 41017 . - . Name=AT1G01070.1.exon1;Parent=transcript:AT1G01070.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01070.1.exon1;rank=1; -1 araport11 five_prime_UTR 40878 41017 . - . Parent=transcript:AT1G01070.1; -1 araport11 mRNA 38752 40945 . - . ID=transcript:AT1G01070.2;biotype=protein_coding;Parent=gene:AT1G01070;transcript_id=AT1G01070.2; -1 araport11 three_prime_UTR 38752 38897 . - . Parent=transcript:AT1G01070.2; -1 araport11 exon 38752 39054 . - . Name=AT1G01070.2.exon5;Parent=transcript:AT1G01070.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01070.2.exon5;rank=5; -1 araport11 CDS 38898 39054 . - 1 ID=CDS:AT1G01070.2;Parent=transcript:AT1G01070.2;protein_id=AT1G01070.2 -1 araport11 exon 39136 39287 . - . Name=AT1G01070.2.exon4;Parent=transcript:AT1G01070.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01070.2.exon4;rank=4; -1 araport11 CDS 39136 39287 . - 0 ID=CDS:AT1G01070.2;Parent=transcript:AT1G01070.2;protein_id=AT1G01070.2 -1 araport11 exon 39409 39814 . - . Name=AT1G01070.2.exon3;Parent=transcript:AT1G01070.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01070.2.exon3;rank=3; -1 araport11 CDS 39409 39814 . - 1 ID=CDS:AT1G01070.2;Parent=transcript:AT1G01070.2;protein_id=AT1G01070.2 -1 araport11 exon 40213 40329 . - . Name=AT1G01070.2.exon2;Parent=transcript:AT1G01070.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01070.2.exon2;rank=2; -1 araport11 CDS 40213 40329 . - 1 ID=CDS:AT1G01070.2;Parent=transcript:AT1G01070.2;protein_id=AT1G01070.2 -1 araport11 CDS 40473 40597 . - 0 ID=CDS:AT1G01070.2;Parent=transcript:AT1G01070.2;protein_id=AT1G01070.2 -1 araport11 exon 40473 40945 . - . Name=AT1G01070.2.exon1;Parent=transcript:AT1G01070.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01070.2.exon1;rank=1; -1 araport11 five_prime_UTR 40598 40945 . - . Parent=transcript:AT1G01070.2; -1 araport11 ncRNA_gene 43087 43295 . - . ID=gene:AT1G04003;biotype=lncRNA;gene_id=AT1G04003;logic_name=araport11; -1 araport11 lnc_RNA 43087 43295 . - . ID=transcript:AT1G04003.1;biotype=lncRNA;Parent=gene:AT1G04003;transcript_id=AT1G04003.1; -1 araport11 exon 43087 43295 . - . Name=AT1G04003.1.exon1;Parent=transcript:AT1G04003.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04003.1.exon1;rank=1; -1 araport11 gene 44970 47059 . - . ID=gene:AT1G01080;biotype=protein_coding;description=RNA-binding (RRM/RBD/RNP motifs) family protein [Source:UniProtKB/TrEMBL%3bAcc:F4HQH8];gene_id=AT1G01080;logic_name=araport11; -1 araport11 mRNA 44970 47059 . - . ID=transcript:AT1G01080.3;biotype=protein_coding;Parent=gene:AT1G01080;transcript_id=AT1G01080.3; -1 araport11 three_prime_UTR 44970 45609 . - . Parent=transcript:AT1G01080.3; -1 araport11 exon 44970 45954 . - . Name=AT1G01080.3.exon3;Parent=transcript:AT1G01080.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01080.3.exon3;rank=3; -1 araport11 CDS 45610 45954 . - 0 ID=CDS:AT1G01080.3;Parent=transcript:AT1G01080.3;protein_id=AT1G01080.3 -1 araport11 exon 46044 46145 . - . Name=AT1G01080.1.exon2;Parent=transcript:AT1G01080.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01080.1.exon2;rank=2; -1 araport11 CDS 46044 46145 . - 0 ID=CDS:AT1G01080.3;Parent=transcript:AT1G01080.3;protein_id=AT1G01080.3 -1 araport11 CDS 46376 46789 . - 0 ID=CDS:AT1G01080.3;Parent=transcript:AT1G01080.3;protein_id=AT1G01080.3 -1 araport11 exon 46376 47059 . - . Name=AT1G01080.1.exon1;Parent=transcript:AT1G01080.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01080.1.exon1;rank=1; -1 araport11 five_prime_UTR 46790 47059 . - . Parent=transcript:AT1G01080.3; -1 araport11 mRNA 44970 47059 . - . ID=transcript:AT1G01080.1;biotype=protein_coding;Parent=gene:AT1G01080;transcript_id=AT1G01080.1; -1 araport11 three_prime_UTR 44970 45502 . - . Parent=transcript:AT1G01080.1; -1 araport11 exon 44970 45559 . - . Name=AT1G01080.1.exon4;Parent=transcript:AT1G01080.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01080.1.exon4;rank=4; -1 araport11 CDS 45503 45559 . - 0 ID=CDS:AT1G01080.1;Parent=transcript:AT1G01080.1;protein_id=AT1G01080.1 -1 araport11 exon 45646 45954 . - . Name=AT1G01080.1.exon3;Parent=transcript:AT1G01080.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01080.1.exon3;rank=3; -1 araport11 CDS 45646 45954 . - 0 ID=CDS:AT1G01080.1;Parent=transcript:AT1G01080.1;protein_id=AT1G01080.1 -1 araport11 exon 46044 46145 . - . Name=AT1G01080.1.exon2;Parent=transcript:AT1G01080.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01080.1.exon2;rank=2; -1 araport11 CDS 46044 46145 . - 0 ID=CDS:AT1G01080.1;Parent=transcript:AT1G01080.1;protein_id=AT1G01080.1 -1 araport11 CDS 46376 46789 . - 0 ID=CDS:AT1G01080.1;Parent=transcript:AT1G01080.1;protein_id=AT1G01080.1 -1 araport11 exon 46376 47059 . - . Name=AT1G01080.1.exon1;Parent=transcript:AT1G01080.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01080.1.exon1;rank=1; -1 araport11 five_prime_UTR 46790 47059 . - . Parent=transcript:AT1G01080.1; -1 araport11 mRNA 45296 47019 . - . ID=transcript:AT1G01080.2;biotype=protein_coding;Parent=gene:AT1G01080;transcript_id=AT1G01080.2; -1 araport11 three_prime_UTR 45296 45502 . - . Parent=transcript:AT1G01080.2; -1 araport11 exon 45296 45559 . - . Name=AT1G01080.2.exon4;Parent=transcript:AT1G01080.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01080.2.exon4;rank=4; -1 araport11 CDS 45503 45559 . - 0 ID=CDS:AT1G01080.2;Parent=transcript:AT1G01080.2;protein_id=AT1G01080.2 -1 araport11 exon 45646 45954 . - . Name=AT1G01080.1.exon3;Parent=transcript:AT1G01080.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01080.1.exon3;rank=3; -1 araport11 CDS 45646 45954 . - 0 ID=CDS:AT1G01080.2;Parent=transcript:AT1G01080.2;protein_id=AT1G01080.2 -1 araport11 exon 46044 46145 . - . Name=AT1G01080.1.exon2;Parent=transcript:AT1G01080.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01080.1.exon2;rank=2; -1 araport11 CDS 46044 46145 . - 0 ID=CDS:AT1G01080.2;Parent=transcript:AT1G01080.2;protein_id=AT1G01080.2 -1 araport11 CDS 46373 46789 . - 0 ID=CDS:AT1G01080.2;Parent=transcript:AT1G01080.2;protein_id=AT1G01080.2 -1 araport11 exon 46373 47019 . - . Name=AT1G01080.2.exon1;Parent=transcript:AT1G01080.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01080.2.exon1;rank=1; -1 araport11 five_prime_UTR 46790 47019 . - . Parent=transcript:AT1G01080.2; -1 araport11 gene 47234 49304 . - . ID=gene:AT1G01090;Name=PDH-E1 ALPHA;biotype=protein_coding;description=Pyruvate dehydrogenase E1 component subunit alpha [Source:UniProtKB/TrEMBL%3bAcc:A0A178W8A7];gene_id=AT1G01090;logic_name=araport11; -1 araport11 mRNA 47234 49304 . - . ID=transcript:AT1G01090.1;biotype=protein_coding;Parent=gene:AT1G01090;transcript_id=AT1G01090.1; -1 araport11 three_prime_UTR 47234 47704 . - . Parent=transcript:AT1G01090.1; -1 araport11 exon 47234 47982 . - . Name=AT1G01090.1.exon3;Parent=transcript:AT1G01090.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01090.1.exon3;rank=3; -1 araport11 CDS 47705 47982 . - 2 ID=CDS:AT1G01090.1;Parent=transcript:AT1G01090.1;protein_id=AT1G01090.1 -1 araport11 exon 48075 48852 . - . Name=AT1G01090.1.exon2;Parent=transcript:AT1G01090.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01090.1.exon2;rank=2; -1 araport11 CDS 48075 48852 . - 0 ID=CDS:AT1G01090.1;Parent=transcript:AT1G01090.1;protein_id=AT1G01090.1 -1 araport11 CDS 48936 49166 . - 0 ID=CDS:AT1G01090.1;Parent=transcript:AT1G01090.1;protein_id=AT1G01090.1 -1 araport11 exon 48936 49304 . - . Name=AT1G01090.1.exon1;Parent=transcript:AT1G01090.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01090.1.exon1;rank=1; -1 araport11 five_prime_UTR 49167 49304 . - . Parent=transcript:AT1G01090.1; -1 araport11 gene 49909 51210 . - . ID=gene:AT1G01100;Name=RPP1A;biotype=protein_coding;description=60S acidic ribosomal protein P1-1 [Source:UniProtKB/Swiss-Prot%3bAcc:Q8LCW9];gene_id=AT1G01100;logic_name=araport11; -1 araport11 mRNA 49909 51210 . - . ID=transcript:AT1G01100.2;biotype=protein_coding;Parent=gene:AT1G01100;transcript_id=AT1G01100.2; -1 araport11 three_prime_UTR 49909 50283 . - . Parent=transcript:AT1G01100.2; -1 araport11 exon 49909 50337 . - . Name=AT1G01100.2.exon4;Parent=transcript:AT1G01100.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01100.2.exon4;rank=4; -1 araport11 CDS 50284 50337 . - 0 ID=CDS:AT1G01100.2;Parent=transcript:AT1G01100.2;protein_id=AT1G01100.2 -1 araport11 exon 50419 50631 . - . Name=AT1G01100.2.exon3;Parent=transcript:AT1G01100.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01100.2.exon3;rank=3; -1 araport11 CDS 50419 50631 . - 0 ID=CDS:AT1G01100.2;Parent=transcript:AT1G01100.2;protein_id=AT1G01100.2 -1 araport11 CDS 50883 50954 . - 0 ID=CDS:AT1G01100.2;Parent=transcript:AT1G01100.2;protein_id=AT1G01100.2 -1 araport11 exon 50883 50963 . - . Name=AT1G01100.2.exon2;Parent=transcript:AT1G01100.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01100.2.exon2;rank=2; -1 araport11 five_prime_UTR 50955 50963 . - . Parent=transcript:AT1G01100.2; -1 araport11 exon 51126 51210 . - . Name=AT1G01100.2.exon1;Parent=transcript:AT1G01100.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01100.2.exon1;rank=1; -1 araport11 five_prime_UTR 51126 51210 . - . Parent=transcript:AT1G01100.2; -1 araport11 mRNA 50090 51108 . - . ID=transcript:AT1G01100.1;biotype=protein_coding;Parent=gene:AT1G01100;transcript_id=AT1G01100.1; -1 araport11 three_prime_UTR 50090 50283 . - . Parent=transcript:AT1G01100.1; -1 araport11 exon 50090 50337 . - . Name=AT1G01100.1.exon4;Parent=transcript:AT1G01100.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01100.1.exon4;rank=4; -1 araport11 CDS 50284 50337 . - 0 ID=CDS:AT1G01100.1;Parent=transcript:AT1G01100.1;protein_id=AT1G01100.1 -1 araport11 exon 50419 50631 . - . Name=AT1G01100.2.exon3;Parent=transcript:AT1G01100.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01100.2.exon3;rank=3; -1 araport11 CDS 50419 50631 . - 0 ID=CDS:AT1G01100.1;Parent=transcript:AT1G01100.1;protein_id=AT1G01100.1 -1 araport11 CDS 50883 50954 . - 0 ID=CDS:AT1G01100.1;Parent=transcript:AT1G01100.1;protein_id=AT1G01100.1 -1 araport11 exon 50883 50963 . - . Name=AT1G01100.2.exon2;Parent=transcript:AT1G01100.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01100.2.exon2;rank=2; -1 araport11 five_prime_UTR 50955 50963 . - . Parent=transcript:AT1G01100.1; -1 araport11 exon 51064 51108 . - . Name=AT1G01100.1.exon1;Parent=transcript:AT1G01100.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01100.1.exon1;rank=1; -1 araport11 five_prime_UTR 51064 51108 . - . Parent=transcript:AT1G01100.1; -1 araport11 mRNA 50090 51187 . - . ID=transcript:AT1G01100.4;biotype=protein_coding;Parent=gene:AT1G01100;transcript_id=AT1G01100.4; -1 araport11 three_prime_UTR 50090 50283 . - . Parent=transcript:AT1G01100.4; -1 araport11 exon 50090 50337 . - . Name=AT1G01100.1.exon4;Parent=transcript:AT1G01100.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01100.1.exon4;rank=4; -1 araport11 CDS 50284 50337 . - 0 ID=CDS:AT1G01100.4;Parent=transcript:AT1G01100.4;protein_id=AT1G01100.4 -1 araport11 exon 50419 50631 . - . Name=AT1G01100.2.exon3;Parent=transcript:AT1G01100.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01100.2.exon3;rank=3; -1 araport11 CDS 50419 50631 . - 0 ID=CDS:AT1G01100.4;Parent=transcript:AT1G01100.4;protein_id=AT1G01100.4 -1 araport11 CDS 50883 50954 . - 0 ID=CDS:AT1G01100.4;Parent=transcript:AT1G01100.4;protein_id=AT1G01100.4 -1 araport11 exon 50883 50963 . - . Name=AT1G01100.2.exon2;Parent=transcript:AT1G01100.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01100.2.exon2;rank=2; -1 araport11 five_prime_UTR 50955 50963 . - . Parent=transcript:AT1G01100.4; -1 araport11 exon 51123 51187 . - . Name=AT1G01100.4.exon1;Parent=transcript:AT1G01100.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01100.4.exon1;rank=1; -1 araport11 five_prime_UTR 51123 51187 . - . Parent=transcript:AT1G01100.4; -1 araport11 mRNA 50090 51197 . - . ID=transcript:AT1G01100.3;biotype=protein_coding;Parent=gene:AT1G01100;transcript_id=AT1G01100.3; -1 araport11 three_prime_UTR 50090 50283 . - . Parent=transcript:AT1G01100.3; -1 araport11 exon 50090 50337 . - . Name=AT1G01100.1.exon4;Parent=transcript:AT1G01100.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01100.1.exon4;rank=5; -1 araport11 CDS 50284 50337 . - 0 ID=CDS:AT1G01100.3;Parent=transcript:AT1G01100.3;protein_id=AT1G01100.3 -1 araport11 exon 50419 50447 . - . Name=AT1G01100.3.exon4;Parent=transcript:AT1G01100.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01100.3.exon4;rank=4; -1 araport11 CDS 50419 50447 . - 2 ID=CDS:AT1G01100.3;Parent=transcript:AT1G01100.3;protein_id=AT1G01100.3 -1 araport11 exon 50496 50631 . - . Name=AT1G01100.3.exon3;Parent=transcript:AT1G01100.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01100.3.exon3;rank=3; -1 araport11 CDS 50496 50631 . - 0 ID=CDS:AT1G01100.3;Parent=transcript:AT1G01100.3;protein_id=AT1G01100.3 -1 araport11 CDS 50883 50954 . - 0 ID=CDS:AT1G01100.3;Parent=transcript:AT1G01100.3;protein_id=AT1G01100.3 -1 araport11 exon 50883 50963 . - . Name=AT1G01100.2.exon2;Parent=transcript:AT1G01100.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01100.2.exon2;rank=2; -1 araport11 five_prime_UTR 50955 50963 . - . Parent=transcript:AT1G01100.3; -1 araport11 exon 51126 51197 . - . Name=AT1G01100.3.exon1;Parent=transcript:AT1G01100.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01100.3.exon1;rank=1; -1 araport11 five_prime_UTR 51126 51197 . - . Parent=transcript:AT1G01100.3; -1 araport11 gene 51953 54737 . + . ID=gene:AT1G01110;Name=IQD18;biotype=protein_coding;description=IQ-domain 18 [Source:UniProtKB/TrEMBL%3bAcc:Q9MAM4];gene_id=AT1G01110;logic_name=araport11; -1 araport11 mRNA 51953 54737 . + . ID=transcript:AT1G01110.2;biotype=protein_coding;Parent=gene:AT1G01110;transcript_id=AT1G01110.2; -1 araport11 five_prime_UTR 51953 52238 . + . Parent=transcript:AT1G01110.2; -1 araport11 exon 51953 52346 . + . Name=AT1G01110.2.exon1;Parent=transcript:AT1G01110.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01110.2.exon1;rank=1; -1 araport11 CDS 52239 52346 . + 0 ID=CDS:AT1G01110.2;Parent=transcript:AT1G01110.2;protein_id=AT1G01110.2 -1 araport11 exon 52434 52730 . + . Name=AT1G01110.2.exon2;Parent=transcript:AT1G01110.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01110.2.exon2;rank=2; -1 araport11 CDS 52434 52730 . + 0 ID=CDS:AT1G01110.2;Parent=transcript:AT1G01110.2;protein_id=AT1G01110.2 -1 araport11 exon 52938 53183 . + . Name=AT1G01110.2.exon3;Parent=transcript:AT1G01110.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01110.2.exon3;rank=3; -1 araport11 CDS 52938 53183 . + 0 ID=CDS:AT1G01110.2;Parent=transcript:AT1G01110.2;protein_id=AT1G01110.2 -1 araport11 exon 53484 53624 . + . Name=AT1G01110.2.exon4;Parent=transcript:AT1G01110.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01110.2.exon4;rank=4; -1 araport11 CDS 53484 53624 . + 0 ID=CDS:AT1G01110.2;Parent=transcript:AT1G01110.2;protein_id=AT1G01110.2 -1 araport11 CDS 53703 54494 . + 0 ID=CDS:AT1G01110.2;Parent=transcript:AT1G01110.2;protein_id=AT1G01110.2 -1 araport11 exon 53703 54737 . + . Name=AT1G01110.2.exon5;Parent=transcript:AT1G01110.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01110.2.exon5;rank=5; -1 araport11 three_prime_UTR 54495 54737 . + . Parent=transcript:AT1G01110.2; -1 araport11 mRNA 52061 54689 . + . ID=transcript:AT1G01110.1;biotype=protein_coding;Parent=gene:AT1G01110;transcript_id=AT1G01110.1; -1 araport11 exon 52061 52730 . + . Name=AT1G01110.1.exon1;Parent=transcript:AT1G01110.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01110.1.exon1;rank=1; -1 araport11 five_prime_UTR 52061 52730 . + . Parent=transcript:AT1G01110.1; -1 araport11 five_prime_UTR 52938 53021 . + . Parent=transcript:AT1G01110.1; -1 araport11 exon 52938 53183 . + . Name=AT1G01110.1.exon2;Parent=transcript:AT1G01110.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01110.1.exon2;rank=2; -1 araport11 CDS 53022 53183 . + 0 ID=CDS:AT1G01110.1;Parent=transcript:AT1G01110.1;protein_id=AT1G01110.1 -1 araport11 exon 53484 53624 . + . Name=AT1G01110.2.exon4;Parent=transcript:AT1G01110.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01110.2.exon4;rank=3; -1 araport11 CDS 53484 53624 . + 0 ID=CDS:AT1G01110.1;Parent=transcript:AT1G01110.1;protein_id=AT1G01110.1 -1 araport11 CDS 53703 54494 . + 0 ID=CDS:AT1G01110.1;Parent=transcript:AT1G01110.1;protein_id=AT1G01110.1 -1 araport11 exon 53703 54689 . + . Name=AT1G01110.1.exon4;Parent=transcript:AT1G01110.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01110.1.exon4;rank=4; -1 araport11 three_prime_UTR 54495 54689 . + . Parent=transcript:AT1G01110.1; -1 araport11 gene 57164 59215 . - . ID=gene:AT1G01120;Name=KCS1;biotype=protein_coding;description=3-ketoacyl-CoA synthase [Source:UniProtKB/TrEMBL%3bAcc:A0A178W124];gene_id=AT1G01120;logic_name=araport11; -1 araport11 mRNA 57164 59215 . - . ID=transcript:AT1G01120.1;biotype=protein_coding;Parent=gene:AT1G01120;transcript_id=AT1G01120.1; -1 araport11 three_prime_UTR 57164 57391 . - . Parent=transcript:AT1G01120.1; -1 araport11 exon 57164 59215 . - . Name=AT1G01120.1.exon1;Parent=transcript:AT1G01120.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01120.1.exon1;rank=1; -1 araport11 CDS 57392 58978 . - 0 ID=CDS:AT1G01120.1;Parent=transcript:AT1G01120.1;protein_id=AT1G01120.1 -1 araport11 five_prime_UTR 58979 59215 . - . Parent=transcript:AT1G01120.1; -1 araport11 gene 61905 63811 . - . ID=gene:AT1G01130;biotype=protein_coding;description=CONTAINS InterPro DOMAIN/s: CBL-interacting protein kinase (InterPro:IPR020660)%2c Calcium/calmodulin-dependent protein kinase-like (InterPro:IPR020636)%3b BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT5G47170.1)%3b Has 176 Blast hit /.../76 proteins in 20 species: Archae - 0%3b Bacteria - 0%3b Metazoa - 0%3b Fungi - 0%3b Plants - 176%3b Viruses - 0%3b Other Eukaryotes - 0 (source: NCBI BLink). [Source:TAIR%3bAcc:AT1G01130];gene_id=AT1G01130;logic_name=araport11; -1 araport11 mRNA 61905 63811 . - . ID=transcript:AT1G01130.1;biotype=protein_coding;Parent=gene:AT1G01130;transcript_id=AT1G01130.1; -1 araport11 exon 61905 61949 . - . Name=AT1G01130.1.exon3;Parent=transcript:AT1G01130.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01130.1.exon3;rank=3; -1 araport11 CDS 61905 61949 . - 0 ID=CDS:AT1G01130.1;Parent=transcript:AT1G01130.1;protein_id=AT1G01130.1 -1 araport11 exon 62050 62124 . - . Name=AT1G01130.1.exon2;Parent=transcript:AT1G01130.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01130.1.exon2;rank=2; -1 araport11 CDS 62050 62124 . - 0 ID=CDS:AT1G01130.1;Parent=transcript:AT1G01130.1;protein_id=AT1G01130.1 -1 araport11 exon 63557 63811 . - . Name=AT1G01130.1.exon1;Parent=transcript:AT1G01130.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01130.1.exon1;rank=1; -1 araport11 CDS 63557 63811 . - 0 ID=CDS:AT1G01130.1;Parent=transcript:AT1G01130.1;protein_id=AT1G01130.1 -1 araport11 gene 64166 67774 . - . ID=gene:AT1G01140;Name=CIPK9;biotype=protein_coding;description=CBL-interacting protein kinase 9 [Source:TAIR%3bAcc:AT1G01140];gene_id=AT1G01140;logic_name=araport11; -1 araport11 mRNA 64166 67774 . - . ID=transcript:AT1G01140.1;biotype=protein_coding;Parent=gene:AT1G01140;transcript_id=AT1G01140.1; -1 araport11 three_prime_UTR 64166 64397 . - . Parent=transcript:AT1G01140.1; -1 araport11 exon 64166 64475 . - . Name=AT1G01140.1.exon14;Parent=transcript:AT1G01140.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01140.1.exon14;rank=14; -1 araport11 CDS 64398 64475 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 64582 64656 . - . Name=AT1G01140.2.exon13;Parent=transcript:AT1G01140.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon13;rank=13; -1 araport11 CDS 64582 64656 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 64751 64807 . - . Name=AT1G01140.2.exon12;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon12;rank=12; -1 araport11 CDS 64751 64807 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 64901 65017 . - . Name=AT1G01140.2.exon11;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon11;rank=11; -1 araport11 CDS 64901 65017 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 65110 65217 . - . Name=AT1G01140.2.exon10;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon10;rank=10; -1 araport11 CDS 65110 65217 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 65331 65456 . - . Name=AT1G01140.2.exon9;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon9;rank=9; -1 araport11 CDS 65331 65456 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 65563 65652 . - . Name=AT1G01140.2.exon8;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon8;rank=8; -1 araport11 CDS 65563 65652 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 65739 65864 . - . Name=AT1G01140.1.exon7;Parent=transcript:AT1G01140.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.1.exon7;rank=7; -1 araport11 CDS 65739 65864 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 66107 66160 . - . Name=AT1G01140.2.exon6;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon6;rank=6; -1 araport11 CDS 66107 66160 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 66262 66342 . - . Name=AT1G01140.2.exon5;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon5;rank=5; -1 araport11 CDS 66262 66342 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 66450 66557 . - . Name=AT1G01140.2.exon4;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon4;rank=4; -1 araport11 CDS 66450 66557 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 66678 66749 . - . Name=AT1G01140.2.exon3;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon3;rank=3; -1 araport11 CDS 66678 66749 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 66835 66897 . - . Name=AT1G01140.2.exon2;Parent=transcript:AT1G01140.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon2;rank=2; -1 araport11 CDS 66835 66897 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 CDS 67324 67512 . - 0 ID=CDS:AT1G01140.1;Parent=transcript:AT1G01140.1;protein_id=AT1G01140.1 -1 araport11 exon 67324 67774 . - . Name=AT1G01140.1.exon1;Parent=transcript:AT1G01140.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01140.1.exon1;rank=1; -1 araport11 five_prime_UTR 67513 67774 . - . Parent=transcript:AT1G01140.1; -1 araport11 mRNA 64167 67625 . - . ID=transcript:AT1G01140.3;biotype=protein_coding;Parent=gene:AT1G01140;transcript_id=AT1G01140.3; -1 araport11 three_prime_UTR 64167 64397 . - . Parent=transcript:AT1G01140.3; -1 araport11 exon 64167 64475 . - . Name=AT1G01140.2.exon14;Parent=transcript:AT1G01140.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01140.2.exon14;rank=14; -1 araport11 CDS 64398 64475 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 64570 64656 . - . Name=AT1G01140.3.exon13;Parent=transcript:AT1G01140.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.3.exon13;rank=13; -1 araport11 CDS 64570 64656 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 64751 64807 . - . Name=AT1G01140.2.exon12;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon12;rank=12; -1 araport11 CDS 64751 64807 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 64901 65017 . - . Name=AT1G01140.2.exon11;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon11;rank=11; -1 araport11 CDS 64901 65017 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 65110 65217 . - . Name=AT1G01140.2.exon10;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon10;rank=10; -1 araport11 CDS 65110 65217 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 65331 65456 . - . Name=AT1G01140.2.exon9;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon9;rank=9; -1 araport11 CDS 65331 65456 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 65563 65652 . - . Name=AT1G01140.2.exon8;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon8;rank=8; -1 araport11 CDS 65563 65652 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 65739 65864 . - . Name=AT1G01140.1.exon7;Parent=transcript:AT1G01140.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.1.exon7;rank=7; -1 araport11 CDS 65739 65864 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 66107 66160 . - . Name=AT1G01140.2.exon6;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon6;rank=6; -1 araport11 CDS 66107 66160 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 66262 66342 . - . Name=AT1G01140.2.exon5;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon5;rank=5; -1 araport11 CDS 66262 66342 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 66450 66557 . - . Name=AT1G01140.2.exon4;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon4;rank=4; -1 araport11 CDS 66450 66557 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 66678 66749 . - . Name=AT1G01140.2.exon3;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon3;rank=3; -1 araport11 CDS 66678 66749 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 66835 66897 . - . Name=AT1G01140.2.exon2;Parent=transcript:AT1G01140.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon2;rank=2; -1 araport11 CDS 66835 66897 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 CDS 67324 67512 . - 0 ID=CDS:AT1G01140.3;Parent=transcript:AT1G01140.3;protein_id=AT1G01140.3 -1 araport11 exon 67324 67625 . - . Name=AT1G01140.2.exon1;Parent=transcript:AT1G01140.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01140.2.exon1;rank=1; -1 araport11 five_prime_UTR 67513 67625 . - . Parent=transcript:AT1G01140.3; -1 araport11 mRNA 64167 67625 . - . ID=transcript:AT1G01140.2;biotype=protein_coding;Parent=gene:AT1G01140;transcript_id=AT1G01140.2; -1 araport11 three_prime_UTR 64167 64397 . - . Parent=transcript:AT1G01140.2; -1 araport11 exon 64167 64475 . - . Name=AT1G01140.2.exon14;Parent=transcript:AT1G01140.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01140.2.exon14;rank=14; -1 araport11 CDS 64398 64475 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 64582 64656 . - . Name=AT1G01140.2.exon13;Parent=transcript:AT1G01140.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon13;rank=13; -1 araport11 CDS 64582 64656 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 64751 64807 . - . Name=AT1G01140.2.exon12;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon12;rank=12; -1 araport11 CDS 64751 64807 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 64901 65017 . - . Name=AT1G01140.2.exon11;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon11;rank=11; -1 araport11 CDS 64901 65017 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 65110 65217 . - . Name=AT1G01140.2.exon10;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon10;rank=10; -1 araport11 CDS 65110 65217 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 65331 65456 . - . Name=AT1G01140.2.exon9;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon9;rank=9; -1 araport11 CDS 65331 65456 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 65563 65652 . - . Name=AT1G01140.2.exon8;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon8;rank=8; -1 araport11 CDS 65563 65652 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 65733 65864 . - . Name=AT1G01140.2.exon7;Parent=transcript:AT1G01140.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon7;rank=7; -1 araport11 CDS 65733 65864 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 66107 66160 . - . Name=AT1G01140.2.exon6;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon6;rank=6; -1 araport11 CDS 66107 66160 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 66262 66342 . - . Name=AT1G01140.2.exon5;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon5;rank=5; -1 araport11 CDS 66262 66342 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 66450 66557 . - . Name=AT1G01140.2.exon4;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon4;rank=4; -1 araport11 CDS 66450 66557 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 66678 66749 . - . Name=AT1G01140.2.exon3;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon3;rank=3; -1 araport11 CDS 66678 66749 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 66835 66897 . - . Name=AT1G01140.2.exon2;Parent=transcript:AT1G01140.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01140.2.exon2;rank=2; -1 araport11 CDS 66835 66897 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 CDS 67324 67512 . - 0 ID=CDS:AT1G01140.2;Parent=transcript:AT1G01140.2;protein_id=AT1G01140.2 -1 araport11 exon 67324 67625 . - . Name=AT1G01140.2.exon1;Parent=transcript:AT1G01140.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01140.2.exon1;rank=1; -1 araport11 five_prime_UTR 67513 67625 . - . Parent=transcript:AT1G01140.2; -1 araport11 gene 69911 72138 . - . ID=gene:AT1G01150;biotype=protein_coding;description=Homeodomain-like protein with RING/FYVE/PHD-type zinc finger domain-containing protein [Source:UniProtKB/TrEMBL%3bAcc:F4HQJ2];gene_id=AT1G01150;logic_name=araport11; -1 araport11 mRNA 69911 72138 . - . ID=transcript:AT1G01150.1;biotype=protein_coding;Parent=gene:AT1G01150;transcript_id=AT1G01150.1; -1 araport11 three_prime_UTR 69911 70114 . - . Parent=transcript:AT1G01150.1; -1 araport11 exon 69911 70285 . - . Name=AT1G01150.1.exon4;Parent=transcript:AT1G01150.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01150.1.exon4;rank=4; -1 araport11 CDS 70115 70285 . - 0 ID=CDS:AT1G01150.1;Parent=transcript:AT1G01150.1;protein_id=AT1G01150.1 -1 araport11 exon 70840 70968 . - . Name=AT1G01150.1.exon3;Parent=transcript:AT1G01150.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01150.1.exon3;rank=3; -1 araport11 CDS 70840 70968 . - 0 ID=CDS:AT1G01150.1;Parent=transcript:AT1G01150.1;protein_id=AT1G01150.1 -1 araport11 exon 71041 71721 . - . Name=AT1G01150.3.exon2;Parent=transcript:AT1G01150.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01150.3.exon2;rank=2; -1 araport11 CDS 71041 71721 . - 0 ID=CDS:AT1G01150.1;Parent=transcript:AT1G01150.1;protein_id=AT1G01150.1 -1 araport11 CDS 71942 71998 . - 0 ID=CDS:AT1G01150.1;Parent=transcript:AT1G01150.1;protein_id=AT1G01150.1 -1 araport11 exon 71942 72138 . - . Name=AT1G01150.3.exon1;Parent=transcript:AT1G01150.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01150.3.exon1;rank=1; -1 araport11 five_prime_UTR 71999 72138 . - . Parent=transcript:AT1G01150.1; -1 araport11 mRNA 70035 72138 . - . ID=transcript:AT1G01150.2;biotype=protein_coding;Parent=gene:AT1G01150;transcript_id=AT1G01150.2; -1 araport11 three_prime_UTR 70035 70114 . - . Parent=transcript:AT1G01150.2; -1 araport11 exon 70035 70233 . - . Name=AT1G01150.2.exon4;Parent=transcript:AT1G01150.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01150.2.exon4;rank=4; -1 araport11 CDS 70115 70233 . - 2 ID=CDS:AT1G01150.2;Parent=transcript:AT1G01150.2;protein_id=AT1G01150.2 -1 araport11 exon 70896 70968 . - . Name=AT1G01150.2.exon3;Parent=transcript:AT1G01150.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01150.2.exon3;rank=3; -1 araport11 CDS 70896 70968 . - 0 ID=CDS:AT1G01150.2;Parent=transcript:AT1G01150.2;protein_id=AT1G01150.2 -1 araport11 exon 71041 71721 . - . Name=AT1G01150.3.exon2;Parent=transcript:AT1G01150.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01150.3.exon2;rank=2; -1 araport11 CDS 71041 71721 . - 0 ID=CDS:AT1G01150.2;Parent=transcript:AT1G01150.2;protein_id=AT1G01150.2 -1 araport11 CDS 71942 71998 . - 0 ID=CDS:AT1G01150.2;Parent=transcript:AT1G01150.2;protein_id=AT1G01150.2 -1 araport11 exon 71942 72138 . - . Name=AT1G01150.3.exon1;Parent=transcript:AT1G01150.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01150.3.exon1;rank=1; -1 araport11 five_prime_UTR 71999 72138 . - . Parent=transcript:AT1G01150.2; -1 araport11 mRNA 70619 72138 . - . ID=transcript:AT1G01150.3;biotype=protein_coding;Parent=gene:AT1G01150;transcript_id=AT1G01150.3; -1 araport11 three_prime_UTR 70619 70827 . - . Parent=transcript:AT1G01150.3; -1 araport11 exon 70619 70968 . - . Name=AT1G01150.3.exon3;Parent=transcript:AT1G01150.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01150.3.exon3;rank=3; -1 araport11 CDS 70828 70968 . - 0 ID=CDS:AT1G01150.3;Parent=transcript:AT1G01150.3;protein_id=AT1G01150.3 -1 araport11 exon 71041 71721 . - . Name=AT1G01150.3.exon2;Parent=transcript:AT1G01150.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01150.3.exon2;rank=2; -1 araport11 CDS 71041 71721 . - 0 ID=CDS:AT1G01150.3;Parent=transcript:AT1G01150.3;protein_id=AT1G01150.3 -1 araport11 CDS 71942 71998 . - 0 ID=CDS:AT1G01150.3;Parent=transcript:AT1G01150.3;protein_id=AT1G01150.3 -1 araport11 exon 71942 72138 . - . Name=AT1G01150.3.exon1;Parent=transcript:AT1G01150.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01150.3.exon1;rank=1; -1 araport11 five_prime_UTR 71999 72138 . - . Parent=transcript:AT1G01150.3; -1 araport11 gene 72339 74096 . + . ID=gene:AT1G01160;Name=GIF2;biotype=protein_coding;description=GRF1-interacting factor 2 [Source:UniProtKB/TrEMBL%3bAcc:F4HQJ3];gene_id=AT1G01160;logic_name=araport11; -1 araport11 mRNA 72339 74096 . + . ID=transcript:AT1G01160.1;biotype=protein_coding;Parent=gene:AT1G01160;transcript_id=AT1G01160.1; -1 araport11 five_prime_UTR 72339 72582 . + . Parent=transcript:AT1G01160.1; -1 araport11 exon 72339 72669 . + . Name=AT1G01160.1.exon1;Parent=transcript:AT1G01160.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01160.1.exon1;rank=1; -1 araport11 CDS 72583 72669 . + 0 ID=CDS:AT1G01160.1;Parent=transcript:AT1G01160.1;protein_id=AT1G01160.1 -1 araport11 exon 73087 73163 . + . Name=AT1G01160.2.exon3;Parent=transcript:AT1G01160.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01160.2.exon3;rank=2; -1 araport11 CDS 73087 73163 . + 0 ID=CDS:AT1G01160.1;Parent=transcript:AT1G01160.1;protein_id=AT1G01160.1 -1 araport11 exon 73287 73395 . + . Name=AT1G01160.2.exon4;Parent=transcript:AT1G01160.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01160.2.exon4;rank=3; -1 araport11 CDS 73287 73395 . + 1 ID=CDS:AT1G01160.1;Parent=transcript:AT1G01160.1;protein_id=AT1G01160.1 -1 araport11 exon 73488 73740 . + . Name=AT1G01160.2.exon5;Parent=transcript:AT1G01160.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01160.2.exon5;rank=4; -1 araport11 CDS 73488 73740 . + 0 ID=CDS:AT1G01160.1;Parent=transcript:AT1G01160.1;protein_id=AT1G01160.1 -1 araport11 CDS 73822 73883 . + 2 ID=CDS:AT1G01160.1;Parent=transcript:AT1G01160.1;protein_id=AT1G01160.1 -1 araport11 exon 73822 74096 . + . Name=AT1G01160.2.exon6;Parent=transcript:AT1G01160.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01160.2.exon6;rank=5; -1 araport11 three_prime_UTR 73884 74096 . + . Parent=transcript:AT1G01160.1; -1 araport11 mRNA 72357 74096 . + . ID=transcript:AT1G01160.2;biotype=protein_coding;Parent=gene:AT1G01160;transcript_id=AT1G01160.2; -1 araport11 five_prime_UTR 72357 72582 . + . Parent=transcript:AT1G01160.2; -1 araport11 exon 72357 72669 . + . Name=AT1G01160.2.exon1;Parent=transcript:AT1G01160.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01160.2.exon1;rank=1; -1 araport11 CDS 72583 72669 . + 0 ID=CDS:AT1G01160.2;Parent=transcript:AT1G01160.2;protein_id=AT1G01160.2 -1 araport11 exon 72915 73016 . + . Name=AT1G01160.2.exon2;Parent=transcript:AT1G01160.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01160.2.exon2;rank=2; -1 araport11 CDS 72915 73016 . + 0 ID=CDS:AT1G01160.2;Parent=transcript:AT1G01160.2;protein_id=AT1G01160.2 -1 araport11 exon 73087 73163 . + . Name=AT1G01160.2.exon3;Parent=transcript:AT1G01160.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01160.2.exon3;rank=3; -1 araport11 CDS 73087 73163 . + 0 ID=CDS:AT1G01160.2;Parent=transcript:AT1G01160.2;protein_id=AT1G01160.2 -1 araport11 exon 73287 73395 . + . Name=AT1G01160.2.exon4;Parent=transcript:AT1G01160.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01160.2.exon4;rank=4; -1 araport11 CDS 73287 73395 . + 1 ID=CDS:AT1G01160.2;Parent=transcript:AT1G01160.2;protein_id=AT1G01160.2 -1 araport11 exon 73488 73740 . + . Name=AT1G01160.2.exon5;Parent=transcript:AT1G01160.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01160.2.exon5;rank=5; -1 araport11 CDS 73488 73740 . + 0 ID=CDS:AT1G01160.2;Parent=transcript:AT1G01160.2;protein_id=AT1G01160.2 -1 araport11 CDS 73822 73883 . + 2 ID=CDS:AT1G01160.2;Parent=transcript:AT1G01160.2;protein_id=AT1G01160.2 -1 araport11 exon 73822 74096 . + . Name=AT1G01160.2.exon6;Parent=transcript:AT1G01160.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01160.2.exon6;rank=6; -1 araport11 three_prime_UTR 73884 74096 . + . Parent=transcript:AT1G01160.2; -1 araport11 ncRNA_gene 72646 73108 . - . ID=gene:AT1G04007;biotype=lncRNA;gene_id=AT1G04007;logic_name=araport11; -1 araport11 lnc_RNA 72646 73108 . - . ID=transcript:AT1G04007.1;biotype=lncRNA;Parent=gene:AT1G04007;transcript_id=AT1G04007.1; -1 araport11 exon 72646 73108 . - . Name=AT1G04007.1.exon1;Parent=transcript:AT1G04007.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04007.1.exon1;rank=1; -1 araport11 gene 73931 74737 . - . ID=gene:AT1G01170;biotype=protein_coding;description=At1g01170 [Source:UniProtKB/TrEMBL%3bAcc:Q2HIQ2];gene_id=AT1G01170;logic_name=araport11; -1 araport11 mRNA 73931 74731 . - . ID=transcript:AT1G01170.2;biotype=protein_coding;Parent=gene:AT1G01170;transcript_id=AT1G01170.2; -1 araport11 three_prime_UTR 73931 74104 . - . Parent=transcript:AT1G01170.2; -1 araport11 exon 73931 74250 . - . Name=AT1G01170.2.exon3;Parent=transcript:AT1G01170.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01170.2.exon3;rank=3; -1 araport11 CDS 74105 74250 . - 2 ID=CDS:AT1G01170.2;Parent=transcript:AT1G01170.2;protein_id=AT1G01170.2 -1 araport11 CDS 74338 74443 . - 0 ID=CDS:AT1G01170.2;Parent=transcript:AT1G01170.2;protein_id=AT1G01170.2 -1 araport11 exon 74338 74449 . - . Name=AT1G01170.2.exon2;Parent=transcript:AT1G01170.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01170.2.exon2;rank=2; -1 araport11 five_prime_UTR 74444 74449 . - . Parent=transcript:AT1G01170.2; -1 araport11 exon 74661 74731 . - . Name=AT1G01170.2.exon1;Parent=transcript:AT1G01170.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01170.2.exon1;rank=1; -1 araport11 five_prime_UTR 74661 74731 . - . Parent=transcript:AT1G01170.2; -1 araport11 mRNA 73931 74737 . - . ID=transcript:AT1G01170.1;biotype=protein_coding;Parent=gene:AT1G01170;transcript_id=AT1G01170.1; -1 araport11 three_prime_UTR 73931 74104 . - . Parent=transcript:AT1G01170.1; -1 araport11 exon 73931 74250 . - . Name=AT1G01170.2.exon3;Parent=transcript:AT1G01170.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01170.2.exon3;rank=3; -1 araport11 CDS 74105 74250 . - 2 ID=CDS:AT1G01170.1;Parent=transcript:AT1G01170.1;protein_id=AT1G01170.1 -1 araport11 CDS 74338 74443 . - 0 ID=CDS:AT1G01170.1;Parent=transcript:AT1G01170.1;protein_id=AT1G01170.1 -1 araport11 exon 74338 74455 . - . Name=AT1G01170.1.exon2;Parent=transcript:AT1G01170.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01170.1.exon2;rank=2; -1 araport11 five_prime_UTR 74444 74455 . - . Parent=transcript:AT1G01170.1; -1 araport11 exon 74661 74737 . - . Name=AT1G01170.1.exon1;Parent=transcript:AT1G01170.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01170.1.exon1;rank=1; -1 araport11 five_prime_UTR 74661 74737 . - . Parent=transcript:AT1G01170.1; -1 araport11 ncRNA_gene 74435 74683 . + . ID=gene:AT1G04013;biotype=lncRNA;gene_id=AT1G04013;logic_name=araport11; -1 araport11 lnc_RNA 74435 74683 . + . ID=transcript:AT1G04013.1;biotype=lncRNA;Parent=gene:AT1G04013;transcript_id=AT1G04013.1; -1 araport11 exon 74435 74683 . + . Name=AT1G04013.1.exon1;Parent=transcript:AT1G04013.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04013.1.exon1;rank=1; -1 araport11 gene 75390 76845 . + . ID=gene:AT1G01180;biotype=protein_coding;description=S-adenosyl-L-methionine-dependent methyltransferases superfamily protein [Source:UniProtKB/TrEMBL%3bAcc:F4HS78];gene_id=AT1G01180;logic_name=araport11; -1 araport11 mRNA 75390 76845 . + . ID=transcript:AT1G01180.1;biotype=protein_coding;Parent=gene:AT1G01180;transcript_id=AT1G01180.1; -1 araport11 five_prime_UTR 75390 75632 . + . Parent=transcript:AT1G01180.1; -1 araport11 exon 75390 76845 . + . Name=AT1G01180.1.exon1;Parent=transcript:AT1G01180.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01180.1.exon1;rank=1; -1 araport11 CDS 75633 76556 . + 0 ID=CDS:AT1G01180.1;Parent=transcript:AT1G01180.1;protein_id=AT1G01180.1 -1 araport11 three_prime_UTR 76557 76845 . + . Parent=transcript:AT1G01180.1; -1 araport11 ncRNA_gene 78927 79037 . - . ID=gene:AT1G01183;Name=MIR165A;biotype=miRNA;description=MIR165/MIR165A%3b miRNA [Source:TAIR%3bAcc:AT1G01183];gene_id=AT1G01183;logic_name=araport11; -1 araport11 miRNA 78927 79037 . - . ID=transcript:at1g01183;biotype=miRNA;Parent=gene:AT1G01183;transcript_id=at1g01183; -1 araport11 exon 78927 79037 . - . Name=at1g01183.exon;Parent=transcript:at1g01183;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=at1g01183.exon;rank=1; -1 araport11 gene 82984 84946 . - . ID=gene:AT1G01190;Name=CYP78A8;biotype=protein_coding;description=CYP78A8 [Source:UniProtKB/TrEMBL%3bAcc:A0A178WIC4];gene_id=AT1G01190;logic_name=araport11; -1 araport11 mRNA 82984 84864 . - . ID=transcript:AT1G01190.1;biotype=protein_coding;Parent=gene:AT1G01190;transcript_id=AT1G01190.1; -1 araport11 three_prime_UTR 82984 83044 . - . Parent=transcript:AT1G01190.1; -1 araport11 exon 82984 83671 . - . Name=AT1G01190.1.exon2;Parent=transcript:AT1G01190.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01190.1.exon2;rank=2; -1 araport11 CDS 83045 83671 . - 0 ID=CDS:AT1G01190.1;Parent=transcript:AT1G01190.1;protein_id=AT1G01190.1 -1 araport11 exon 83884 84864 . - . Name=AT1G01190.1.exon1;Parent=transcript:AT1G01190.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01190.1.exon1;rank=1; -1 araport11 CDS 83884 84864 . - 0 ID=CDS:AT1G01190.1;Parent=transcript:AT1G01190.1;protein_id=AT1G01190.1 -1 araport11 mRNA 83045 84946 . - . ID=transcript:AT1G01190.2;biotype=protein_coding;Parent=gene:AT1G01190;transcript_id=AT1G01190.2; -1 araport11 exon 83045 83671 . - . Name=AT1G01190.2.exon2;Parent=transcript:AT1G01190.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01190.2.exon2;rank=2; -1 araport11 CDS 83045 83671 . - 0 ID=CDS:AT1G01190.2;Parent=transcript:AT1G01190.2;protein_id=AT1G01190.2 -1 araport11 CDS 83884 84879 . - 0 ID=CDS:AT1G01190.2;Parent=transcript:AT1G01190.2;protein_id=AT1G01190.2 -1 araport11 exon 83884 84946 . - . Name=AT1G01190.2.exon1;Parent=transcript:AT1G01190.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01190.2.exon1;rank=1; -1 araport11 five_prime_UTR 84880 84946 . - . Parent=transcript:AT1G01190.2; -1 araport11 gene 86486 88409 . - . ID=gene:AT1G01200;Name=RABA3;biotype=protein_coding;description=RABA3 [Source:UniProtKB/TrEMBL%3bAcc:A0A178W3F7];gene_id=AT1G01200;logic_name=araport11; -1 araport11 mRNA 86486 88409 . - . ID=transcript:AT1G01200.1;biotype=protein_coding;Parent=gene:AT1G01200;transcript_id=AT1G01200.1; -1 araport11 three_prime_UTR 86486 86714 . - . Parent=transcript:AT1G01200.1; -1 araport11 exon 86486 87162 . - . Name=AT1G01200.1.exon2;Parent=transcript:AT1G01200.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01200.1.exon2;rank=2; -1 araport11 CDS 86715 87162 . - 1 ID=CDS:AT1G01200.1;Parent=transcript:AT1G01200.1;protein_id=AT1G01200.1 -1 araport11 CDS 87880 88145 . - 0 ID=CDS:AT1G01200.1;Parent=transcript:AT1G01200.1;protein_id=AT1G01200.1 -1 araport11 exon 87880 88409 . - . Name=AT1G01200.1.exon1;Parent=transcript:AT1G01200.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01200.1.exon1;rank=1; -1 araport11 five_prime_UTR 88146 88409 . - . Parent=transcript:AT1G01200.1; -1 araport11 gene 88622 90502 . + . ID=gene:AT1G01210;biotype=protein_coding;description=DNA-directed RNA polymerase subunit [Source:UniProtKB/TrEMBL%3bAcc:Q9LNK0];gene_id=AT1G01210;logic_name=araport11; -1 araport11 mRNA 88622 89745 . + . ID=transcript:AT1G01210.2;biotype=protein_coding;Parent=gene:AT1G01210;transcript_id=AT1G01210.2; -1 araport11 exon 88622 88730 . + . Name=AT1G01210.2.exon1;Parent=transcript:AT1G01210.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01210.2.exon1;rank=1; -1 araport11 five_prime_UTR 88622 88730 . + . Parent=transcript:AT1G01210.2; -1 araport11 five_prime_UTR 88954 88976 . + . Parent=transcript:AT1G01210.2; -1 araport11 exon 88954 89081 . + . Name=AT1G01210.2.exon2;Parent=transcript:AT1G01210.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01210.2.exon2;rank=2; -1 araport11 CDS 88977 89081 . + 0 ID=CDS:AT1G01210.2;Parent=transcript:AT1G01210.2;protein_id=AT1G01210.2 -1 araport11 exon 89173 89263 . + . Name=AT1G01210.3.exon2;Parent=transcript:AT1G01210.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01210.3.exon2;rank=3; -1 araport11 CDS 89173 89263 . + 0 ID=CDS:AT1G01210.2;Parent=transcript:AT1G01210.2;protein_id=AT1G01210.2 -1 araport11 CDS 89405 89529 . + 2 ID=CDS:AT1G01210.2;Parent=transcript:AT1G01210.2;protein_id=AT1G01210.2 -1 araport11 exon 89405 89745 . + . Name=AT1G01210.1.exon3;Parent=transcript:AT1G01210.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01210.1.exon3;rank=4; -1 araport11 three_prime_UTR 89530 89745 . + . Parent=transcript:AT1G01210.2; -1 araport11 mRNA 88883 90502 . + . ID=transcript:AT1G01210.3;biotype=protein_coding;Parent=gene:AT1G01210;transcript_id=AT1G01210.3; -1 araport11 five_prime_UTR 88883 88976 . + . Parent=transcript:AT1G01210.3; -1 araport11 exon 88883 89081 . + . Name=AT1G01210.3.exon1;Parent=transcript:AT1G01210.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01210.3.exon1;rank=1; -1 araport11 CDS 88977 89081 . + 0 ID=CDS:AT1G01210.3;Parent=transcript:AT1G01210.3;protein_id=AT1G01210.3 -1 araport11 exon 89173 89263 . + . Name=AT1G01210.3.exon2;Parent=transcript:AT1G01210.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01210.3.exon2;rank=2; -1 araport11 CDS 89173 89263 . + 0 ID=CDS:AT1G01210.3;Parent=transcript:AT1G01210.3;protein_id=AT1G01210.3 -1 araport11 CDS 89405 89529 . + 2 ID=CDS:AT1G01210.3;Parent=transcript:AT1G01210.3;protein_id=AT1G01210.3 -1 araport11 exon 89405 89579 . + . Name=AT1G01210.3.exon3;Parent=transcript:AT1G01210.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01210.3.exon3;rank=3; -1 araport11 three_prime_UTR 89530 89579 . + . Parent=transcript:AT1G01210.3; -1 araport11 exon 90162 90502 . + . Name=AT1G01210.3.exon4;Parent=transcript:AT1G01210.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01210.3.exon4;rank=4; -1 araport11 three_prime_UTR 90162 90502 . + . Parent=transcript:AT1G01210.3; -1 araport11 mRNA 88890 89745 . + . ID=transcript:AT1G01210.1;biotype=protein_coding;Parent=gene:AT1G01210;transcript_id=AT1G01210.1; -1 araport11 five_prime_UTR 88890 88976 . + . Parent=transcript:AT1G01210.1; -1 araport11 exon 88890 89081 . + . Name=AT1G01210.1.exon1;Parent=transcript:AT1G01210.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01210.1.exon1;rank=1; -1 araport11 CDS 88977 89081 . + 0 ID=CDS:AT1G01210.1;Parent=transcript:AT1G01210.1;protein_id=AT1G01210.1 -1 araport11 exon 89173 89263 . + . Name=AT1G01210.3.exon2;Parent=transcript:AT1G01210.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01210.3.exon2;rank=2; -1 araport11 CDS 89173 89263 . + 0 ID=CDS:AT1G01210.1;Parent=transcript:AT1G01210.1;protein_id=AT1G01210.1 -1 araport11 CDS 89405 89529 . + 2 ID=CDS:AT1G01210.1;Parent=transcript:AT1G01210.1;protein_id=AT1G01210.1 -1 araport11 exon 89405 89745 . + . Name=AT1G01210.1.exon3;Parent=transcript:AT1G01210.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01210.1.exon3;rank=3; -1 araport11 three_prime_UTR 89530 89745 . + . Parent=transcript:AT1G01210.1; -1 araport11 ncRNA_gene 90169 90401 . - . ID=gene:AT1G04017;biotype=lncRNA;gene_id=AT1G04017;logic_name=araport11; -1 araport11 lnc_RNA 90169 90401 . - . ID=transcript:AT1G04017.1;biotype=lncRNA;Parent=gene:AT1G04017;transcript_id=AT1G04017.1; -1 araport11 exon 90169 90401 . - . Name=AT1G04017.1.exon1;Parent=transcript:AT1G04017.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04017.1.exon1;rank=1; -1 araport11 gene 91342 95681 . + . ID=gene:AT1G01220;Name=FKGP;biotype=protein_coding;description=Bifunctional fucokinase/fucose pyrophosphorylase [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LNJ9];gene_id=AT1G01220;logic_name=araport11; -1 araport11 mRNA 91342 95681 . + . ID=transcript:AT1G01220.2;biotype=protein_coding;Parent=gene:AT1G01220;transcript_id=AT1G01220.2; -1 araport11 exon 91342 91633 . + . Name=AT1G01220.4.exon1;Parent=transcript:AT1G01220.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.4.exon1;rank=1; -1 araport11 five_prime_UTR 91342 91633 . + . Parent=transcript:AT1G01220.2; -1 araport11 five_prime_UTR 91743 92582 . + . Parent=transcript:AT1G01220.2; -1 araport11 exon 91743 92933 . + . Name=AT1G01220.2.exon2;Parent=transcript:AT1G01220.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01220.2.exon2;rank=2; -1 araport11 CDS 92583 92933 . + 0 ID=CDS:AT1G01220.2;Parent=transcript:AT1G01220.2;protein_id=AT1G01220.2 -1 araport11 exon 93045 93171 . + . Name=AT1G01220.6.exon4;Parent=transcript:AT1G01220.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.6.exon4;rank=3; -1 araport11 CDS 93045 93171 . + 0 ID=CDS:AT1G01220.2;Parent=transcript:AT1G01220.2;protein_id=AT1G01220.2 -1 araport11 exon 93271 94281 . + . Name=AT1G01220.6.exon5;Parent=transcript:AT1G01220.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01220.6.exon5;rank=4; -1 araport11 CDS 93271 94281 . + 2 ID=CDS:AT1G01220.2;Parent=transcript:AT1G01220.2;protein_id=AT1G01220.2 -1 araport11 exon 94357 95075 . + . Name=AT1G01220.6.exon6;Parent=transcript:AT1G01220.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.6.exon6;rank=5; -1 araport11 CDS 94357 95075 . + 2 ID=CDS:AT1G01220.2;Parent=transcript:AT1G01220.2;protein_id=AT1G01220.2 -1 araport11 CDS 95160 95552 . + 0 ID=CDS:AT1G01220.2;Parent=transcript:AT1G01220.2;protein_id=AT1G01220.2 -1 araport11 exon 95160 95681 . + . Name=AT1G01220.4.exon8;Parent=transcript:AT1G01220.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01220.4.exon8;rank=6; -1 araport11 three_prime_UTR 95553 95681 . + . Parent=transcript:AT1G01220.2; -1 araport11 mRNA 91342 95681 . + . ID=transcript:AT1G01220.3;biotype=protein_coding;Parent=gene:AT1G01220;transcript_id=AT1G01220.3; -1 araport11 exon 91342 91633 . + . Name=AT1G01220.4.exon1;Parent=transcript:AT1G01220.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.4.exon1;rank=1; -1 araport11 five_prime_UTR 91342 91633 . + . Parent=transcript:AT1G01220.3; -1 araport11 five_prime_UTR 91743 92245 . + . Parent=transcript:AT1G01220.3; -1 araport11 exon 91743 92501 . + . Name=AT1G01220.3.exon2;Parent=transcript:AT1G01220.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01220.3.exon2;rank=2; -1 araport11 CDS 92246 92501 . + 0 ID=CDS:AT1G01220.3;Parent=transcript:AT1G01220.3;protein_id=AT1G01220.3 -1 araport11 exon 92569 92933 . + . Name=AT1G01220.4.exon4;Parent=transcript:AT1G01220.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.4.exon4;rank=3; -1 araport11 CDS 92569 92933 . + 2 ID=CDS:AT1G01220.3;Parent=transcript:AT1G01220.3;protein_id=AT1G01220.3 -1 araport11 exon 93045 93171 . + . Name=AT1G01220.6.exon4;Parent=transcript:AT1G01220.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.6.exon4;rank=4; -1 araport11 CDS 93045 93171 . + 0 ID=CDS:AT1G01220.3;Parent=transcript:AT1G01220.3;protein_id=AT1G01220.3 -1 araport11 exon 93271 94281 . + . Name=AT1G01220.6.exon5;Parent=transcript:AT1G01220.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01220.6.exon5;rank=5; -1 araport11 CDS 93271 94281 . + 2 ID=CDS:AT1G01220.3;Parent=transcript:AT1G01220.3;protein_id=AT1G01220.3 -1 araport11 exon 94357 95075 . + . Name=AT1G01220.6.exon6;Parent=transcript:AT1G01220.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.6.exon6;rank=6; -1 araport11 CDS 94357 95075 . + 2 ID=CDS:AT1G01220.3;Parent=transcript:AT1G01220.3;protein_id=AT1G01220.3 -1 araport11 CDS 95160 95552 . + 0 ID=CDS:AT1G01220.3;Parent=transcript:AT1G01220.3;protein_id=AT1G01220.3 -1 araport11 exon 95160 95681 . + . Name=AT1G01220.4.exon8;Parent=transcript:AT1G01220.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01220.4.exon8;rank=7; -1 araport11 three_prime_UTR 95553 95681 . + . Parent=transcript:AT1G01220.3; -1 araport11 mRNA 91342 95681 . + . ID=transcript:AT1G01220.1;biotype=protein_coding;Parent=gene:AT1G01220;transcript_id=AT1G01220.1; -1 araport11 exon 91342 91633 . + . Name=AT1G01220.4.exon1;Parent=transcript:AT1G01220.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.4.exon1;rank=1; -1 araport11 five_prime_UTR 91342 91633 . + . Parent=transcript:AT1G01220.1; -1 araport11 five_prime_UTR 91743 91749 . + . Parent=transcript:AT1G01220.1; -1 araport11 exon 91743 92070 . + . Name=AT1G01220.1.exon2;Parent=transcript:AT1G01220.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01220.1.exon2;rank=2; -1 araport11 CDS 91750 92070 . + 0 ID=CDS:AT1G01220.1;Parent=transcript:AT1G01220.1;protein_id=AT1G01220.1 -1 araport11 exon 92270 92501 . + . Name=AT1G01220.4.exon3;Parent=transcript:AT1G01220.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.4.exon3;rank=3; -1 araport11 CDS 92270 92501 . + 0 ID=CDS:AT1G01220.1;Parent=transcript:AT1G01220.1;protein_id=AT1G01220.1 -1 araport11 exon 92569 92933 . + . Name=AT1G01220.4.exon4;Parent=transcript:AT1G01220.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.4.exon4;rank=4; -1 araport11 CDS 92569 92933 . + 2 ID=CDS:AT1G01220.1;Parent=transcript:AT1G01220.1;protein_id=AT1G01220.1 -1 araport11 exon 93045 93171 . + . Name=AT1G01220.6.exon4;Parent=transcript:AT1G01220.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.6.exon4;rank=5; -1 araport11 CDS 93045 93171 . + 0 ID=CDS:AT1G01220.1;Parent=transcript:AT1G01220.1;protein_id=AT1G01220.1 -1 araport11 exon 93271 94281 . + . Name=AT1G01220.6.exon5;Parent=transcript:AT1G01220.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01220.6.exon5;rank=6; -1 araport11 CDS 93271 94281 . + 2 ID=CDS:AT1G01220.1;Parent=transcript:AT1G01220.1;protein_id=AT1G01220.1 -1 araport11 exon 94357 95075 . + . Name=AT1G01220.6.exon6;Parent=transcript:AT1G01220.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.6.exon6;rank=7; -1 araport11 CDS 94357 95075 . + 2 ID=CDS:AT1G01220.1;Parent=transcript:AT1G01220.1;protein_id=AT1G01220.1 -1 araport11 CDS 95160 95552 . + 0 ID=CDS:AT1G01220.1;Parent=transcript:AT1G01220.1;protein_id=AT1G01220.1 -1 araport11 exon 95160 95681 . + . Name=AT1G01220.4.exon8;Parent=transcript:AT1G01220.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01220.4.exon8;rank=8; -1 araport11 three_prime_UTR 95553 95681 . + . Parent=transcript:AT1G01220.1; -1 araport11 mRNA 91342 95681 . + . ID=transcript:AT1G01220.4;biotype=protein_coding;Parent=gene:AT1G01220;transcript_id=AT1G01220.4; -1 araport11 exon 91342 91633 . + . Name=AT1G01220.4.exon1;Parent=transcript:AT1G01220.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.4.exon1;rank=1; -1 araport11 five_prime_UTR 91342 91633 . + . Parent=transcript:AT1G01220.4; -1 araport11 exon 91743 92089 . + . Name=AT1G01220.4.exon2;Parent=transcript:AT1G01220.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.4.exon2;rank=2; -1 araport11 five_prime_UTR 91743 92089 . + . Parent=transcript:AT1G01220.4; -1 araport11 exon 92270 92501 . + . Name=AT1G01220.4.exon3;Parent=transcript:AT1G01220.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.4.exon3;rank=3; -1 araport11 CDS 92270 92501 . + 0 ID=CDS:AT1G01220.4;Parent=transcript:AT1G01220.4;protein_id=AT1G01220.4 -1 araport11 exon 92569 92933 . + . Name=AT1G01220.4.exon4;Parent=transcript:AT1G01220.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.4.exon4;rank=4; -1 araport11 CDS 92569 92933 . + 2 ID=CDS:AT1G01220.4;Parent=transcript:AT1G01220.4;protein_id=AT1G01220.4 -1 araport11 exon 93045 93171 . + . Name=AT1G01220.6.exon4;Parent=transcript:AT1G01220.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.6.exon4;rank=5; -1 araport11 CDS 93045 93171 . + 0 ID=CDS:AT1G01220.4;Parent=transcript:AT1G01220.4;protein_id=AT1G01220.4 -1 araport11 exon 93271 94281 . + . Name=AT1G01220.6.exon5;Parent=transcript:AT1G01220.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01220.6.exon5;rank=6; -1 araport11 CDS 93271 94281 . + 2 ID=CDS:AT1G01220.4;Parent=transcript:AT1G01220.4;protein_id=AT1G01220.4 -1 araport11 exon 94357 95075 . + . Name=AT1G01220.6.exon6;Parent=transcript:AT1G01220.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.6.exon6;rank=7; -1 araport11 CDS 94357 95075 . + 2 ID=CDS:AT1G01220.4;Parent=transcript:AT1G01220.4;protein_id=AT1G01220.4 -1 araport11 CDS 95160 95552 . + 0 ID=CDS:AT1G01220.4;Parent=transcript:AT1G01220.4;protein_id=AT1G01220.4 -1 araport11 exon 95160 95681 . + . Name=AT1G01220.4.exon8;Parent=transcript:AT1G01220.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01220.4.exon8;rank=8; -1 araport11 three_prime_UTR 95553 95681 . + . Parent=transcript:AT1G01220.4; -1 araport11 mRNA 91376 95674 . + . ID=transcript:AT1G01220.6;biotype=protein_coding;Parent=gene:AT1G01220;transcript_id=AT1G01220.6; -1 araport11 exon 91376 91633 . + . Name=AT1G01220.6.exon1;Parent=transcript:AT1G01220.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.6.exon1;rank=1; -1 araport11 five_prime_UTR 91376 91633 . + . Parent=transcript:AT1G01220.6; -1 araport11 exon 91743 92070 . + . Name=AT1G01220.6.exon2;Parent=transcript:AT1G01220.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.6.exon2;rank=2; -1 araport11 five_prime_UTR 91743 92070 . + . Parent=transcript:AT1G01220.6; -1 araport11 five_prime_UTR 92270 92582 . + . Parent=transcript:AT1G01220.6; -1 araport11 exon 92270 92933 . + . Name=AT1G01220.6.exon3;Parent=transcript:AT1G01220.6;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01220.6.exon3;rank=3; -1 araport11 CDS 92583 92933 . + 0 ID=CDS:AT1G01220.6;Parent=transcript:AT1G01220.6;protein_id=AT1G01220.6 -1 araport11 exon 93045 93171 . + . Name=AT1G01220.6.exon4;Parent=transcript:AT1G01220.6;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.6.exon4;rank=4; -1 araport11 CDS 93045 93171 . + 0 ID=CDS:AT1G01220.6;Parent=transcript:AT1G01220.6;protein_id=AT1G01220.6 -1 araport11 exon 93271 94281 . + . Name=AT1G01220.6.exon5;Parent=transcript:AT1G01220.6;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01220.6.exon5;rank=5; -1 araport11 CDS 93271 94281 . + 2 ID=CDS:AT1G01220.6;Parent=transcript:AT1G01220.6;protein_id=AT1G01220.6 -1 araport11 exon 94357 95075 . + . Name=AT1G01220.6.exon6;Parent=transcript:AT1G01220.6;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.6.exon6;rank=6; -1 araport11 CDS 94357 95075 . + 2 ID=CDS:AT1G01220.6;Parent=transcript:AT1G01220.6;protein_id=AT1G01220.6 -1 araport11 CDS 95160 95552 . + 0 ID=CDS:AT1G01220.6;Parent=transcript:AT1G01220.6;protein_id=AT1G01220.6 -1 araport11 exon 95160 95674 . + . Name=AT1G01220.6.exon7;Parent=transcript:AT1G01220.6;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01220.6.exon7;rank=7; -1 araport11 three_prime_UTR 95553 95674 . + . Parent=transcript:AT1G01220.6; -1 araport11 mRNA 91376 95676 . + . ID=transcript:AT1G01220.5;biotype=protein_coding;Parent=gene:AT1G01220;transcript_id=AT1G01220.5; -1 araport11 exon 91376 91633 . + . Name=AT1G01220.6.exon1;Parent=transcript:AT1G01220.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.6.exon1;rank=1; -1 araport11 five_prime_UTR 91376 91633 . + . Parent=transcript:AT1G01220.5; -1 araport11 exon 91743 92089 . + . Name=AT1G01220.4.exon2;Parent=transcript:AT1G01220.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01220.4.exon2;rank=2; -1 araport11 five_prime_UTR 91743 92089 . + . Parent=transcript:AT1G01220.5; -1 araport11 five_prime_UTR 92270 92582 . + . Parent=transcript:AT1G01220.5; -1 araport11 exon 92270 92933 . + . Name=AT1G01220.6.exon3;Parent=transcript:AT1G01220.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01220.6.exon3;rank=3; -1 araport11 CDS 92583 92933 . + 0 ID=CDS:AT1G01220.5;Parent=transcript:AT1G01220.5;protein_id=AT1G01220.5 -1 araport11 exon 93045 93171 . + . Name=AT1G01220.6.exon4;Parent=transcript:AT1G01220.5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.6.exon4;rank=4; -1 araport11 CDS 93045 93171 . + 0 ID=CDS:AT1G01220.5;Parent=transcript:AT1G01220.5;protein_id=AT1G01220.5 -1 araport11 exon 93271 94281 . + . Name=AT1G01220.6.exon5;Parent=transcript:AT1G01220.5;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01220.6.exon5;rank=5; -1 araport11 CDS 93271 94281 . + 2 ID=CDS:AT1G01220.5;Parent=transcript:AT1G01220.5;protein_id=AT1G01220.5 -1 araport11 exon 94357 95075 . + . Name=AT1G01220.6.exon6;Parent=transcript:AT1G01220.5;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.6.exon6;rank=6; -1 araport11 CDS 94357 95075 . + 2 ID=CDS:AT1G01220.5;Parent=transcript:AT1G01220.5;protein_id=AT1G01220.5 -1 araport11 CDS 95160 95552 . + 0 ID=CDS:AT1G01220.5;Parent=transcript:AT1G01220.5;protein_id=AT1G01220.5 -1 araport11 exon 95160 95676 . + . Name=AT1G01220.5.exon7;Parent=transcript:AT1G01220.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01220.5.exon7;rank=7; -1 araport11 three_prime_UTR 95553 95676 . + . Parent=transcript:AT1G01220.5; -1 araport11 mRNA 91642 95674 . + . ID=transcript:AT1G01220.7;biotype=protein_coding;Parent=gene:AT1G01220;transcript_id=AT1G01220.7; -1 araport11 five_prime_UTR 91642 91749 . + . Parent=transcript:AT1G01220.7; -1 araport11 exon 91642 92070 . + . Name=AT1G01220.7.exon1;Parent=transcript:AT1G01220.7;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01220.7.exon1;rank=1; -1 araport11 CDS 91750 92070 . + 0 ID=CDS:AT1G01220.7;Parent=transcript:AT1G01220.7;protein_id=AT1G01220.7 -1 araport11 exon 92270 92501 . + . Name=AT1G01220.4.exon3;Parent=transcript:AT1G01220.7;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.4.exon3;rank=2; -1 araport11 CDS 92270 92501 . + 0 ID=CDS:AT1G01220.7;Parent=transcript:AT1G01220.7;protein_id=AT1G01220.7 -1 araport11 exon 92569 92933 . + . Name=AT1G01220.4.exon4;Parent=transcript:AT1G01220.7;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.4.exon4;rank=3; -1 araport11 CDS 92569 92933 . + 2 ID=CDS:AT1G01220.7;Parent=transcript:AT1G01220.7;protein_id=AT1G01220.7 -1 araport11 exon 93045 93171 . + . Name=AT1G01220.6.exon4;Parent=transcript:AT1G01220.7;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.6.exon4;rank=4; -1 araport11 CDS 93045 93171 . + 0 ID=CDS:AT1G01220.7;Parent=transcript:AT1G01220.7;protein_id=AT1G01220.7 -1 araport11 exon 93271 94281 . + . Name=AT1G01220.6.exon5;Parent=transcript:AT1G01220.7;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01220.6.exon5;rank=5; -1 araport11 CDS 93271 94281 . + 2 ID=CDS:AT1G01220.7;Parent=transcript:AT1G01220.7;protein_id=AT1G01220.7 -1 araport11 exon 94357 95075 . + . Name=AT1G01220.6.exon6;Parent=transcript:AT1G01220.7;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.6.exon6;rank=6; -1 araport11 CDS 94357 95075 . + 2 ID=CDS:AT1G01220.7;Parent=transcript:AT1G01220.7;protein_id=AT1G01220.7 -1 araport11 CDS 95160 95552 . + 0 ID=CDS:AT1G01220.7;Parent=transcript:AT1G01220.7;protein_id=AT1G01220.7 -1 araport11 exon 95160 95674 . + . Name=AT1G01220.6.exon7;Parent=transcript:AT1G01220.7;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01220.6.exon7;rank=7; -1 araport11 three_prime_UTR 95553 95674 . + . Parent=transcript:AT1G01220.7; -1 araport11 mRNA 91692 95681 . + . ID=transcript:AT1G01220.8;biotype=protein_coding;Parent=gene:AT1G01220;transcript_id=AT1G01220.8; -1 araport11 five_prime_UTR 91692 92245 . + . Parent=transcript:AT1G01220.8; -1 araport11 exon 91692 92501 . + . Name=AT1G01220.8.exon1;Parent=transcript:AT1G01220.8;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01220.8.exon1;rank=1; -1 araport11 CDS 92246 92501 . + 0 ID=CDS:AT1G01220.8;Parent=transcript:AT1G01220.8;protein_id=AT1G01220.8 -1 araport11 exon 92569 92933 . + . Name=AT1G01220.4.exon4;Parent=transcript:AT1G01220.8;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.4.exon4;rank=2; -1 araport11 CDS 92569 92933 . + 2 ID=CDS:AT1G01220.8;Parent=transcript:AT1G01220.8;protein_id=AT1G01220.8 -1 araport11 exon 93045 93171 . + . Name=AT1G01220.6.exon4;Parent=transcript:AT1G01220.8;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01220.6.exon4;rank=3; -1 araport11 CDS 93045 93171 . + 0 ID=CDS:AT1G01220.8;Parent=transcript:AT1G01220.8;protein_id=AT1G01220.8 -1 araport11 exon 93271 94281 . + . Name=AT1G01220.6.exon5;Parent=transcript:AT1G01220.8;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01220.6.exon5;rank=4; -1 araport11 CDS 93271 94281 . + 2 ID=CDS:AT1G01220.8;Parent=transcript:AT1G01220.8;protein_id=AT1G01220.8 -1 araport11 exon 94357 95075 . + . Name=AT1G01220.6.exon6;Parent=transcript:AT1G01220.8;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01220.6.exon6;rank=5; -1 araport11 CDS 94357 95075 . + 2 ID=CDS:AT1G01220.8;Parent=transcript:AT1G01220.8;protein_id=AT1G01220.8 -1 araport11 CDS 95160 95552 . + 0 ID=CDS:AT1G01220.8;Parent=transcript:AT1G01220.8;protein_id=AT1G01220.8 -1 araport11 exon 95160 95681 . + . Name=AT1G01220.4.exon8;Parent=transcript:AT1G01220.8;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01220.4.exon8;rank=6; -1 araport11 three_prime_UTR 95553 95681 . + . Parent=transcript:AT1G01220.8; -1 araport11 ncRNA_gene 91356 91685 . - . ID=gene:AT1G04023;biotype=lncRNA;gene_id=AT1G04023;logic_name=araport11; -1 araport11 lnc_RNA 91356 91685 . - . ID=transcript:AT1G04023.1;biotype=lncRNA;Parent=gene:AT1G04023;transcript_id=AT1G04023.1; -1 araport11 exon 91356 91685 . - . Name=AT1G04023.1.exon1;Parent=transcript:AT1G04023.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04023.1.exon1;rank=1; -1 araport11 gene 95935 97407 . + . ID=gene:AT1G01225;biotype=protein_coding;description=At1g01225 [Source:UniProtKB/TrEMBL%3bAcc:Q29PY0];gene_id=AT1G01225;logic_name=araport11; -1 araport11 mRNA 95935 97407 . + . ID=transcript:AT1G01225.1;biotype=protein_coding;Parent=gene:AT1G01225;transcript_id=AT1G01225.1; -1 araport11 five_prime_UTR 95935 96063 . + . Parent=transcript:AT1G01225.1; -1 araport11 exon 95935 96157 . + . Name=AT1G01225.1.exon1;Parent=transcript:AT1G01225.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01225.1.exon1;rank=1; -1 araport11 CDS 96064 96157 . + 0 ID=CDS:AT1G01225.1;Parent=transcript:AT1G01225.1;protein_id=AT1G01225.1 -1 araport11 CDS 96554 97242 . + 2 ID=CDS:AT1G01225.1;Parent=transcript:AT1G01225.1;protein_id=AT1G01225.1 -1 araport11 exon 96554 97407 . + . Name=AT1G01225.1.exon2;Parent=transcript:AT1G01225.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01225.1.exon2;rank=2; -1 araport11 three_prime_UTR 97243 97407 . + . Parent=transcript:AT1G01225.1; -1 araport11 gene 97412 99240 . + . ID=gene:AT1G01230;biotype=protein_coding;description=ORMDL family protein [Source:UniProtKB/TrEMBL%3bAcc:Q9C5I0];gene_id=AT1G01230;logic_name=araport11; -1 araport11 mRNA 97412 99240 . + . ID=transcript:AT1G01230.1;biotype=protein_coding;Parent=gene:AT1G01230;transcript_id=AT1G01230.1; -1 araport11 five_prime_UTR 97412 97619 . + . Parent=transcript:AT1G01230.1; -1 araport11 exon 97412 97805 . + . Name=AT1G01230.1.exon1;Parent=transcript:AT1G01230.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01230.1.exon1;rank=1; -1 araport11 CDS 97620 97805 . + 0 ID=CDS:AT1G01230.1;Parent=transcript:AT1G01230.1;protein_id=AT1G01230.1 -1 araport11 exon 98457 98605 . + . Name=AT1G01230.1.exon2;Parent=transcript:AT1G01230.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01230.1.exon2;rank=2; -1 araport11 CDS 98457 98605 . + 0 ID=CDS:AT1G01230.1;Parent=transcript:AT1G01230.1;protein_id=AT1G01230.1 -1 araport11 CDS 98908 99046 . + 1 ID=CDS:AT1G01230.1;Parent=transcript:AT1G01230.1;protein_id=AT1G01230.1 -1 araport11 exon 98908 99240 . + . Name=AT1G01230.1.exon3;Parent=transcript:AT1G01230.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01230.1.exon3;rank=3; -1 araport11 three_prime_UTR 99047 99240 . + . Parent=transcript:AT1G01230.1; -1 araport11 gene 99865 101987 . + . ID=gene:AT1G01240;biotype=protein_coding;description=At1g01240/F6F3_11 [Source:UniProtKB/TrEMBL%3bAcc:Q9LNJ7];gene_id=AT1G01240;logic_name=araport11; -1 araport11 mRNA 99865 101840 . + . ID=transcript:AT1G01240.4;biotype=protein_coding;Parent=gene:AT1G01240;transcript_id=AT1G01240.4; -1 araport11 exon 99865 100031 . + . Name=AT1G01240.4.exon1;Parent=transcript:AT1G01240.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.4.exon1;rank=1; -1 araport11 five_prime_UTR 99865 100031 . + . Parent=transcript:AT1G01240.4; -1 araport11 exon 100111 100220 . + . Name=AT1G01240.4.exon2;Parent=transcript:AT1G01240.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.4.exon2;rank=2; -1 araport11 five_prime_UTR 100111 100220 . + . Parent=transcript:AT1G01240.4; -1 araport11 five_prime_UTR 100657 100682 . + . Parent=transcript:AT1G01240.4; -1 araport11 exon 100657 101840 . + . Name=AT1G01240.4.exon3;Parent=transcript:AT1G01240.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.4.exon3;rank=3; -1 araport11 CDS 100683 101678 . + 0 ID=CDS:AT1G01240.4;Parent=transcript:AT1G01240.4;protein_id=AT1G01240.4 -1 araport11 three_prime_UTR 101679 101840 . + . Parent=transcript:AT1G01240.4; -1 araport11 mRNA 99866 101987 . + . ID=transcript:AT1G01240.3;biotype=protein_coding;Parent=gene:AT1G01240;transcript_id=AT1G01240.3; -1 araport11 five_prime_UTR 99866 100682 . + . Parent=transcript:AT1G01240.3; -1 araport11 exon 99866 101987 . + . Name=AT1G01240.3.exon1;Parent=transcript:AT1G01240.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.3.exon1;rank=1; -1 araport11 CDS 100683 101678 . + 0 ID=CDS:AT1G01240.3;Parent=transcript:AT1G01240.3;protein_id=AT1G01240.3 -1 araport11 three_prime_UTR 101679 101987 . + . Parent=transcript:AT1G01240.3; -1 araport11 mRNA 99866 101987 . + . ID=transcript:AT1G01240.1;biotype=protein_coding;Parent=gene:AT1G01240;transcript_id=AT1G01240.1; -1 araport11 exon 99866 100031 . + . Name=AT1G01240.1.exon1;Parent=transcript:AT1G01240.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.1.exon1;rank=1; -1 araport11 five_prime_UTR 99866 100031 . + . Parent=transcript:AT1G01240.1; -1 araport11 five_prime_UTR 100657 100682 . + . Parent=transcript:AT1G01240.1; -1 araport11 exon 100657 101987 . + . Name=AT1G01240.2.exon2;Parent=transcript:AT1G01240.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.2.exon2;rank=2; -1 araport11 CDS 100683 101678 . + 0 ID=CDS:AT1G01240.1;Parent=transcript:AT1G01240.1;protein_id=AT1G01240.1 -1 araport11 three_prime_UTR 101679 101987 . + . Parent=transcript:AT1G01240.1; -1 araport11 mRNA 99866 101987 . + . ID=transcript:AT1G01240.2;biotype=protein_coding;Parent=gene:AT1G01240;transcript_id=AT1G01240.2; -1 araport11 exon 99866 100220 . + . Name=AT1G01240.2.exon1;Parent=transcript:AT1G01240.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.2.exon1;rank=1; -1 araport11 five_prime_UTR 99866 100220 . + . Parent=transcript:AT1G01240.2; -1 araport11 five_prime_UTR 100657 100682 . + . Parent=transcript:AT1G01240.2; -1 araport11 exon 100657 101987 . + . Name=AT1G01240.2.exon2;Parent=transcript:AT1G01240.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.2.exon2;rank=2; -1 araport11 CDS 100683 101678 . + 0 ID=CDS:AT1G01240.2;Parent=transcript:AT1G01240.2;protein_id=AT1G01240.2 -1 araport11 three_prime_UTR 101679 101987 . + . Parent=transcript:AT1G01240.2; -1 araport11 mRNA 99872 101882 . + . ID=transcript:AT1G01240.5;biotype=protein_coding;Parent=gene:AT1G01240;transcript_id=AT1G01240.5; -1 araport11 exon 99872 100031 . + . Name=AT1G01240.5.exon1;Parent=transcript:AT1G01240.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.5.exon1;rank=1; -1 araport11 five_prime_UTR 99872 100031 . + . Parent=transcript:AT1G01240.5; -1 araport11 five_prime_UTR 100111 100682 . + . Parent=transcript:AT1G01240.5; -1 araport11 exon 100111 101882 . + . Name=AT1G01240.5.exon2;Parent=transcript:AT1G01240.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01240.5.exon2;rank=2; -1 araport11 CDS 100683 101678 . + 0 ID=CDS:AT1G01240.5;Parent=transcript:AT1G01240.5;protein_id=AT1G01240.5 -1 araport11 three_prime_UTR 101679 101882 . + . Parent=transcript:AT1G01240.5; -1 araport11 gene 104440 105330 . - . ID=gene:AT1G01250;Name=ERF023;biotype=protein_coding;description=Ethylene-responsive transcription factor ERF023 [Source:UniProtKB/Swiss-Prot%3bAcc:Q1ECI2];gene_id=AT1G01250;logic_name=araport11; -1 araport11 mRNA 104440 105330 . - . ID=transcript:AT1G01250.1;biotype=protein_coding;Parent=gene:AT1G01250;transcript_id=AT1G01250.1; -1 araport11 three_prime_UTR 104440 104730 . - . Parent=transcript:AT1G01250.1; -1 araport11 exon 104440 105330 . - . Name=AT1G01250.1.exon1;Parent=transcript:AT1G01250.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01250.1.exon1;rank=1; -1 araport11 CDS 104731 105309 . - 0 ID=CDS:AT1G01250.1;Parent=transcript:AT1G01250.1;protein_id=AT1G01250.1 -1 araport11 five_prime_UTR 105310 105330 . - . Parent=transcript:AT1G01250.1; -1 araport11 gene 108946 111699 . + . ID=gene:AT1G01260;Name=BHLH13;biotype=protein_coding;description=Transcription factor bHLH13 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LNJ5];gene_id=AT1G01260;logic_name=araport11; -1 araport11 mRNA 108946 111699 . + . ID=transcript:AT1G01260.3;biotype=protein_coding;Parent=gene:AT1G01260;transcript_id=AT1G01260.3; -1 araport11 exon 108946 109330 . + . Name=AT1G01260.3.exon1;Parent=transcript:AT1G01260.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01260.3.exon1;rank=1; -1 araport11 five_prime_UTR 108946 109330 . + . Parent=transcript:AT1G01260.3; -1 araport11 five_prime_UTR 109406 109594 . + . Parent=transcript:AT1G01260.3; -1 araport11 exon 109406 111699 . + . Name=AT1G01260.3.exon2;Parent=transcript:AT1G01260.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01260.3.exon2;rank=2; -1 araport11 CDS 109595 111367 . + 0 ID=CDS:AT1G01260.3;Parent=transcript:AT1G01260.3;protein_id=AT1G01260.3 -1 araport11 three_prime_UTR 111368 111699 . + . Parent=transcript:AT1G01260.3; -1 araport11 mRNA 108991 111699 . + . ID=transcript:AT1G01260.1;biotype=protein_coding;Parent=gene:AT1G01260;transcript_id=AT1G01260.1; -1 araport11 five_prime_UTR 108991 109594 . + . Parent=transcript:AT1G01260.1; -1 araport11 exon 108991 111699 . + . Name=AT1G01260.1.exon1;Parent=transcript:AT1G01260.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01260.1.exon1;rank=1; -1 araport11 CDS 109595 111367 . + 0 ID=CDS:AT1G01260.1;Parent=transcript:AT1G01260.1;protein_id=AT1G01260.1 -1 araport11 three_prime_UTR 111368 111699 . + . Parent=transcript:AT1G01260.1; -1 araport11 mRNA 109076 111535 . + . ID=transcript:AT1G01260.2;biotype=protein_coding;Parent=gene:AT1G01260;transcript_id=AT1G01260.2; -1 araport11 exon 109076 109330 . + . Name=AT1G01260.2.exon1;Parent=transcript:AT1G01260.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01260.2.exon1;rank=1; -1 araport11 five_prime_UTR 109076 109330 . + . Parent=transcript:AT1G01260.2; -1 araport11 five_prime_UTR 109413 109594 . + . Parent=transcript:AT1G01260.2; -1 araport11 exon 109413 111535 . + . Name=AT1G01260.2.exon2;Parent=transcript:AT1G01260.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01260.2.exon2;rank=2; -1 araport11 CDS 109595 111367 . + 0 ID=CDS:AT1G01260.2;Parent=transcript:AT1G01260.2;protein_id=AT1G01260.2 -1 araport11 three_prime_UTR 111368 111535 . + . Parent=transcript:AT1G01260.2; -1 araport11 ncRNA_gene 111890 111961 . - . ID=gene:AT1G01270;biotype=tRNA;description=pre-tRNA [Source:TAIR%3bAcc:AT1G01270];gene_id=AT1G01270;logic_name=araport11; -1 araport11 tRNA 111890 111961 . - . ID=transcript:AT1G01270.1;biotype=tRNA;Parent=gene:AT1G01270;transcript_id=AT1G01270.1; -1 araport11 exon 111890 111961 . - . Name=AT1G01270.1.exon1;Parent=transcript:AT1G01270.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01270.1.exon1;rank=1; -1 araport11 gene 112263 113947 . + . ID=gene:AT1G01280;Name=CYP703A2;biotype=protein_coding;description=CYP703A2 [Source:UniProtKB/TrEMBL%3bAcc:A0A178WMS1];gene_id=AT1G01280;logic_name=araport11; -1 araport11 mRNA 112263 113947 . + . ID=transcript:AT1G01280.1;biotype=protein_coding;Parent=gene:AT1G01280;transcript_id=AT1G01280.1; -1 araport11 five_prime_UTR 112263 112289 . + . Parent=transcript:AT1G01280.1; -1 araport11 exon 112263 113195 . + . Name=AT1G01280.1.exon1;Parent=transcript:AT1G01280.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01280.1.exon1;rank=1; -1 araport11 CDS 112290 113195 . + 0 ID=CDS:AT1G01280.1;Parent=transcript:AT1G01280.1;protein_id=AT1G01280.1 -1 araport11 CDS 113279 113905 . + 0 ID=CDS:AT1G01280.1;Parent=transcript:AT1G01280.1;protein_id=AT1G01280.1 -1 araport11 exon 113279 113947 . + . Name=AT1G01280.1.exon2;Parent=transcript:AT1G01280.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01280.1.exon2;rank=2; -1 araport11 three_prime_UTR 113906 113947 . + . Parent=transcript:AT1G01280.1; -1 araport11 gene 114202 116407 . + . ID=gene:AT1G01290;Name=CNX3;biotype=protein_coding;description=Cyclic pyranopterin monophosphate synthase%2c mitochondrial [Source:UniProtKB/Swiss-Prot%3bAcc:Q39056];gene_id=AT1G01290;logic_name=araport11; -1 araport11 mRNA 114202 116407 . + . ID=transcript:AT1G01290.1;biotype=protein_coding;Parent=gene:AT1G01290;transcript_id=AT1G01290.1; -1 araport11 five_prime_UTR 114202 114298 . + . Parent=transcript:AT1G01290.1; -1 araport11 exon 114202 114433 . + . Name=AT1G01290.1.exon1;Parent=transcript:AT1G01290.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01290.1.exon1;rank=1; -1 araport11 CDS 114299 114433 . + 0 ID=CDS:AT1G01290.1;Parent=transcript:AT1G01290.1;protein_id=AT1G01290.1 -1 araport11 CDS 114619 115296 . + 0 ID=CDS:AT1G01290.1;Parent=transcript:AT1G01290.1;protein_id=AT1G01290.1 -1 araport11 exon 114619 116407 . + . Name=AT1G01290.1.exon2;Parent=transcript:AT1G01290.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01290.1.exon2;rank=2; -1 araport11 three_prime_UTR 115297 116407 . + . Parent=transcript:AT1G01290.1; -1 araport11 mRNA 114202 116407 . + . ID=transcript:AT1G01290.2;biotype=protein_coding;Parent=gene:AT1G01290;transcript_id=AT1G01290.2; -1 araport11 five_prime_UTR 114202 114298 . + . Parent=transcript:AT1G01290.2; -1 araport11 exon 114202 114433 . + . Name=AT1G01290.1.exon1;Parent=transcript:AT1G01290.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01290.1.exon1;rank=1; -1 araport11 CDS 114299 114433 . + 0 ID=CDS:AT1G01290.2;Parent=transcript:AT1G01290.2;protein_id=AT1G01290.2 -1 araport11 CDS 114619 115296 . + 0 ID=CDS:AT1G01290.2;Parent=transcript:AT1G01290.2;protein_id=AT1G01290.2 -1 araport11 exon 114619 115339 . + . Name=AT1G01290.2.exon2;Parent=transcript:AT1G01290.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01290.2.exon2;rank=2; -1 araport11 three_prime_UTR 115297 115339 . + . Parent=transcript:AT1G01290.2; -1 araport11 exon 115961 116407 . + . Name=AT1G01290.2.exon3;Parent=transcript:AT1G01290.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01290.2.exon3;rank=3; -1 araport11 three_prime_UTR 115961 116407 . + . Parent=transcript:AT1G01290.2; -1 araport11 gene 116784 118845 . + . ID=gene:AT1G01300;Name=APF2;biotype=protein_coding;description=Aspartyl protease family protein 2 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LNJ3];gene_id=AT1G01300;logic_name=araport11; -1 araport11 mRNA 116784 118845 . + . ID=transcript:AT1G01300.1;biotype=protein_coding;Parent=gene:AT1G01300;transcript_id=AT1G01300.1; -1 araport11 five_prime_UTR 116784 117064 . + . Parent=transcript:AT1G01300.1; -1 araport11 exon 116784 118845 . + . Name=AT1G01300.1.exon1;Parent=transcript:AT1G01300.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01300.1.exon1;rank=1; -1 araport11 CDS 117065 118522 . + 0 ID=CDS:AT1G01300.1;Parent=transcript:AT1G01300.1;protein_id=AT1G01300.1 -1 araport11 three_prime_UTR 118523 118845 . + . Parent=transcript:AT1G01300.1; -1 araport11 gene 119381 119997 . + . ID=gene:AT1G01305;biotype=protein_coding;description=Putative uncharacterized protein [Source:UniProtKB/TrEMBL%3bAcc:Q1G401];gene_id=AT1G01305;logic_name=araport11; -1 araport11 mRNA 119381 119997 . + . ID=transcript:AT1G01305.1;biotype=protein_coding;Parent=gene:AT1G01305;transcript_id=AT1G01305.1; -1 araport11 five_prime_UTR 119381 119428 . + . Parent=transcript:AT1G01305.1; -1 araport11 exon 119381 119997 . + . Name=AT1G01305.1.exon1;Parent=transcript:AT1G01305.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01305.1.exon1;rank=1; -1 araport11 CDS 119429 119854 . + 0 ID=CDS:AT1G01305.1;Parent=transcript:AT1G01305.1;protein_id=AT1G01305.1 -1 araport11 three_prime_UTR 119855 119997 . + . Parent=transcript:AT1G01305.1; -1 araport11 gene 120154 121130 . + . ID=gene:AT1G01310;biotype=protein_coding;description=At1g01310 [Source:UniProtKB/TrEMBL%3bAcc:Q6ID87];gene_id=AT1G01310;logic_name=araport11; -1 araport11 mRNA 120154 121130 . + . ID=transcript:AT1G01310.1;biotype=protein_coding;Parent=gene:AT1G01310;transcript_id=AT1G01310.1; -1 araport11 five_prime_UTR 120154 120220 . + . Parent=transcript:AT1G01310.1; -1 araport11 exon 120154 121130 . + . Name=AT1G01310.1.exon1;Parent=transcript:AT1G01310.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01310.1.exon1;rank=1; -1 araport11 CDS 120221 120946 . + 0 ID=CDS:AT1G01310.1;Parent=transcript:AT1G01310.1;protein_id=AT1G01310.1 -1 araport11 three_prime_UTR 120947 121130 . + . Parent=transcript:AT1G01310.1; -1 araport11 gene 121067 130577 . - . ID=gene:AT1G01320;biotype=protein_coding;description=Tetratricopeptide repeat (TPR)-like superfamily protein [Source:UniProtKB/TrEMBL%3bAcc:F4HS99];gene_id=AT1G01320;logic_name=araport11; -1 araport11 mRNA 121067 130573 . - . ID=transcript:AT1G01320.3;biotype=protein_coding;Parent=gene:AT1G01320;transcript_id=AT1G01320.3; -1 araport11 exon 121067 121406 . - . Name=AT1G01320.3.exon25;Parent=transcript:AT1G01320.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01320.3.exon25;rank=25; -1 araport11 three_prime_UTR 121067 121406 . - . Parent=transcript:AT1G01320.3; -1 araport11 three_prime_UTR 121493 121581 . - . Parent=transcript:AT1G01320.3; -1 araport11 exon 121493 123501 . - . Name=AT1G01320.3.exon24;Parent=transcript:AT1G01320.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01320.3.exon24;rank=24; -1 araport11 CDS 121582 123501 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 123579 123669 . - . Name=AT1G01320.3.exon23;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon23;rank=23; -1 araport11 CDS 123579 123669 . - 1 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 123785 123897 . - . Name=AT1G01320.3.exon22;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon22;rank=22; -1 araport11 CDS 123785 123897 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 123992 124123 . - . Name=AT1G01320.3.exon21;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon21;rank=21; -1 araport11 CDS 123992 124123 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 124211 124394 . - . Name=AT1G01320.3.exon20;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon20;rank=20; -1 araport11 CDS 124211 124394 . - 1 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 124499 124632 . - . Name=AT1G01320.3.exon19;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon19;rank=19; -1 araport11 CDS 124499 124632 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 124714 124818 . - . Name=AT1G01320.3.exon18;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon18;rank=18; -1 araport11 CDS 124714 124818 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 124921 125022 . - . Name=AT1G01320.3.exon17;Parent=transcript:AT1G01320.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon17;rank=17; -1 araport11 CDS 124921 125022 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 125134 125226 . - . Name=AT1G01320.3.exon16;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon16;rank=16; -1 araport11 CDS 125134 125226 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 125329 125655 . - . Name=AT1G01320.3.exon15;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon15;rank=15; -1 araport11 CDS 125329 125655 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 125742 125843 . - . Name=AT1G01320.3.exon14;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon14;rank=14; -1 araport11 CDS 125742 125843 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 125936 125998 . - . Name=AT1G01320.3.exon13;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon13;rank=13; -1 araport11 CDS 125936 125998 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 126076 126589 . - . Name=AT1G01320.3.exon12;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon12;rank=12; -1 araport11 CDS 126076 126589 . - 1 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 126686 126840 . - . Name=AT1G01320.3.exon11;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon11;rank=11; -1 araport11 CDS 126686 126840 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 126935 127453 . - . Name=AT1G01320.3.exon10;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon10;rank=10; -1 araport11 CDS 126935 127453 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 127532 127573 . - . Name=AT1G01320.3.exon9;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon9;rank=9; -1 araport11 CDS 127532 127573 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 127651 127782 . - . Name=AT1G01320.3.exon8;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon8;rank=8; -1 araport11 CDS 127651 127782 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 127868 127935 . - . Name=AT1G01320.3.exon7;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01320.3.exon7;rank=7; -1 araport11 CDS 127868 127935 . - 2 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 128028 128312 . - . Name=AT1G01320.3.exon6;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01320.3.exon6;rank=6; -1 araport11 CDS 128028 128312 . - 2 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 128479 128551 . - . Name=AT1G01320.3.exon5;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01320.3.exon5;rank=5; -1 araport11 CDS 128479 128551 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 128968 129060 . - . Name=AT1G01320.3.exon4;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon4;rank=4; -1 araport11 CDS 128968 129060 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 129853 129914 . - . Name=AT1G01320.3.exon3;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01320.3.exon3;rank=3; -1 araport11 CDS 129853 129914 . - 2 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 CDS 130039 130099 . - 0 ID=CDS:AT1G01320.3;Parent=transcript:AT1G01320.3;protein_id=AT1G01320.3 -1 araport11 exon 130039 130149 . - . Name=AT1G01320.3.exon2;Parent=transcript:AT1G01320.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01320.3.exon2;rank=2; -1 araport11 five_prime_UTR 130100 130149 . - . Parent=transcript:AT1G01320.3; -1 araport11 exon 130372 130573 . - . Name=AT1G01320.3.exon1;Parent=transcript:AT1G01320.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01320.3.exon1;rank=1; -1 araport11 five_prime_UTR 130372 130573 . - . Parent=transcript:AT1G01320.3; -1 araport11 mRNA 121067 130577 . - . ID=transcript:AT1G01320.2;biotype=protein_coding;Parent=gene:AT1G01320;transcript_id=AT1G01320.2; -1 araport11 exon 121067 121406 . - . Name=AT1G01320.3.exon25;Parent=transcript:AT1G01320.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01320.3.exon25;rank=25; -1 araport11 three_prime_UTR 121067 121406 . - . Parent=transcript:AT1G01320.2; -1 araport11 three_prime_UTR 121493 121581 . - . Parent=transcript:AT1G01320.2; -1 araport11 exon 121493 123495 . - . Name=AT1G01320.2.exon24;Parent=transcript:AT1G01320.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01320.2.exon24;rank=24; -1 araport11 CDS 121582 123495 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 123579 123669 . - . Name=AT1G01320.3.exon23;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon23;rank=23; -1 araport11 CDS 123579 123669 . - 1 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 123785 123897 . - . Name=AT1G01320.3.exon22;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon22;rank=22; -1 araport11 CDS 123785 123897 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 123992 124123 . - . Name=AT1G01320.3.exon21;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon21;rank=21; -1 araport11 CDS 123992 124123 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 124211 124394 . - . Name=AT1G01320.3.exon20;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon20;rank=20; -1 araport11 CDS 124211 124394 . - 1 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 124499 124632 . - . Name=AT1G01320.3.exon19;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon19;rank=19; -1 araport11 CDS 124499 124632 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 124714 124818 . - . Name=AT1G01320.3.exon18;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon18;rank=18; -1 araport11 CDS 124714 124818 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 124921 125022 . - . Name=AT1G01320.3.exon17;Parent=transcript:AT1G01320.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon17;rank=17; -1 araport11 CDS 124921 125022 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 125134 125226 . - . Name=AT1G01320.3.exon16;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon16;rank=16; -1 araport11 CDS 125134 125226 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 125329 125655 . - . Name=AT1G01320.3.exon15;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon15;rank=15; -1 araport11 CDS 125329 125655 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 125742 125843 . - . Name=AT1G01320.3.exon14;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon14;rank=14; -1 araport11 CDS 125742 125843 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 125936 125998 . - . Name=AT1G01320.3.exon13;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon13;rank=13; -1 araport11 CDS 125936 125998 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 126076 126589 . - . Name=AT1G01320.3.exon12;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon12;rank=12; -1 araport11 CDS 126076 126589 . - 1 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 126686 126840 . - . Name=AT1G01320.3.exon11;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon11;rank=11; -1 araport11 CDS 126686 126840 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 126935 127453 . - . Name=AT1G01320.3.exon10;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon10;rank=10; -1 araport11 CDS 126935 127453 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 127532 127573 . - . Name=AT1G01320.3.exon9;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon9;rank=9; -1 araport11 CDS 127532 127573 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 127651 127782 . - . Name=AT1G01320.3.exon8;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon8;rank=8; -1 araport11 CDS 127651 127782 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 127868 127935 . - . Name=AT1G01320.3.exon7;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01320.3.exon7;rank=7; -1 araport11 CDS 127868 127935 . - 2 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 128028 128312 . - . Name=AT1G01320.3.exon6;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01320.3.exon6;rank=6; -1 araport11 CDS 128028 128312 . - 2 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 128479 128551 . - . Name=AT1G01320.3.exon5;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01320.3.exon5;rank=5; -1 araport11 CDS 128479 128551 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 128968 129060 . - . Name=AT1G01320.3.exon4;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon4;rank=4; -1 araport11 CDS 128968 129060 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 129853 129914 . - . Name=AT1G01320.3.exon3;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01320.3.exon3;rank=3; -1 araport11 CDS 129853 129914 . - 2 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 CDS 130039 130099 . - 0 ID=CDS:AT1G01320.2;Parent=transcript:AT1G01320.2;protein_id=AT1G01320.2 -1 araport11 exon 130039 130149 . - . Name=AT1G01320.3.exon2;Parent=transcript:AT1G01320.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01320.3.exon2;rank=2; -1 araport11 five_prime_UTR 130100 130149 . - . Parent=transcript:AT1G01320.2; -1 araport11 exon 130372 130577 . - . Name=AT1G01320.2.exon1;Parent=transcript:AT1G01320.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01320.2.exon1;rank=1; -1 araport11 five_prime_UTR 130372 130577 . - . Parent=transcript:AT1G01320.2; -1 araport11 mRNA 121124 130570 . - . ID=transcript:AT1G01320.1;biotype=protein_coding;Parent=gene:AT1G01320;transcript_id=AT1G01320.1; -1 araport11 exon 121124 121406 . - . Name=AT1G01320.1.exon25;Parent=transcript:AT1G01320.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01320.1.exon25;rank=25; -1 araport11 three_prime_UTR 121124 121406 . - . Parent=transcript:AT1G01320.1; -1 araport11 three_prime_UTR 121493 121581 . - . Parent=transcript:AT1G01320.1; -1 araport11 exon 121493 123501 . - . Name=AT1G01320.3.exon24;Parent=transcript:AT1G01320.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01320.3.exon24;rank=24; -1 araport11 CDS 121582 123501 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 123579 123669 . - . Name=AT1G01320.3.exon23;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon23;rank=23; -1 araport11 CDS 123579 123669 . - 1 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 123785 123897 . - . Name=AT1G01320.3.exon22;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon22;rank=22; -1 araport11 CDS 123785 123897 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 123992 124123 . - . Name=AT1G01320.3.exon21;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon21;rank=21; -1 araport11 CDS 123992 124123 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 124211 124394 . - . Name=AT1G01320.3.exon20;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon20;rank=20; -1 araport11 CDS 124211 124394 . - 1 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 124499 124632 . - . Name=AT1G01320.3.exon19;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon19;rank=19; -1 araport11 CDS 124499 124632 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 124714 124818 . - . Name=AT1G01320.3.exon18;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon18;rank=18; -1 araport11 CDS 124714 124818 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 124921 125046 . - . Name=AT1G01320.1.exon17;Parent=transcript:AT1G01320.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.1.exon17;rank=17; -1 araport11 CDS 124921 125046 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 125134 125226 . - . Name=AT1G01320.3.exon16;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon16;rank=16; -1 araport11 CDS 125134 125226 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 125329 125655 . - . Name=AT1G01320.3.exon15;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon15;rank=15; -1 araport11 CDS 125329 125655 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 125742 125843 . - . Name=AT1G01320.3.exon14;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon14;rank=14; -1 araport11 CDS 125742 125843 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 125936 125998 . - . Name=AT1G01320.3.exon13;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon13;rank=13; -1 araport11 CDS 125936 125998 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 126076 126589 . - . Name=AT1G01320.3.exon12;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01320.3.exon12;rank=12; -1 araport11 CDS 126076 126589 . - 1 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 126686 126840 . - . Name=AT1G01320.3.exon11;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01320.3.exon11;rank=11; -1 araport11 CDS 126686 126840 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 126935 127453 . - . Name=AT1G01320.3.exon10;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon10;rank=10; -1 araport11 CDS 126935 127453 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 127532 127573 . - . Name=AT1G01320.3.exon9;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon9;rank=9; -1 araport11 CDS 127532 127573 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 127651 127782 . - . Name=AT1G01320.3.exon8;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon8;rank=8; -1 araport11 CDS 127651 127782 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 127868 127935 . - . Name=AT1G01320.3.exon7;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01320.3.exon7;rank=7; -1 araport11 CDS 127868 127935 . - 2 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 128028 128312 . - . Name=AT1G01320.3.exon6;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01320.3.exon6;rank=6; -1 araport11 CDS 128028 128312 . - 2 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 128479 128551 . - . Name=AT1G01320.3.exon5;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01320.3.exon5;rank=5; -1 araport11 CDS 128479 128551 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 128968 129060 . - . Name=AT1G01320.3.exon4;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01320.3.exon4;rank=4; -1 araport11 CDS 128968 129060 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 129853 129914 . - . Name=AT1G01320.3.exon3;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01320.3.exon3;rank=3; -1 araport11 CDS 129853 129914 . - 2 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 CDS 130039 130099 . - 0 ID=CDS:AT1G01320.1;Parent=transcript:AT1G01320.1;protein_id=AT1G01320.1 -1 araport11 exon 130039 130149 . - . Name=AT1G01320.3.exon2;Parent=transcript:AT1G01320.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01320.3.exon2;rank=2; -1 araport11 five_prime_UTR 130100 130149 . - . Parent=transcript:AT1G01320.1; -1 araport11 exon 130372 130570 . - . Name=AT1G01320.1.exon1;Parent=transcript:AT1G01320.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01320.1.exon1;rank=1; -1 araport11 five_prime_UTR 130372 130570 . - . Parent=transcript:AT1G01320.1; -1 araport11 gene 130736 130858 . + . ID=gene:AT1G01335;Name=AREP1;biotype=protein_coding;description=Auxin-responsive endogenous peptide 1 [Source:UniProtKB/Swiss-Prot%3bAcc:P0DKH9];gene_id=AT1G01335;logic_name=araport11; -1 araport11 mRNA 130736 130858 . + . ID=transcript:AT1G01335.1;biotype=protein_coding;Parent=gene:AT1G01335;transcript_id=AT1G01335.1; -1 araport11 exon 130736 130858 . + . Name=AT1G01335.1.exon1;Parent=transcript:AT1G01335.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01335.1.exon1;rank=1; -1 araport11 CDS 130736 130858 . + 0 ID=CDS:AT1G01335.1;Parent=transcript:AT1G01335.1;protein_id=AT1G01335.1 -1 araport11 gene 132270 135924 . - . ID=gene:AT1G01340;Name=CNGC10;biotype=protein_coding;description=Probable cyclic nucleotide-gated ion channel 10 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LNJ0];gene_id=AT1G01340;logic_name=araport11; -1 araport11 mRNA 132270 135924 . - . ID=transcript:AT1G01340.2;biotype=protein_coding;Parent=gene:AT1G01340;transcript_id=AT1G01340.2; -1 araport11 three_prime_UTR 132270 132413 . - . Parent=transcript:AT1G01340.2; -1 araport11 exon 132270 132744 . - . Name=AT1G01340.2.exon9;Parent=transcript:AT1G01340.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01340.2.exon9;rank=9; -1 araport11 CDS 132414 132744 . - 1 ID=CDS:AT1G01340.2;Parent=transcript:AT1G01340.2;protein_id=AT1G01340.2 -1 araport11 exon 132824 133218 . - . Name=AT1G01340.1.exon6;Parent=transcript:AT1G01340.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01340.1.exon6;rank=8; -1 araport11 CDS 132824 133218 . - 0 ID=CDS:AT1G01340.2;Parent=transcript:AT1G01340.2;protein_id=AT1G01340.2 -1 araport11 exon 133303 133539 . - . Name=AT1G01340.1.exon5;Parent=transcript:AT1G01340.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01340.1.exon5;rank=7; -1 araport11 CDS 133303 133539 . - 0 ID=CDS:AT1G01340.2;Parent=transcript:AT1G01340.2;protein_id=AT1G01340.2 -1 araport11 exon 133641 133752 . - . Name=AT1G01340.1.exon4;Parent=transcript:AT1G01340.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01340.1.exon4;rank=6; -1 araport11 CDS 133641 133752 . - 1 ID=CDS:AT1G01340.2;Parent=transcript:AT1G01340.2;protein_id=AT1G01340.2 -1 araport11 exon 133911 134206 . - . Name=AT1G01340.1.exon3;Parent=transcript:AT1G01340.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01340.1.exon3;rank=5; -1 araport11 CDS 133911 134206 . - 0 ID=CDS:AT1G01340.2;Parent=transcript:AT1G01340.2;protein_id=AT1G01340.2 -1 araport11 exon 134289 134501 . - . Name=AT1G01340.1.exon2;Parent=transcript:AT1G01340.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01340.1.exon2;rank=4; -1 araport11 CDS 134289 134501 . - 0 ID=CDS:AT1G01340.2;Parent=transcript:AT1G01340.2;protein_id=AT1G01340.2 -1 araport11 exon 134582 135104 . - . Name=AT1G01340.2.exon3;Parent=transcript:AT1G01340.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01340.2.exon3;rank=3; -1 araport11 CDS 134582 135104 . - 1 ID=CDS:AT1G01340.2;Parent=transcript:AT1G01340.2;protein_id=AT1G01340.2 -1 araport11 CDS 135188 135216 . - 0 ID=CDS:AT1G01340.2;Parent=transcript:AT1G01340.2;protein_id=AT1G01340.2 -1 araport11 exon 135188 135269 . - . Name=AT1G01340.2.exon2;Parent=transcript:AT1G01340.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01340.2.exon2;rank=2; -1 araport11 five_prime_UTR 135217 135269 . - . Parent=transcript:AT1G01340.2; -1 araport11 exon 135708 135924 . - . Name=AT1G01340.2.exon1;Parent=transcript:AT1G01340.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01340.2.exon1;rank=1; -1 araport11 five_prime_UTR 135708 135924 . - . Parent=transcript:AT1G01340.2; -1 araport11 mRNA 132328 135322 . - . ID=transcript:AT1G01340.1;biotype=protein_coding;Parent=gene:AT1G01340;transcript_id=AT1G01340.1; -1 araport11 three_prime_UTR 132328 132413 . - . Parent=transcript:AT1G01340.1; -1 araport11 exon 132328 132744 . - . Name=AT1G01340.1.exon7;Parent=transcript:AT1G01340.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01340.1.exon7;rank=7; -1 araport11 CDS 132414 132744 . - 1 ID=CDS:AT1G01340.1;Parent=transcript:AT1G01340.1;protein_id=AT1G01340.1 -1 araport11 exon 132824 133218 . - . Name=AT1G01340.1.exon6;Parent=transcript:AT1G01340.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01340.1.exon6;rank=6; -1 araport11 CDS 132824 133218 . - 0 ID=CDS:AT1G01340.1;Parent=transcript:AT1G01340.1;protein_id=AT1G01340.1 -1 araport11 exon 133303 133539 . - . Name=AT1G01340.1.exon5;Parent=transcript:AT1G01340.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01340.1.exon5;rank=5; -1 araport11 CDS 133303 133539 . - 0 ID=CDS:AT1G01340.1;Parent=transcript:AT1G01340.1;protein_id=AT1G01340.1 -1 araport11 exon 133641 133752 . - . Name=AT1G01340.1.exon4;Parent=transcript:AT1G01340.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01340.1.exon4;rank=4; -1 araport11 CDS 133641 133752 . - 1 ID=CDS:AT1G01340.1;Parent=transcript:AT1G01340.1;protein_id=AT1G01340.1 -1 araport11 exon 133911 134206 . - . Name=AT1G01340.1.exon3;Parent=transcript:AT1G01340.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01340.1.exon3;rank=3; -1 araport11 CDS 133911 134206 . - 0 ID=CDS:AT1G01340.1;Parent=transcript:AT1G01340.1;protein_id=AT1G01340.1 -1 araport11 exon 134289 134501 . - . Name=AT1G01340.1.exon2;Parent=transcript:AT1G01340.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01340.1.exon2;rank=2; -1 araport11 CDS 134289 134501 . - 0 ID=CDS:AT1G01340.1;Parent=transcript:AT1G01340.1;protein_id=AT1G01340.1 -1 araport11 CDS 134582 135118 . - 0 ID=CDS:AT1G01340.1;Parent=transcript:AT1G01340.1;protein_id=AT1G01340.1 -1 araport11 exon 134582 135322 . - . Name=AT1G01340.1.exon1;Parent=transcript:AT1G01340.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01340.1.exon1;rank=1; -1 araport11 five_prime_UTR 135119 135322 . - . Parent=transcript:AT1G01340.1; -1 araport11 gene 136090 138162 . + . ID=gene:AT1G01350;biotype=protein_coding;description=Zinc finger CCCH domain-containing protein 1 [Source:UniProtKB/Swiss-Prot%3bAcc:Q8GX84];gene_id=AT1G01350;logic_name=araport11; -1 araport11 mRNA 136090 138162 . + . ID=transcript:AT1G01350.1;biotype=protein_coding;Parent=gene:AT1G01350;transcript_id=AT1G01350.1; -1 araport11 exon 136090 136234 . + . Name=AT1G01350.1.exon1;Parent=transcript:AT1G01350.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01350.1.exon1;rank=1; -1 araport11 five_prime_UTR 136090 136234 . + . Parent=transcript:AT1G01350.1; -1 araport11 five_prime_UTR 136667 136731 . + . Parent=transcript:AT1G01350.1; -1 araport11 exon 136667 136816 . + . Name=AT1G01350.1.exon2;Parent=transcript:AT1G01350.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01350.1.exon2;rank=2; -1 araport11 CDS 136732 136816 . + 0 ID=CDS:AT1G01350.1;Parent=transcript:AT1G01350.1;protein_id=AT1G01350.1 -1 araport11 exon 136935 137758 . + . Name=AT1G01350.1.exon3;Parent=transcript:AT1G01350.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01350.1.exon3;rank=3; -1 araport11 CDS 136935 137758 . + 2 ID=CDS:AT1G01350.1;Parent=transcript:AT1G01350.1;protein_id=AT1G01350.1 -1 araport11 CDS 137848 137970 . + 0 ID=CDS:AT1G01350.1;Parent=transcript:AT1G01350.1;protein_id=AT1G01350.1 -1 araport11 exon 137848 138162 . + . Name=AT1G01350.1.exon4;Parent=transcript:AT1G01350.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01350.1.exon4;rank=4; -1 araport11 three_prime_UTR 137971 138162 . + . Parent=transcript:AT1G01350.1; -1 araport11 gene 138489 139680 . + . ID=gene:AT1G01355;biotype=protein_coding;description=Putative endonuclease or glycosyl hydrolase [Source:UniProtKB/TrEMBL%3bAcc:F4HSA3];gene_id=AT1G01355;logic_name=araport11; -1 araport11 mRNA 138489 139671 . + . ID=transcript:AT1G01355.2;biotype=protein_coding;Parent=gene:AT1G01355;transcript_id=AT1G01355.2; -1 araport11 five_prime_UTR 138489 138721 . + . Parent=transcript:AT1G01355.2; -1 araport11 exon 138489 138778 . + . Name=AT1G01355.2.exon1;Parent=transcript:AT1G01355.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01355.2.exon1;rank=1; -1 araport11 CDS 138722 138778 . + 0 ID=CDS:AT1G01355.2;Parent=transcript:AT1G01355.2;protein_id=AT1G01355.2 -1 araport11 exon 138875 138914 . + . Name=AT1G01355.2.exon2;Parent=transcript:AT1G01355.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01355.2.exon2;rank=2; -1 araport11 CDS 138875 138914 . + 0 ID=CDS:AT1G01355.2;Parent=transcript:AT1G01355.2;protein_id=AT1G01355.2 -1 araport11 exon 138989 139114 . + . Name=AT1G01355.2.exon3;Parent=transcript:AT1G01355.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01355.2.exon3;rank=3; -1 araport11 CDS 138989 139114 . + 2 ID=CDS:AT1G01355.2;Parent=transcript:AT1G01355.2;protein_id=AT1G01355.2 -1 araport11 exon 139203 139345 . + . Name=AT1G01355.3.exon4;Parent=transcript:AT1G01355.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01355.3.exon4;rank=4; -1 araport11 CDS 139203 139345 . + 2 ID=CDS:AT1G01355.2;Parent=transcript:AT1G01355.2;protein_id=AT1G01355.2 -1 araport11 CDS 139488 139568 . + 0 ID=CDS:AT1G01355.2;Parent=transcript:AT1G01355.2;protein_id=AT1G01355.2 -1 araport11 exon 139488 139671 . + . Name=AT1G01355.2.exon5;Parent=transcript:AT1G01355.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01355.2.exon5;rank=5; -1 araport11 three_prime_UTR 139569 139671 . + . Parent=transcript:AT1G01355.2; -1 araport11 mRNA 138513 139651 . + . ID=transcript:AT1G01355.3;biotype=protein_coding;Parent=gene:AT1G01355;transcript_id=AT1G01355.3; -1 araport11 exon 138513 138541 . + . Name=AT1G01355.3.exon1;Parent=transcript:AT1G01355.3;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01355.3.exon1;rank=1; -1 araport11 CDS 138513 138541 . + 0 ID=CDS:AT1G01355.3;Parent=transcript:AT1G01355.3;protein_id=AT1G01355.3 -1 araport11 exon 138597 138778 . + . Name=AT1G01355.3.exon2;Parent=transcript:AT1G01355.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01355.3.exon2;rank=2; -1 araport11 CDS 138597 138778 . + 1 ID=CDS:AT1G01355.3;Parent=transcript:AT1G01355.3;protein_id=AT1G01355.3 -1 araport11 exon 138875 139114 . + . Name=AT1G01355.3.exon3;Parent=transcript:AT1G01355.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01355.3.exon3;rank=3; -1 araport11 CDS 138875 139114 . + 2 ID=CDS:AT1G01355.3;Parent=transcript:AT1G01355.3;protein_id=AT1G01355.3 -1 araport11 exon 139203 139345 . + . Name=AT1G01355.3.exon4;Parent=transcript:AT1G01355.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01355.3.exon4;rank=4; -1 araport11 CDS 139203 139345 . + 2 ID=CDS:AT1G01355.3;Parent=transcript:AT1G01355.3;protein_id=AT1G01355.3 -1 araport11 CDS 139488 139568 . + 0 ID=CDS:AT1G01355.3;Parent=transcript:AT1G01355.3;protein_id=AT1G01355.3 -1 araport11 exon 139488 139651 . + . Name=AT1G01355.3.exon5;Parent=transcript:AT1G01355.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01355.3.exon5;rank=5; -1 araport11 three_prime_UTR 139569 139651 . + . Parent=transcript:AT1G01355.3; -1 araport11 mRNA 138513 139680 . + . ID=transcript:AT1G01355.1;biotype=protein_coding;Parent=gene:AT1G01355;transcript_id=AT1G01355.1; -1 araport11 exon 138513 138541 . + . Name=AT1G01355.3.exon1;Parent=transcript:AT1G01355.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01355.3.exon1;rank=1; -1 araport11 CDS 138513 138541 . + 0 ID=CDS:AT1G01355.1;Parent=transcript:AT1G01355.1;protein_id=AT1G01355.1 -1 araport11 exon 138597 138778 . + . Name=AT1G01355.3.exon2;Parent=transcript:AT1G01355.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01355.3.exon2;rank=2; -1 araport11 CDS 138597 138778 . + 1 ID=CDS:AT1G01355.1;Parent=transcript:AT1G01355.1;protein_id=AT1G01355.1 -1 araport11 exon 138863 139114 . + . Name=AT1G01355.1.exon3;Parent=transcript:AT1G01355.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01355.1.exon3;rank=3; -1 araport11 CDS 138863 139114 . + 2 ID=CDS:AT1G01355.1;Parent=transcript:AT1G01355.1;protein_id=AT1G01355.1 -1 araport11 exon 139203 139345 . + . Name=AT1G01355.3.exon4;Parent=transcript:AT1G01355.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01355.3.exon4;rank=4; -1 araport11 CDS 139203 139345 . + 2 ID=CDS:AT1G01355.1;Parent=transcript:AT1G01355.1;protein_id=AT1G01355.1 -1 araport11 CDS 139488 139568 . + 0 ID=CDS:AT1G01355.1;Parent=transcript:AT1G01355.1;protein_id=AT1G01355.1 -1 araport11 exon 139488 139680 . + . Name=AT1G01355.1.exon5;Parent=transcript:AT1G01355.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01355.1.exon5;rank=5; -1 araport11 three_prime_UTR 139569 139680 . + . Parent=transcript:AT1G01355.1; -1 araport11 gene 141870 143261 . + . ID=gene:AT1G01360;Name=PYL9;biotype=protein_coding;description=RCAR1 [Source:UniProtKB/TrEMBL%3bAcc:A0A178W4H4];gene_id=AT1G01360;logic_name=araport11; -1 araport11 mRNA 141870 143261 . + . ID=transcript:AT1G01360.1;biotype=protein_coding;Parent=gene:AT1G01360;transcript_id=AT1G01360.1; -1 araport11 five_prime_UTR 141870 142137 . + . Parent=transcript:AT1G01360.1; -1 araport11 exon 141870 142281 . + . Name=AT1G01360.1.exon1;Parent=transcript:AT1G01360.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01360.1.exon1;rank=1; -1 araport11 CDS 142138 142281 . + 0 ID=CDS:AT1G01360.1;Parent=transcript:AT1G01360.1;protein_id=AT1G01360.1 -1 araport11 exon 142424 142639 . + . Name=AT1G01360.1.exon2;Parent=transcript:AT1G01360.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01360.1.exon2;rank=2; -1 araport11 CDS 142424 142639 . + 0 ID=CDS:AT1G01360.1;Parent=transcript:AT1G01360.1;protein_id=AT1G01360.1 -1 araport11 CDS 142711 142914 . + 0 ID=CDS:AT1G01360.1;Parent=transcript:AT1G01360.1;protein_id=AT1G01360.1 -1 araport11 exon 142711 143261 . + . Name=AT1G01360.1.exon3;Parent=transcript:AT1G01360.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01360.1.exon3;rank=3; -1 araport11 three_prime_UTR 142915 143261 . + . Parent=transcript:AT1G01360.1; -1 araport11 gene 143489 146479 . + . ID=gene:AT1G01370;Name=HTR12;biotype=protein_coding;description=Histone H3-like centromeric protein HTR12 [Source:UniProtKB/Swiss-Prot%3bAcc:Q8RVQ9];gene_id=AT1G01370;logic_name=araport11; -1 araport11 mRNA 143489 146042 . + . ID=transcript:AT1G01370.1;biotype=protein_coding;Parent=gene:AT1G01370;transcript_id=AT1G01370.1; -1 araport11 exon 143489 143676 . + . Name=AT1G01370.3.exon1;Parent=transcript:AT1G01370.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01370.3.exon1;rank=1; -1 araport11 five_prime_UTR 143489 143676 . + . Parent=transcript:AT1G01370.1; -1 araport11 five_prime_UTR 143764 143772 . + . Parent=transcript:AT1G01370.1; -1 araport11 exon 143764 143824 . + . Name=AT1G01370.3.exon2;Parent=transcript:AT1G01370.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01370.3.exon2;rank=2; -1 araport11 CDS 143773 143824 . + 0 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 exon 143934 143977 . + . Name=AT1G01370.3.exon3;Parent=transcript:AT1G01370.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon3;rank=3; -1 araport11 CDS 143934 143977 . + 2 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 exon 144064 144109 . + . Name=AT1G01370.3.exon4;Parent=transcript:AT1G01370.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon4;rank=4; -1 araport11 CDS 144064 144109 . + 0 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 exon 144193 144227 . + . Name=AT1G01370.3.exon5;Parent=transcript:AT1G01370.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon5;rank=5; -1 araport11 CDS 144193 144227 . + 2 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 exon 144315 144351 . + . Name=AT1G01370.3.exon6;Parent=transcript:AT1G01370.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon6;rank=6; -1 araport11 CDS 144315 144351 . + 0 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 exon 144447 144559 . + . Name=AT1G01370.3.exon7;Parent=transcript:AT1G01370.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon7;rank=7; -1 araport11 CDS 144447 144559 . + 2 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 exon 144927 145004 . + . Name=AT1G01370.3.exon8;Parent=transcript:AT1G01370.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01370.3.exon8;rank=8; -1 araport11 CDS 144927 145004 . + 0 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 exon 145132 145207 . + . Name=AT1G01370.3.exon9;Parent=transcript:AT1G01370.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon9;rank=9; -1 araport11 CDS 145132 145207 . + 0 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 CDS 145345 145400 . + 2 ID=CDS:AT1G01370.1;Parent=transcript:AT1G01370.1;protein_id=AT1G01370.1 -1 araport11 exon 145345 146042 . + . Name=AT1G01370.1.exon10;Parent=transcript:AT1G01370.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01370.1.exon10;rank=10; -1 araport11 three_prime_UTR 145401 146042 . + . Parent=transcript:AT1G01370.1; -1 araport11 mRNA 143489 146042 . + . ID=transcript:AT1G01370.2;biotype=protein_coding;Parent=gene:AT1G01370;transcript_id=AT1G01370.2; -1 araport11 five_prime_UTR 143489 143772 . + . Parent=transcript:AT1G01370.2; -1 araport11 exon 143489 143824 . + . Name=AT1G01370.2.exon1;Parent=transcript:AT1G01370.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01370.2.exon1;rank=1; -1 araport11 CDS 143773 143824 . + 0 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 exon 143934 143977 . + . Name=AT1G01370.3.exon3;Parent=transcript:AT1G01370.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon3;rank=2; -1 araport11 CDS 143934 143977 . + 2 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 exon 144064 144109 . + . Name=AT1G01370.3.exon4;Parent=transcript:AT1G01370.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon4;rank=3; -1 araport11 CDS 144064 144109 . + 0 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 exon 144193 144227 . + . Name=AT1G01370.3.exon5;Parent=transcript:AT1G01370.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon5;rank=4; -1 araport11 CDS 144193 144227 . + 2 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 exon 144315 144351 . + . Name=AT1G01370.3.exon6;Parent=transcript:AT1G01370.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon6;rank=5; -1 araport11 CDS 144315 144351 . + 0 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 exon 144447 144559 . + . Name=AT1G01370.3.exon7;Parent=transcript:AT1G01370.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon7;rank=6; -1 araport11 CDS 144447 144559 . + 2 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 exon 144927 145004 . + . Name=AT1G01370.3.exon8;Parent=transcript:AT1G01370.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01370.3.exon8;rank=7; -1 araport11 CDS 144927 145004 . + 0 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 exon 145132 145207 . + . Name=AT1G01370.3.exon9;Parent=transcript:AT1G01370.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon9;rank=8; -1 araport11 CDS 145132 145207 . + 0 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 CDS 145345 145400 . + 2 ID=CDS:AT1G01370.2;Parent=transcript:AT1G01370.2;protein_id=AT1G01370.2 -1 araport11 exon 145345 146042 . + . Name=AT1G01370.1.exon10;Parent=transcript:AT1G01370.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01370.1.exon10;rank=9; -1 araport11 three_prime_UTR 145401 146042 . + . Parent=transcript:AT1G01370.2; -1 araport11 mRNA 143489 146479 . + . ID=transcript:AT1G01370.3;biotype=protein_coding;Parent=gene:AT1G01370;transcript_id=AT1G01370.3; -1 araport11 exon 143489 143676 . + . Name=AT1G01370.3.exon1;Parent=transcript:AT1G01370.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01370.3.exon1;rank=1; -1 araport11 five_prime_UTR 143489 143676 . + . Parent=transcript:AT1G01370.3; -1 araport11 five_prime_UTR 143764 143772 . + . Parent=transcript:AT1G01370.3; -1 araport11 exon 143764 143824 . + . Name=AT1G01370.3.exon2;Parent=transcript:AT1G01370.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01370.3.exon2;rank=2; -1 araport11 CDS 143773 143824 . + 0 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 exon 143934 143977 . + . Name=AT1G01370.3.exon3;Parent=transcript:AT1G01370.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon3;rank=3; -1 araport11 CDS 143934 143977 . + 2 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 exon 144064 144109 . + . Name=AT1G01370.3.exon4;Parent=transcript:AT1G01370.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon4;rank=4; -1 araport11 CDS 144064 144109 . + 0 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 exon 144193 144227 . + . Name=AT1G01370.3.exon5;Parent=transcript:AT1G01370.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon5;rank=5; -1 araport11 CDS 144193 144227 . + 2 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 exon 144315 144351 . + . Name=AT1G01370.3.exon6;Parent=transcript:AT1G01370.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon6;rank=6; -1 araport11 CDS 144315 144351 . + 0 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 exon 144447 144559 . + . Name=AT1G01370.3.exon7;Parent=transcript:AT1G01370.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon7;rank=7; -1 araport11 CDS 144447 144559 . + 2 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 exon 144927 145004 . + . Name=AT1G01370.3.exon8;Parent=transcript:AT1G01370.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01370.3.exon8;rank=8; -1 araport11 CDS 144927 145004 . + 0 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 exon 145132 145207 . + . Name=AT1G01370.3.exon9;Parent=transcript:AT1G01370.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon9;rank=9; -1 araport11 CDS 145132 145207 . + 0 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 CDS 145345 145400 . + 2 ID=CDS:AT1G01370.3;Parent=transcript:AT1G01370.3;protein_id=AT1G01370.3 -1 araport11 exon 145345 145435 . + . Name=AT1G01370.3.exon10;Parent=transcript:AT1G01370.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01370.3.exon10;rank=10; -1 araport11 three_prime_UTR 145401 145435 . + . Parent=transcript:AT1G01370.3; -1 araport11 exon 146164 146479 . + . Name=AT1G01370.3.exon11;Parent=transcript:AT1G01370.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01370.3.exon11;rank=11; -1 araport11 three_prime_UTR 146164 146479 . + . Parent=transcript:AT1G01370.3; -1 araport11 mRNA 143522 145676 . + . ID=transcript:AT1G01370.4;biotype=protein_coding;Parent=gene:AT1G01370;transcript_id=AT1G01370.4; -1 araport11 exon 143522 143676 . + . Name=AT1G01370.4.exon1;Parent=transcript:AT1G01370.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01370.4.exon1;rank=1; -1 araport11 five_prime_UTR 143522 143676 . + . Parent=transcript:AT1G01370.4; -1 araport11 five_prime_UTR 143761 143772 . + . Parent=transcript:AT1G01370.4; -1 araport11 exon 143761 143824 . + . Name=AT1G01370.4.exon2;Parent=transcript:AT1G01370.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01370.4.exon2;rank=2; -1 araport11 CDS 143773 143824 . + 0 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 exon 143934 143977 . + . Name=AT1G01370.3.exon3;Parent=transcript:AT1G01370.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon3;rank=3; -1 araport11 CDS 143934 143977 . + 2 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 exon 144064 144109 . + . Name=AT1G01370.3.exon4;Parent=transcript:AT1G01370.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon4;rank=4; -1 araport11 CDS 144064 144109 . + 0 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 exon 144193 144227 . + . Name=AT1G01370.3.exon5;Parent=transcript:AT1G01370.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon5;rank=5; -1 araport11 CDS 144193 144227 . + 2 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 exon 144315 144351 . + . Name=AT1G01370.3.exon6;Parent=transcript:AT1G01370.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon6;rank=6; -1 araport11 CDS 144315 144351 . + 0 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 exon 144447 144559 . + . Name=AT1G01370.3.exon7;Parent=transcript:AT1G01370.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01370.3.exon7;rank=7; -1 araport11 CDS 144447 144559 . + 2 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 exon 144927 145004 . + . Name=AT1G01370.3.exon8;Parent=transcript:AT1G01370.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01370.3.exon8;rank=8; -1 araport11 CDS 144927 145004 . + 0 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 exon 145132 145207 . + . Name=AT1G01370.3.exon9;Parent=transcript:AT1G01370.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01370.3.exon9;rank=9; -1 araport11 CDS 145132 145207 . + 0 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 CDS 145345 145400 . + 2 ID=CDS:AT1G01370.4;Parent=transcript:AT1G01370.4;protein_id=AT1G01370.4 -1 araport11 exon 145345 145676 . + . Name=AT1G01370.4.exon10;Parent=transcript:AT1G01370.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01370.4.exon10;rank=10; -1 araport11 three_prime_UTR 145401 145676 . + . Parent=transcript:AT1G01370.4; -1 araport11 gene 147043 148014 . + . ID=gene:AT1G01380;Name=ETC1;biotype=protein_coding;description=MYB-like transcription factor ETC1 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LNI5];gene_id=AT1G01380;logic_name=araport11; -1 araport11 mRNA 147043 148014 . + . ID=transcript:AT1G01380.2;biotype=protein_coding;Parent=gene:AT1G01380;transcript_id=AT1G01380.2; -1 araport11 five_prime_UTR 147043 147266 . + . Parent=transcript:AT1G01380.2; -1 araport11 exon 147043 147333 . + . Name=AT1G01380.2.exon1;Parent=transcript:AT1G01380.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01380.2.exon1;rank=1; -1 araport11 CDS 147267 147333 . + 0 ID=CDS:AT1G01380.2;Parent=transcript:AT1G01380.2;protein_id=AT1G01380.2 -1 araport11 CDS 147452 147567 . + 2 ID=CDS:AT1G01380.2;Parent=transcript:AT1G01380.2;protein_id=AT1G01380.2 -1 araport11 exon 147452 148014 . + . Name=AT1G01380.2.exon2;Parent=transcript:AT1G01380.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01380.2.exon2;rank=2; -1 araport11 three_prime_UTR 147568 148014 . + . Parent=transcript:AT1G01380.2; -1 araport11 mRNA 147043 148014 . + . ID=transcript:AT1G01380.1;biotype=protein_coding;Parent=gene:AT1G01380;transcript_id=AT1G01380.1; -1 araport11 five_prime_UTR 147043 147266 . + . Parent=transcript:AT1G01380.1; -1 araport11 exon 147043 147333 . + . Name=AT1G01380.2.exon1;Parent=transcript:AT1G01380.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01380.2.exon1;rank=1; -1 araport11 CDS 147267 147333 . + 0 ID=CDS:AT1G01380.1;Parent=transcript:AT1G01380.1;protein_id=AT1G01380.1 -1 araport11 exon 147452 147539 . + . Name=AT1G01380.1.exon2;Parent=transcript:AT1G01380.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01380.1.exon2;rank=2; -1 araport11 CDS 147452 147539 . + 2 ID=CDS:AT1G01380.1;Parent=transcript:AT1G01380.1;protein_id=AT1G01380.1 -1 araport11 CDS 147644 147740 . + 1 ID=CDS:AT1G01380.1;Parent=transcript:AT1G01380.1;protein_id=AT1G01380.1 -1 araport11 exon 147644 148014 . + . Name=AT1G01380.1.exon3;Parent=transcript:AT1G01380.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01380.1.exon3;rank=3; -1 araport11 three_prime_UTR 147741 148014 . + . Parent=transcript:AT1G01380.1; -1 araport11 mRNA 147153 147942 . + . ID=transcript:AT1G01380.3;biotype=protein_coding;Parent=gene:AT1G01380;transcript_id=AT1G01380.3; -1 araport11 five_prime_UTR 147153 147266 . + . Parent=transcript:AT1G01380.3; -1 araport11 exon 147153 147333 . + . Name=AT1G01380.3.exon1;Parent=transcript:AT1G01380.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01380.3.exon1;rank=1; -1 araport11 CDS 147267 147333 . + 0 ID=CDS:AT1G01380.3;Parent=transcript:AT1G01380.3;protein_id=AT1G01380.3 -1 araport11 exon 147452 147528 . + . Name=AT1G01380.3.exon2;Parent=transcript:AT1G01380.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01380.3.exon2;rank=2; -1 araport11 CDS 147452 147528 . + 2 ID=CDS:AT1G01380.3;Parent=transcript:AT1G01380.3;protein_id=AT1G01380.3 -1 araport11 CDS 147644 147694 . + 0 ID=CDS:AT1G01380.3;Parent=transcript:AT1G01380.3;protein_id=AT1G01380.3 -1 araport11 exon 147644 147942 . + . Name=AT1G01380.3.exon3;Parent=transcript:AT1G01380.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01380.3.exon3;rank=3; -1 araport11 three_prime_UTR 147695 147942 . + . Parent=transcript:AT1G01380.3; -1 araport11 gene 148013 149848 . - . ID=gene:AT1G01390;biotype=protein_coding;description=UDP-Glycosyltransferase superfamily protein [Source:TAIR%3bAcc:AT1G01390];gene_id=AT1G01390;logic_name=araport11; -1 araport11 mRNA 148013 149848 . - . ID=transcript:AT1G01390.2;biotype=protein_coding;Parent=gene:AT1G01390;transcript_id=AT1G01390.2; -1 araport11 three_prime_UTR 148013 148318 . - . Parent=transcript:AT1G01390.2; -1 araport11 exon 148013 149848 . - . Name=AT1G01390.2.exon1;Parent=transcript:AT1G01390.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01390.2.exon1;rank=1; -1 araport11 CDS 148319 149812 . - 0 ID=CDS:AT1G01390.2;Parent=transcript:AT1G01390.2;protein_id=AT1G01390.2 -1 araport11 five_prime_UTR 149813 149848 . - . Parent=transcript:AT1G01390.2; -1 araport11 mRNA 148018 149806 . - . ID=transcript:AT1G01390.1;biotype=protein_coding;Parent=gene:AT1G01390;transcript_id=AT1G01390.1; -1 araport11 three_prime_UTR 148018 148318 . - . Parent=transcript:AT1G01390.1; -1 araport11 exon 148018 149806 . - . Name=AT1G01390.1.exon1;Parent=transcript:AT1G01390.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01390.1.exon1;rank=1; -1 araport11 CDS 148319 149761 . - 0 ID=CDS:AT1G01390.1;Parent=transcript:AT1G01390.1;protein_id=AT1G01390.1 -1 araport11 five_prime_UTR 149762 149806 . - . Parent=transcript:AT1G01390.1; -1 araport11 gene 150689 152210 . - . ID=gene:AT1G01400;biotype=protein_coding;description=F6F3.20 protein [Source:UniProtKB/TrEMBL%3bAcc:Q9LNI3];gene_id=AT1G01400;logic_name=araport11; -1 araport11 mRNA 150689 152210 . - . ID=transcript:AT1G01400.1;biotype=protein_coding;Parent=gene:AT1G01400;transcript_id=AT1G01400.1; -1 araport11 three_prime_UTR 150689 151157 . - . Parent=transcript:AT1G01400.1; -1 araport11 exon 150689 151298 . - . Name=AT1G01400.1.exon4;Parent=transcript:AT1G01400.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01400.1.exon4;rank=4; -1 araport11 CDS 151158 151298 . - 0 ID=CDS:AT1G01400.1;Parent=transcript:AT1G01400.1;protein_id=AT1G01400.1 -1 araport11 exon 151393 151731 . - . Name=AT1G01400.1.exon3;Parent=transcript:AT1G01400.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01400.1.exon3;rank=3; -1 araport11 CDS 151393 151731 . - 0 ID=CDS:AT1G01400.1;Parent=transcript:AT1G01400.1;protein_id=AT1G01400.1 -1 araport11 exon 151932 152002 . - . Name=AT1G01400.1.exon2;Parent=transcript:AT1G01400.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01400.1.exon2;rank=2; -1 araport11 CDS 151932 152002 . - 2 ID=CDS:AT1G01400.1;Parent=transcript:AT1G01400.1;protein_id=AT1G01400.1 -1 araport11 CDS 152086 152149 . - 0 ID=CDS:AT1G01400.1;Parent=transcript:AT1G01400.1;protein_id=AT1G01400.1 -1 araport11 exon 152086 152210 . - . Name=AT1G01400.1.exon1;Parent=transcript:AT1G01400.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01400.1.exon1;rank=1; -1 araport11 five_prime_UTR 152150 152210 . - . Parent=transcript:AT1G01400.1; -1 araport11 gene 153113 154198 . + . ID=gene:AT1G01410;Name=APUM22;biotype=protein_coding;description=Putative pumilio homolog 22 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LNI2];gene_id=AT1G01410;logic_name=araport11; -1 araport11 mRNA 153113 154198 . + . ID=transcript:AT1G01410.1;biotype=protein_coding;Parent=gene:AT1G01410;transcript_id=AT1G01410.1; -1 araport11 exon 153113 154198 . + . Name=AT1G01410.1.exon1;Parent=transcript:AT1G01410.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01410.1.exon1;rank=1; -1 araport11 CDS 153113 154198 . + 0 ID=CDS:AT1G01410.1;Parent=transcript:AT1G01410.1;protein_id=AT1G01410.1 -1 araport11 gene 154367 156178 . - . ID=gene:AT1G01420;Name=UGT72B3;biotype=protein_coding;description=UDP-glucosyl transferase 72B3 [Source:TAIR%3bAcc:AT1G01420];gene_id=AT1G01420;logic_name=araport11; -1 araport11 mRNA 154367 156178 . - . ID=transcript:AT1G01420.2;biotype=protein_coding;Parent=gene:AT1G01420;transcript_id=AT1G01420.2; -1 araport11 three_prime_UTR 154367 154565 . - . Parent=transcript:AT1G01420.2; -1 araport11 exon 154367 156178 . - . Name=AT1G01420.2.exon1;Parent=transcript:AT1G01420.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01420.2.exon1;rank=1; -1 araport11 CDS 154566 156020 . - 0 ID=CDS:AT1G01420.2;Parent=transcript:AT1G01420.2;protein_id=AT1G01420.2 -1 araport11 five_prime_UTR 156021 156178 . - . Parent=transcript:AT1G01420.2; -1 araport11 mRNA 154492 156011 . - . ID=transcript:AT1G01420.1;biotype=protein_coding;Parent=gene:AT1G01420;transcript_id=AT1G01420.1; -1 araport11 three_prime_UTR 154492 154565 . - . Parent=transcript:AT1G01420.1; -1 araport11 exon 154492 156011 . - . Name=AT1G01420.1.exon1;Parent=transcript:AT1G01420.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01420.1.exon1;rank=1; -1 araport11 CDS 154566 156011 . - 0 ID=CDS:AT1G01420.1;Parent=transcript:AT1G01420.1;protein_id=AT1G01420.1 -1 araport11 gene 156477 158823 . - . ID=gene:AT1G01430;Name=TBL25;biotype=protein_coding;description=Mannan O-acetyltransferase 3 [Source:UniProtKB/TrEMBL%3bAcc:A0A346P850];gene_id=AT1G01430;logic_name=araport11; -1 araport11 mRNA 156477 158823 . - . ID=transcript:AT1G01430.1;biotype=protein_coding;Parent=gene:AT1G01430;transcript_id=AT1G01430.1; -1 araport11 three_prime_UTR 156477 156952 . - . Parent=transcript:AT1G01430.1; -1 araport11 exon 156477 157756 . - . Name=AT1G01430.1.exon3;Parent=transcript:AT1G01430.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01430.1.exon3;rank=3; -1 araport11 CDS 156953 157756 . - 0 ID=CDS:AT1G01430.1;Parent=transcript:AT1G01430.1;protein_id=AT1G01430.1 -1 araport11 exon 157829 158112 . - . Name=AT1G01430.1.exon2;Parent=transcript:AT1G01430.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01430.1.exon2;rank=2; -1 araport11 CDS 157829 158112 . - 2 ID=CDS:AT1G01430.1;Parent=transcript:AT1G01430.1;protein_id=AT1G01430.1 -1 araport11 CDS 158254 158536 . - 0 ID=CDS:AT1G01430.1;Parent=transcript:AT1G01430.1;protein_id=AT1G01430.1 -1 araport11 exon 158254 158823 . - . Name=AT1G01430.1.exon1;Parent=transcript:AT1G01430.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01430.1.exon1;rank=1; -1 araport11 five_prime_UTR 158537 158823 . - . Parent=transcript:AT1G01430.1; -1 araport11 gene 159628 162953 . - . ID=gene:AT1G01440;biotype=protein_coding;description=At1g01440 [Source:UniProtKB/TrEMBL%3bAcc:Q6NQ63];gene_id=AT1G01440;logic_name=araport11; -1 araport11 mRNA 159628 162953 . - . ID=transcript:AT1G01440.1;biotype=protein_coding;Parent=gene:AT1G01440;transcript_id=AT1G01440.1; -1 araport11 three_prime_UTR 159628 159934 . - . Parent=transcript:AT1G01440.1; -1 araport11 exon 159628 159992 . - . Name=AT1G01440.1.exon5;Parent=transcript:AT1G01440.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01440.1.exon5;rank=5; -1 araport11 CDS 159935 159992 . - 1 ID=CDS:AT1G01440.1;Parent=transcript:AT1G01440.1;protein_id=AT1G01440.1 -1 araport11 exon 160079 160302 . - . Name=AT1G01440.1.exon4;Parent=transcript:AT1G01440.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01440.1.exon4;rank=4; -1 araport11 CDS 160079 160302 . - 0 ID=CDS:AT1G01440.1;Parent=transcript:AT1G01440.1;protein_id=AT1G01440.1 -1 araport11 exon 160418 160478 . - . Name=AT1G01440.1.exon3;Parent=transcript:AT1G01440.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01440.1.exon3;rank=3; -1 araport11 CDS 160418 160478 . - 1 ID=CDS:AT1G01440.1;Parent=transcript:AT1G01440.1;protein_id=AT1G01440.1 -1 araport11 CDS 160568 162219 . - 0 ID=CDS:AT1G01440.1;Parent=transcript:AT1G01440.1;protein_id=AT1G01440.1 -1 araport11 exon 160568 162280 . - . Name=AT1G01440.1.exon2;Parent=transcript:AT1G01440.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01440.1.exon2;rank=2; -1 araport11 five_prime_UTR 162220 162280 . - . Parent=transcript:AT1G01440.1; -1 araport11 exon 162487 162953 . - . Name=AT1G01440.1.exon1;Parent=transcript:AT1G01440.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01440.1.exon1;rank=1; -1 araport11 five_prime_UTR 162487 162953 . - . Parent=transcript:AT1G01440.1; -1 araport11 ncRNA_gene 163278 166353 . + . ID=gene:AT1G01448;biotype=lncRNA;description=other RNA [Source:TAIR%3bAcc:AT1G01448];gene_id=AT1G01448;logic_name=araport11; -1 araport11 lnc_RNA 163278 166353 . + . ID=transcript:AT1G01448.1;biotype=lncRNA;Parent=gene:AT1G01448;transcript_id=AT1G01448.1; -1 araport11 exon 163278 163516 . + . Name=AT1G01448.1.exon1;Parent=transcript:AT1G01448.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon1;rank=1; -1 araport11 exon 163934 164103 . + . Name=AT1G01448.1.exon2;Parent=transcript:AT1G01448.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon2;rank=2; -1 araport11 exon 164225 164686 . + . Name=AT1G01448.1.exon3;Parent=transcript:AT1G01448.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon3;rank=3; -1 araport11 exon 164771 165380 . + . Name=AT1G01448.1.exon4;Parent=transcript:AT1G01448.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon4;rank=4; -1 araport11 exon 165449 166353 . + . Name=AT1G01448.1.exon5;Parent=transcript:AT1G01448.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon5;rank=5; -1 araport11 lnc_RNA 163278 166353 . + . ID=transcript:AT1G01448.2;biotype=lncRNA;Parent=gene:AT1G01448;transcript_id=AT1G01448.2; -1 araport11 exon 163278 163516 . + . Name=AT1G01448.1.exon1;Parent=transcript:AT1G01448.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon1;rank=1; -1 araport11 exon 163934 164103 . + . Name=AT1G01448.1.exon2;Parent=transcript:AT1G01448.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon2;rank=2; -1 araport11 exon 164225 164686 . + . Name=AT1G01448.1.exon3;Parent=transcript:AT1G01448.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon3;rank=3; -1 araport11 exon 164771 165380 . + . Name=AT1G01448.1.exon4;Parent=transcript:AT1G01448.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon4;rank=4; -1 araport11 exon 165449 165656 . + . Name=AT1G01448.2.exon5;Parent=transcript:AT1G01448.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.2.exon5;rank=5; -1 araport11 exon 165769 166353 . + . Name=AT1G01448.2.exon6;Parent=transcript:AT1G01448.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.2.exon6;rank=6; -1 araport11 lnc_RNA 163302 166307 . + . ID=transcript:AT1G01448.3;biotype=lncRNA;Parent=gene:AT1G01448;transcript_id=AT1G01448.3; -1 araport11 exon 163302 163516 . + . Name=AT1G01448.3.exon1;Parent=transcript:AT1G01448.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.3.exon1;rank=1; -1 araport11 exon 163934 164103 . + . Name=AT1G01448.1.exon2;Parent=transcript:AT1G01448.3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon2;rank=2; -1 araport11 exon 164225 164686 . + . Name=AT1G01448.1.exon3;Parent=transcript:AT1G01448.3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon3;rank=3; -1 araport11 exon 164771 165380 . + . Name=AT1G01448.1.exon4;Parent=transcript:AT1G01448.3;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.1.exon4;rank=4; -1 araport11 exon 165449 165656 . + . Name=AT1G01448.2.exon5;Parent=transcript:AT1G01448.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.2.exon5;rank=5; -1 araport11 exon 165983 166307 . + . Name=AT1G01448.3.exon6;Parent=transcript:AT1G01448.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01448.3.exon6;rank=6; -1 araport11 gene 164105 165517 . - . ID=gene:AT1G01450;biotype=protein_coding;description=Protein kinase superfamily protein [Source:UniProtKB/TrEMBL%3bAcc:F4HSB4];gene_id=AT1G01450;logic_name=araport11; -1 araport11 mRNA 164105 165517 . - . ID=transcript:AT1G01450.1;biotype=protein_coding;Parent=gene:AT1G01450;transcript_id=AT1G01450.1; -1 araport11 exon 164105 165517 . - . Name=AT1G01450.1.exon1;Parent=transcript:AT1G01450.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01450.1.exon1;rank=1; -1 araport11 CDS 164105 165517 . - 0 ID=CDS:AT1G01450.1;Parent=transcript:AT1G01450.1;protein_id=AT1G01450.1 -1 araport11 gene 166589 168088 . - . ID=gene:AT1G01453;biotype=protein_coding;description=unknown protein%3b FUNCTIONS IN: molecular_function unknown%3b INVOLVED IN: biological_process unknown%3b LOCATED IN: cellular_component unknown%3b BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT4G01110.1)%3b Has 30201 Blast hits to 17322 /.../ins in 780 species: Archae - 12%3b Bacteria - 1396%3b Metazoa - 17338%3b Fungi - 3422%3b Plants - 5037%3b Viruses - 0%3b Other Eukaryotes - 2996 (source: NCBI BLink). [Source:TAIR%3bAcc:AT1G01453];gene_id=AT1G01453;logic_name=araport11; -1 araport11 mRNA 166589 168088 . - . ID=transcript:AT1G01453.1;biotype=protein_coding;Parent=gene:AT1G01453;transcript_id=AT1G01453.1; -1 araport11 three_prime_UTR 166589 166852 . - . Parent=transcript:AT1G01453.1; -1 araport11 exon 166589 166871 . - . Name=AT1G01453.1.exon2;Parent=transcript:AT1G01453.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01453.1.exon2;rank=2; -1 araport11 CDS 166853 166871 . - 1 ID=CDS:AT1G01453.1;Parent=transcript:AT1G01453.1;protein_id=AT1G01453.1 -1 araport11 CDS 167014 167798 . - 0 ID=CDS:AT1G01453.1;Parent=transcript:AT1G01453.1;protein_id=AT1G01453.1 -1 araport11 exon 167014 168088 . - . Name=AT1G01453.1.exon1;Parent=transcript:AT1G01453.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01453.1.exon1;rank=1; -1 araport11 five_prime_UTR 167799 168088 . - . Parent=transcript:AT1G01453.1; -1 araport11 mRNA 166618 167842 . - . ID=transcript:AT1G01453.2;biotype=protein_coding;Parent=gene:AT1G01453;transcript_id=AT1G01453.2; -1 araport11 three_prime_UTR 166618 166928 . - . Parent=transcript:AT1G01453.2; -1 araport11 exon 166618 167842 . - . Name=AT1G01453.2.exon1;Parent=transcript:AT1G01453.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01453.2.exon1;rank=1; -1 araport11 CDS 166929 167798 . - 0 ID=CDS:AT1G01453.2;Parent=transcript:AT1G01453.2;protein_id=AT1G01453.2 -1 araport11 five_prime_UTR 167799 167842 . - . Parent=transcript:AT1G01453.2; -1 araport11 gene 168559 171386 . + . ID=gene:AT1G01460;Name=PIP5K10;biotype=protein_coding;description=Phosphatidylinositol 4-phosphate 5-kinase 10 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LMN1];gene_id=AT1G01460;logic_name=araport11; -1 araport11 mRNA 168559 171386 . + . ID=transcript:AT1G01460.1;biotype=protein_coding;Parent=gene:AT1G01460;transcript_id=AT1G01460.1; -1 araport11 exon 168559 168801 . + . Name=AT1G01460.1.exon1;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01460.1.exon1;rank=1; -1 araport11 five_prime_UTR 168559 168801 . + . Parent=transcript:AT1G01460.1; -1 araport11 five_prime_UTR 169037 169114 . + . Parent=transcript:AT1G01460.1; -1 araport11 exon 169037 169257 . + . Name=AT1G01460.1.exon2;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01460.1.exon2;rank=2; -1 araport11 CDS 169115 169257 . + 0 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 exon 169347 169509 . + . Name=AT1G01460.1.exon3;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01460.1.exon3;rank=3; -1 araport11 CDS 169347 169509 . + 1 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 exon 169600 169710 . + . Name=AT1G01460.1.exon4;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01460.1.exon4;rank=4; -1 araport11 CDS 169600 169710 . + 0 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 exon 169806 169993 . + . Name=AT1G01460.1.exon5;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01460.1.exon5;rank=5; -1 araport11 CDS 169806 169993 . + 0 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 exon 170071 170162 . + . Name=AT1G01460.1.exon6;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01460.1.exon6;rank=6; -1 araport11 CDS 170071 170162 . + 1 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 exon 170266 170313 . + . Name=AT1G01460.1.exon7;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01460.1.exon7;rank=7; -1 araport11 CDS 170266 170313 . + 2 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 exon 170412 170507 . + . Name=AT1G01460.1.exon8;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01460.1.exon8;rank=8; -1 araport11 CDS 170412 170507 . + 2 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 exon 170622 170760 . + . Name=AT1G01460.1.exon9;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01460.1.exon9;rank=9; -1 araport11 CDS 170622 170760 . + 2 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 CDS 170851 171154 . + 1 ID=CDS:AT1G01460.1;Parent=transcript:AT1G01460.1;protein_id=AT1G01460.1 -1 araport11 exon 170851 171386 . + . Name=AT1G01460.1.exon10;Parent=transcript:AT1G01460.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01460.1.exon10;rank=10; -1 araport11 three_prime_UTR 171155 171386 . + . Parent=transcript:AT1G01460.1; -1 araport11 gene 171525 172948 . - . ID=gene:AT1G01470;Name=LEA14;biotype=protein_coding;description=LSR3 [Source:UniProtKB/TrEMBL%3bAcc:A0A178W160];gene_id=AT1G01470;logic_name=araport11; -1 araport11 mRNA 171525 172948 . - . ID=transcript:AT1G01470.1;biotype=protein_coding;Parent=gene:AT1G01470;transcript_id=AT1G01470.1; -1 araport11 three_prime_UTR 171525 172294 . - . Parent=transcript:AT1G01470.1; -1 araport11 exon 171525 172544 . - . Name=AT1G01470.1.exon2;Parent=transcript:AT1G01470.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01470.1.exon2;rank=2; -1 araport11 CDS 172295 172544 . - 1 ID=CDS:AT1G01470.1;Parent=transcript:AT1G01470.1;protein_id=AT1G01470.1 -1 araport11 CDS 172621 172826 . - 0 ID=CDS:AT1G01470.1;Parent=transcript:AT1G01470.1;protein_id=AT1G01470.1 -1 araport11 exon 172621 172948 . - . Name=AT1G01470.1.exon1;Parent=transcript:AT1G01470.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01470.1.exon1;rank=1; -1 araport11 five_prime_UTR 172827 172948 . - . Parent=transcript:AT1G01470.1; -1 araport11 gene 175706 178406 . + . ID=gene:AT1G01480;Name=ACS2;biotype=protein_coding;description=1-aminocyclopropane-1-carboxylate synthase 2 [Source:UniProtKB/Swiss-Prot%3bAcc:Q06402];gene_id=AT1G01480;logic_name=araport11; -1 araport11 mRNA 175706 178406 . + . ID=transcript:AT1G01480.1;biotype=protein_coding;Parent=gene:AT1G01480;transcript_id=AT1G01480.1; -1 araport11 five_prime_UTR 175706 175861 . + . Parent=transcript:AT1G01480.1; -1 araport11 exon 175706 176032 . + . Name=AT1G01480.1.exon1;Parent=transcript:AT1G01480.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01480.1.exon1;rank=1; -1 araport11 CDS 175862 176032 . + 0 ID=CDS:AT1G01480.1;Parent=transcript:AT1G01480.1;protein_id=AT1G01480.1 -1 araport11 exon 176207 176338 . + . Name=AT1G01480.1.exon2;Parent=transcript:AT1G01480.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01480.1.exon2;rank=2; -1 araport11 CDS 176207 176338 . + 0 ID=CDS:AT1G01480.1;Parent=transcript:AT1G01480.1;protein_id=AT1G01480.1 -1 araport11 exon 176592 176752 . + . Name=AT1G01480.1.exon3;Parent=transcript:AT1G01480.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01480.1.exon3;rank=3; -1 araport11 CDS 176592 176752 . + 0 ID=CDS:AT1G01480.1;Parent=transcript:AT1G01480.1;protein_id=AT1G01480.1 -1 araport11 CDS 177025 178051 . + 1 ID=CDS:AT1G01480.1;Parent=transcript:AT1G01480.1;protein_id=AT1G01480.1 -1 araport11 exon 177025 178406 . + . Name=AT1G01480.1.exon4;Parent=transcript:AT1G01480.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01480.1.exon4;rank=4; -1 araport11 three_prime_UTR 178052 178406 . + . Parent=transcript:AT1G01480.1; -1 araport11 mRNA 176141 178400 . + . ID=transcript:AT1G01480.2;biotype=protein_coding;Parent=gene:AT1G01480;transcript_id=AT1G01480.2; -1 araport11 exon 176141 176338 . + . Name=AT1G01480.2.exon1;Parent=transcript:AT1G01480.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01480.2.exon1;rank=1; -1 araport11 five_prime_UTR 176141 176338 . + . Parent=transcript:AT1G01480.2; -1 araport11 five_prime_UTR 176592 176606 . + . Parent=transcript:AT1G01480.2; -1 araport11 exon 176592 176752 . + . Name=AT1G01480.2.exon2;Parent=transcript:AT1G01480.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01480.2.exon2;rank=2; -1 araport11 CDS 176607 176752 . + 0 ID=CDS:AT1G01480.2;Parent=transcript:AT1G01480.2;protein_id=AT1G01480.2 -1 araport11 CDS 177025 178051 . + 1 ID=CDS:AT1G01480.2;Parent=transcript:AT1G01480.2;protein_id=AT1G01480.2 -1 araport11 exon 177025 178400 . + . Name=AT1G01480.2.exon3;Parent=transcript:AT1G01480.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01480.2.exon3;rank=3; -1 araport11 three_prime_UTR 178052 178400 . + . Parent=transcript:AT1G01480.2; -1 araport11 gene 180017 182749 . - . ID=gene:AT1G01490;biotype=protein_coding;description=Heavy metal transport/detoxification superfamily protein [Source:TAIR%3bAcc:AT1G01490];gene_id=AT1G01490;logic_name=araport11; -1 araport11 mRNA 180017 182534 . - . ID=transcript:AT1G01490.3;biotype=protein_coding;Parent=gene:AT1G01490;transcript_id=AT1G01490.3; -1 araport11 three_prime_UTR 180017 180400 . - . Parent=transcript:AT1G01490.3; -1 araport11 exon 180017 180852 . - . Name=AT1G01490.3.exon3;Parent=transcript:AT1G01490.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01490.3.exon3;rank=3; -1 araport11 CDS 180401 180835 . - 0 ID=CDS:AT1G01490.3;Parent=transcript:AT1G01490.3;protein_id=AT1G01490.3 -1 araport11 five_prime_UTR 180836 180852 . - . Parent=transcript:AT1G01490.3; -1 araport11 exon 181347 182135 . - . Name=AT1G01490.3.exon2;Parent=transcript:AT1G01490.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01490.3.exon2;rank=2; -1 araport11 five_prime_UTR 181347 182135 . - . Parent=transcript:AT1G01490.3; -1 araport11 exon 182253 182534 . - . Name=AT1G01490.3.exon1;Parent=transcript:AT1G01490.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01490.3.exon1;rank=1; -1 araport11 five_prime_UTR 182253 182534 . - . Parent=transcript:AT1G01490.3; -1 araport11 mRNA 180018 182497 . - . ID=transcript:AT1G01490.4;biotype=protein_coding;Parent=gene:AT1G01490;transcript_id=AT1G01490.4; -1 araport11 three_prime_UTR 180018 180400 . - . Parent=transcript:AT1G01490.4; -1 araport11 exon 180018 180852 . - . Name=AT1G01490.4.exon4;Parent=transcript:AT1G01490.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01490.4.exon4;rank=4; -1 araport11 CDS 180401 180852 . - 2 ID=CDS:AT1G01490.4;Parent=transcript:AT1G01490.4;protein_id=AT1G01490.4 -1 araport11 exon 181347 181422 . - . Name=AT1G01490.2.exon3;Parent=transcript:AT1G01490.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01490.2.exon3;rank=3; -1 araport11 CDS 181347 181422 . - 0 ID=CDS:AT1G01490.4;Parent=transcript:AT1G01490.4;protein_id=AT1G01490.4 -1 araport11 CDS 181594 181680 . - 0 ID=CDS:AT1G01490.4;Parent=transcript:AT1G01490.4;protein_id=AT1G01490.4 -1 araport11 exon 181594 182135 . - . Name=AT1G01490.4.exon2;Parent=transcript:AT1G01490.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01490.4.exon2;rank=2; -1 araport11 five_prime_UTR 181681 182135 . - . Parent=transcript:AT1G01490.4; -1 araport11 exon 182253 182497 . - . Name=AT1G01490.4.exon1;Parent=transcript:AT1G01490.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01490.4.exon1;rank=1; -1 araport11 five_prime_UTR 182253 182497 . - . Parent=transcript:AT1G01490.4; -1 araport11 mRNA 180056 182749 . - . ID=transcript:AT1G01490.1;biotype=protein_coding;Parent=gene:AT1G01490;transcript_id=AT1G01490.1; -1 araport11 three_prime_UTR 180056 180400 . - . Parent=transcript:AT1G01490.1; -1 araport11 exon 180056 180852 . - . Name=AT1G01490.2.exon4;Parent=transcript:AT1G01490.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01490.2.exon4;rank=3; -1 araport11 CDS 180401 180852 . - 2 ID=CDS:AT1G01490.1;Parent=transcript:AT1G01490.1;protein_id=AT1G01490.1 -1 araport11 exon 181347 181422 . - . Name=AT1G01490.2.exon3;Parent=transcript:AT1G01490.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01490.2.exon3;rank=2; -1 araport11 CDS 181347 181422 . - 0 ID=CDS:AT1G01490.1;Parent=transcript:AT1G01490.1;protein_id=AT1G01490.1 -1 araport11 CDS 182061 182066 . - 0 ID=CDS:AT1G01490.1;Parent=transcript:AT1G01490.1;protein_id=AT1G01490.1 -1 araport11 exon 182061 182749 . - . Name=AT1G01490.1.exon1;Parent=transcript:AT1G01490.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01490.1.exon1;rank=1; -1 araport11 five_prime_UTR 182067 182749 . - . Parent=transcript:AT1G01490.1; -1 araport11 mRNA 180056 182749 . - . ID=transcript:AT1G01490.2;biotype=protein_coding;Parent=gene:AT1G01490;transcript_id=AT1G01490.2; -1 araport11 three_prime_UTR 180056 180400 . - . Parent=transcript:AT1G01490.2; -1 araport11 exon 180056 180852 . - . Name=AT1G01490.2.exon4;Parent=transcript:AT1G01490.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01490.2.exon4;rank=4; -1 araport11 CDS 180401 180852 . - 2 ID=CDS:AT1G01490.2;Parent=transcript:AT1G01490.2;protein_id=AT1G01490.2 -1 araport11 exon 181347 181422 . - . Name=AT1G01490.2.exon3;Parent=transcript:AT1G01490.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01490.2.exon3;rank=3; -1 araport11 CDS 181347 181422 . - 0 ID=CDS:AT1G01490.2;Parent=transcript:AT1G01490.2;protein_id=AT1G01490.2 -1 araport11 CDS 182061 182066 . - 0 ID=CDS:AT1G01490.2;Parent=transcript:AT1G01490.2;protein_id=AT1G01490.2 -1 araport11 exon 182061 182135 . - . Name=AT1G01490.2.exon2;Parent=transcript:AT1G01490.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01490.2.exon2;rank=2; -1 araport11 five_prime_UTR 182067 182135 . - . Parent=transcript:AT1G01490.2; -1 araport11 exon 182253 182749 . - . Name=AT1G01490.2.exon1;Parent=transcript:AT1G01490.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01490.2.exon1;rank=1; -1 araport11 five_prime_UTR 182253 182749 . - . Parent=transcript:AT1G01490.2; -1 araport11 gene 185033 187135 . + . ID=gene:AT1G01500;biotype=protein_coding;description=Uncharacterized protein At1g01500 [Source:UniProtKB/Swiss-Prot%3bAcc:Q8GUH2];gene_id=AT1G01500;logic_name=araport11; -1 araport11 mRNA 185033 187135 . + . ID=transcript:AT1G01500.1;biotype=protein_coding;Parent=gene:AT1G01500;transcript_id=AT1G01500.1; -1 araport11 five_prime_UTR 185033 185259 . + . Parent=transcript:AT1G01500.1; -1 araport11 exon 185033 186009 . + . Name=AT1G01500.1.exon1;Parent=transcript:AT1G01500.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01500.1.exon1;rank=1; -1 araport11 CDS 185260 186009 . + 0 ID=CDS:AT1G01500.1;Parent=transcript:AT1G01500.1;protein_id=AT1G01500.1 -1 araport11 CDS 186340 186573 . + 0 ID=CDS:AT1G01500.1;Parent=transcript:AT1G01500.1;protein_id=AT1G01500.1 -1 araport11 exon 186340 187135 . + . Name=AT1G01500.1.exon2;Parent=transcript:AT1G01500.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01500.1.exon2;rank=2; -1 araport11 three_prime_UTR 186574 187135 . + . Parent=transcript:AT1G01500.1; -1 araport11 gene 187145 190472 . + . ID=gene:AT1G01510;Name=AN;biotype=protein_coding;description=C-terminal binding protein AN [Source:UniProtKB/Swiss-Prot%3bAcc:O23702];gene_id=AT1G01510;logic_name=araport11; -1 araport11 mRNA 187145 190472 . + . ID=transcript:AT1G01510.1;biotype=protein_coding;Parent=gene:AT1G01510;transcript_id=AT1G01510.1; -1 araport11 five_prime_UTR 187145 187234 . + . Parent=transcript:AT1G01510.1; -1 araport11 exon 187145 187822 . + . Name=AT1G01510.1.exon1;Parent=transcript:AT1G01510.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01510.1.exon1;rank=1; -1 araport11 CDS 187235 187822 . + 0 ID=CDS:AT1G01510.1;Parent=transcript:AT1G01510.1;protein_id=AT1G01510.1 -1 araport11 exon 188011 188176 . + . Name=AT1G01510.1.exon2;Parent=transcript:AT1G01510.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01510.1.exon2;rank=2; -1 araport11 CDS 188011 188176 . + 0 ID=CDS:AT1G01510.1;Parent=transcript:AT1G01510.1;protein_id=AT1G01510.1 -1 araport11 exon 188284 188414 . + . Name=AT1G01510.1.exon3;Parent=transcript:AT1G01510.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01510.1.exon3;rank=3; -1 araport11 CDS 188284 188414 . + 2 ID=CDS:AT1G01510.1;Parent=transcript:AT1G01510.1;protein_id=AT1G01510.1 -1 araport11 exon 188529 189320 . + . Name=AT1G01510.1.exon4;Parent=transcript:AT1G01510.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01510.1.exon4;rank=4; -1 araport11 CDS 188529 189320 . + 0 ID=CDS:AT1G01510.1;Parent=transcript:AT1G01510.1;protein_id=AT1G01510.1 -1 araport11 exon 189417 189464 . + . Name=AT1G01510.1.exon5;Parent=transcript:AT1G01510.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01510.1.exon5;rank=5; -1 araport11 CDS 189417 189464 . + 0 ID=CDS:AT1G01510.1;Parent=transcript:AT1G01510.1;protein_id=AT1G01510.1 -1 araport11 exon 189562 189675 . + . Name=AT1G01510.1.exon6;Parent=transcript:AT1G01510.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01510.1.exon6;rank=6; -1 araport11 CDS 189562 189675 . + 0 ID=CDS:AT1G01510.1;Parent=transcript:AT1G01510.1;protein_id=AT1G01510.1 -1 araport11 CDS 189765 189836 . + 0 ID=CDS:AT1G01510.1;Parent=transcript:AT1G01510.1;protein_id=AT1G01510.1 -1 araport11 exon 189765 190472 . + . Name=AT1G01510.1.exon7;Parent=transcript:AT1G01510.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01510.1.exon7;rank=7; -1 araport11 three_prime_UTR 189837 190472 . + . Parent=transcript:AT1G01510.1; -1 araport11 gene 190408 192436 . + . ID=gene:AT1G01520;biotype=protein_coding;description=ASG4 [Source:UniProtKB/TrEMBL%3bAcc:A0A384LJW3];gene_id=AT1G01520;logic_name=araport11; -1 araport11 mRNA 190408 192436 . + . ID=transcript:AT1G01520.4;biotype=protein_coding;Parent=gene:AT1G01520;transcript_id=AT1G01520.4; -1 araport11 five_prime_UTR 190408 190595 . + . Parent=transcript:AT1G01520.4; -1 araport11 exon 190408 190828 . + . Name=AT1G01520.4.exon1;Parent=transcript:AT1G01520.4;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01520.4.exon1;rank=1; -1 araport11 CDS 190596 190828 . + 0 ID=CDS:AT1G01520.4;Parent=transcript:AT1G01520.4;protein_id=AT1G01520.4 -1 araport11 exon 190941 190998 . + . Name=AT1G01520.4.exon2;Parent=transcript:AT1G01520.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01520.4.exon2;rank=2; -1 araport11 CDS 190941 190998 . + 1 ID=CDS:AT1G01520.4;Parent=transcript:AT1G01520.4;protein_id=AT1G01520.4 -1 araport11 exon 191138 191258 . + . Name=AT1G01520.4.exon3;Parent=transcript:AT1G01520.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01520.4.exon3;rank=3; -1 araport11 CDS 191138 191258 . + 0 ID=CDS:AT1G01520.4;Parent=transcript:AT1G01520.4;protein_id=AT1G01520.4 -1 araport11 exon 191341 191475 . + . Name=AT1G01520.4.exon4;Parent=transcript:AT1G01520.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.4.exon4;rank=4; -1 araport11 CDS 191341 191475 . + 2 ID=CDS:AT1G01520.4;Parent=transcript:AT1G01520.4;protein_id=AT1G01520.4 -1 araport11 exon 191579 191692 . + . Name=AT1G01520.5.exon4;Parent=transcript:AT1G01520.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.5.exon4;rank=5; -1 araport11 CDS 191579 191692 . + 2 ID=CDS:AT1G01520.4;Parent=transcript:AT1G01520.4;protein_id=AT1G01520.4 -1 araport11 CDS 191780 191895 . + 2 ID=CDS:AT1G01520.4;Parent=transcript:AT1G01520.4;protein_id=AT1G01520.4 -1 araport11 exon 191780 192026 . + . Name=AT1G01520.4.exon6;Parent=transcript:AT1G01520.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01520.4.exon6;rank=6; -1 araport11 three_prime_UTR 191896 192026 . + . Parent=transcript:AT1G01520.4; -1 araport11 exon 192107 192436 . + . Name=AT1G01520.4.exon7;Parent=transcript:AT1G01520.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01520.4.exon7;rank=7; -1 araport11 three_prime_UTR 192107 192436 . + . Parent=transcript:AT1G01520.4; -1 araport11 mRNA 190408 192436 . + . ID=transcript:AT1G01520.2;biotype=protein_coding;Parent=gene:AT1G01520;transcript_id=AT1G01520.2; -1 araport11 five_prime_UTR 190408 190595 . + . Parent=transcript:AT1G01520.2; -1 araport11 exon 190408 190828 . + . Name=AT1G01520.4.exon1;Parent=transcript:AT1G01520.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01520.4.exon1;rank=1; -1 araport11 CDS 190596 190828 . + 0 ID=CDS:AT1G01520.2;Parent=transcript:AT1G01520.2;protein_id=AT1G01520.2 -1 araport11 exon 190941 190998 . + . Name=AT1G01520.4.exon2;Parent=transcript:AT1G01520.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01520.4.exon2;rank=2; -1 araport11 CDS 190941 190998 . + 1 ID=CDS:AT1G01520.2;Parent=transcript:AT1G01520.2;protein_id=AT1G01520.2 -1 araport11 exon 191138 191258 . + . Name=AT1G01520.4.exon3;Parent=transcript:AT1G01520.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01520.4.exon3;rank=3; -1 araport11 CDS 191138 191258 . + 0 ID=CDS:AT1G01520.2;Parent=transcript:AT1G01520.2;protein_id=AT1G01520.2 -1 araport11 exon 191341 191475 . + . Name=AT1G01520.4.exon4;Parent=transcript:AT1G01520.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.4.exon4;rank=4; -1 araport11 CDS 191341 191475 . + 2 ID=CDS:AT1G01520.2;Parent=transcript:AT1G01520.2;protein_id=AT1G01520.2 -1 araport11 exon 191579 191692 . + . Name=AT1G01520.5.exon4;Parent=transcript:AT1G01520.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.5.exon4;rank=5; -1 araport11 CDS 191579 191692 . + 2 ID=CDS:AT1G01520.2;Parent=transcript:AT1G01520.2;protein_id=AT1G01520.2 -1 araport11 CDS 191780 191895 . + 2 ID=CDS:AT1G01520.2;Parent=transcript:AT1G01520.2;protein_id=AT1G01520.2 -1 araport11 exon 191780 192436 . + . Name=AT1G01520.2.exon6;Parent=transcript:AT1G01520.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01520.2.exon6;rank=6; -1 araport11 three_prime_UTR 191896 192436 . + . Parent=transcript:AT1G01520.2; -1 araport11 mRNA 190408 192436 . + . ID=transcript:AT1G01520.3;biotype=protein_coding;Parent=gene:AT1G01520;transcript_id=AT1G01520.3; -1 araport11 five_prime_UTR 190408 190595 . + . Parent=transcript:AT1G01520.3; -1 araport11 exon 190408 190828 . + . Name=AT1G01520.4.exon1;Parent=transcript:AT1G01520.3;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01520.4.exon1;rank=1; -1 araport11 CDS 190596 190828 . + 0 ID=CDS:AT1G01520.3;Parent=transcript:AT1G01520.3;protein_id=AT1G01520.3 -1 araport11 exon 190941 190998 . + . Name=AT1G01520.4.exon2;Parent=transcript:AT1G01520.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01520.4.exon2;rank=2; -1 araport11 CDS 190941 190998 . + 1 ID=CDS:AT1G01520.3;Parent=transcript:AT1G01520.3;protein_id=AT1G01520.3 -1 araport11 exon 191138 191258 . + . Name=AT1G01520.4.exon3;Parent=transcript:AT1G01520.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01520.4.exon3;rank=3; -1 araport11 CDS 191138 191258 . + 0 ID=CDS:AT1G01520.3;Parent=transcript:AT1G01520.3;protein_id=AT1G01520.3 -1 araport11 exon 191341 191475 . + . Name=AT1G01520.4.exon4;Parent=transcript:AT1G01520.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.4.exon4;rank=4; -1 araport11 CDS 191341 191475 . + 2 ID=CDS:AT1G01520.3;Parent=transcript:AT1G01520.3;protein_id=AT1G01520.3 -1 araport11 exon 191579 191692 . + . Name=AT1G01520.5.exon4;Parent=transcript:AT1G01520.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.5.exon4;rank=5; -1 araport11 CDS 191579 191692 . + 2 ID=CDS:AT1G01520.3;Parent=transcript:AT1G01520.3;protein_id=AT1G01520.3 -1 araport11 exon 191780 191889 . + . Name=AT1G01520.5.exon5;Parent=transcript:AT1G01520.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01520.5.exon5;rank=6; -1 araport11 CDS 191780 191889 . + 2 ID=CDS:AT1G01520.3;Parent=transcript:AT1G01520.3;protein_id=AT1G01520.3 -1 araport11 CDS 191967 192059 . + 0 ID=CDS:AT1G01520.3;Parent=transcript:AT1G01520.3;protein_id=AT1G01520.3 -1 araport11 exon 191967 192436 . + . Name=AT1G01520.3.exon7;Parent=transcript:AT1G01520.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01520.3.exon7;rank=7; -1 araport11 three_prime_UTR 192060 192436 . + . Parent=transcript:AT1G01520.3; -1 araport11 mRNA 190408 192436 . + . ID=transcript:AT1G01520.1;biotype=protein_coding;Parent=gene:AT1G01520;transcript_id=AT1G01520.1; -1 araport11 five_prime_UTR 190408 190595 . + . Parent=transcript:AT1G01520.1; -1 araport11 exon 190408 190828 . + . Name=AT1G01520.4.exon1;Parent=transcript:AT1G01520.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01520.4.exon1;rank=1; -1 araport11 CDS 190596 190828 . + 0 ID=CDS:AT1G01520.1;Parent=transcript:AT1G01520.1;protein_id=AT1G01520.1 -1 araport11 exon 190941 190998 . + . Name=AT1G01520.4.exon2;Parent=transcript:AT1G01520.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01520.4.exon2;rank=2; -1 araport11 CDS 190941 190998 . + 1 ID=CDS:AT1G01520.1;Parent=transcript:AT1G01520.1;protein_id=AT1G01520.1 -1 araport11 exon 191138 191258 . + . Name=AT1G01520.4.exon3;Parent=transcript:AT1G01520.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01520.4.exon3;rank=3; -1 araport11 CDS 191138 191258 . + 0 ID=CDS:AT1G01520.1;Parent=transcript:AT1G01520.1;protein_id=AT1G01520.1 -1 araport11 exon 191341 191475 . + . Name=AT1G01520.4.exon4;Parent=transcript:AT1G01520.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.4.exon4;rank=4; -1 araport11 CDS 191341 191475 . + 2 ID=CDS:AT1G01520.1;Parent=transcript:AT1G01520.1;protein_id=AT1G01520.1 -1 araport11 exon 191579 191692 . + . Name=AT1G01520.5.exon4;Parent=transcript:AT1G01520.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.5.exon4;rank=5; -1 araport11 CDS 191579 191692 . + 2 ID=CDS:AT1G01520.1;Parent=transcript:AT1G01520.1;protein_id=AT1G01520.1 -1 araport11 exon 191780 191889 . + . Name=AT1G01520.5.exon5;Parent=transcript:AT1G01520.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01520.5.exon5;rank=6; -1 araport11 CDS 191780 191889 . + 2 ID=CDS:AT1G01520.1;Parent=transcript:AT1G01520.1;protein_id=AT1G01520.1 -1 araport11 exon 191967 192026 . + . Name=AT1G01520.5.exon6;Parent=transcript:AT1G01520.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01520.5.exon6;rank=7; -1 araport11 CDS 191967 192026 . + 0 ID=CDS:AT1G01520.1;Parent=transcript:AT1G01520.1;protein_id=AT1G01520.1 -1 araport11 CDS 192107 192139 . + 0 ID=CDS:AT1G01520.1;Parent=transcript:AT1G01520.1;protein_id=AT1G01520.1 -1 araport11 exon 192107 192436 . + . Name=AT1G01520.5.exon7;Parent=transcript:AT1G01520.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01520.5.exon7;rank=8; -1 araport11 three_prime_UTR 192140 192436 . + . Parent=transcript:AT1G01520.1; -1 araport11 mRNA 190478 192436 . + . ID=transcript:AT1G01520.5;biotype=protein_coding;Parent=gene:AT1G01520;transcript_id=AT1G01520.5; -1 araport11 exon 190478 190828 . + . Name=AT1G01520.5.exon1;Parent=transcript:AT1G01520.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01520.5.exon1;rank=1; -1 araport11 five_prime_UTR 190478 190828 . + . Parent=transcript:AT1G01520.5; -1 araport11 exon 190941 190998 . + . Name=AT1G01520.5.exon2;Parent=transcript:AT1G01520.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01520.5.exon2;rank=2; -1 araport11 five_prime_UTR 190941 190998 . + . Parent=transcript:AT1G01520.5; -1 araport11 five_prime_UTR 191138 191180 . + . Parent=transcript:AT1G01520.5; -1 araport11 exon 191138 191475 . + . Name=AT1G01520.5.exon3;Parent=transcript:AT1G01520.5;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01520.5.exon3;rank=3; -1 araport11 CDS 191181 191475 . + 0 ID=CDS:AT1G01520.5;Parent=transcript:AT1G01520.5;protein_id=AT1G01520.5 -1 araport11 exon 191579 191692 . + . Name=AT1G01520.5.exon4;Parent=transcript:AT1G01520.5;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01520.5.exon4;rank=4; -1 araport11 CDS 191579 191692 . + 2 ID=CDS:AT1G01520.5;Parent=transcript:AT1G01520.5;protein_id=AT1G01520.5 -1 araport11 exon 191780 191889 . + . Name=AT1G01520.5.exon5;Parent=transcript:AT1G01520.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01520.5.exon5;rank=5; -1 araport11 CDS 191780 191889 . + 2 ID=CDS:AT1G01520.5;Parent=transcript:AT1G01520.5;protein_id=AT1G01520.5 -1 araport11 exon 191967 192026 . + . Name=AT1G01520.5.exon6;Parent=transcript:AT1G01520.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01520.5.exon6;rank=6; -1 araport11 CDS 191967 192026 . + 0 ID=CDS:AT1G01520.5;Parent=transcript:AT1G01520.5;protein_id=AT1G01520.5 -1 araport11 CDS 192107 192139 . + 0 ID=CDS:AT1G01520.5;Parent=transcript:AT1G01520.5;protein_id=AT1G01520.5 -1 araport11 exon 192107 192436 . + . Name=AT1G01520.5.exon7;Parent=transcript:AT1G01520.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01520.5.exon7;rank=7; -1 araport11 three_prime_UTR 192140 192436 . + . Parent=transcript:AT1G01520.5; -1 araport11 gene 192634 193670 . - . ID=gene:AT1G01530;Name=AGL28;biotype=protein_coding;description=AGL28 [Source:UniProtKB/TrEMBL%3bAcc:A0A178WE04];gene_id=AT1G01530;logic_name=araport11; -1 araport11 mRNA 192634 193670 . - . ID=transcript:AT1G01530.1;biotype=protein_coding;Parent=gene:AT1G01530;transcript_id=AT1G01530.1; -1 araport11 three_prime_UTR 192634 192639 . - . Parent=transcript:AT1G01530.1; -1 araport11 exon 192634 193071 . - . Name=AT1G01530.1.exon2;Parent=transcript:AT1G01530.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01530.1.exon2;rank=2; -1 araport11 CDS 192640 193071 . - 0 ID=CDS:AT1G01530.1;Parent=transcript:AT1G01530.1;protein_id=AT1G01530.1 -1 araport11 CDS 193351 193662 . - 0 ID=CDS:AT1G01530.1;Parent=transcript:AT1G01530.1;protein_id=AT1G01530.1 -1 araport11 exon 193351 193670 . - . Name=AT1G01530.1.exon1;Parent=transcript:AT1G01530.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01530.1.exon1;rank=1; -1 araport11 five_prime_UTR 193663 193670 . - . Parent=transcript:AT1G01530.1; -1 araport11 gene 195645 198787 . + . ID=gene:AT1G01540;biotype=protein_coding;description=Probable serine/threonine-protein kinase At1g01540 [Source:UniProtKB/Swiss-Prot%3bAcc:Q3EDL4];gene_id=AT1G01540;logic_name=araport11; -1 araport11 mRNA 195645 198787 . + . ID=transcript:AT1G01540.2;biotype=protein_coding;Parent=gene:AT1G01540;transcript_id=AT1G01540.2; -1 araport11 five_prime_UTR 195645 195979 . + . Parent=transcript:AT1G01540.2; -1 araport11 exon 195645 196542 . + . Name=AT1G01540.2.exon1;Parent=transcript:AT1G01540.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01540.2.exon1;rank=1; -1 araport11 CDS 195980 196542 . + 0 ID=CDS:AT1G01540.2;Parent=transcript:AT1G01540.2;protein_id=AT1G01540.2 -1 araport11 exon 197115 197219 . + . Name=AT1G01540.2.exon2;Parent=transcript:AT1G01540.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01540.2.exon2;rank=2; -1 araport11 CDS 197115 197219 . + 1 ID=CDS:AT1G01540.2;Parent=transcript:AT1G01540.2;protein_id=AT1G01540.2 -1 araport11 exon 197300 197422 . + . Name=AT1G01540.2.exon3;Parent=transcript:AT1G01540.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01540.2.exon3;rank=3; -1 araport11 CDS 197300 197422 . + 1 ID=CDS:AT1G01540.2;Parent=transcript:AT1G01540.2;protein_id=AT1G01540.2 -1 araport11 exon 197501 197671 . + . Name=AT1G01540.2.exon4;Parent=transcript:AT1G01540.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01540.2.exon4;rank=4; -1 araport11 CDS 197501 197671 . + 1 ID=CDS:AT1G01540.2;Parent=transcript:AT1G01540.2;protein_id=AT1G01540.2 -1 araport11 exon 197775 197904 . + . Name=AT1G01540.2.exon5;Parent=transcript:AT1G01540.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01540.2.exon5;rank=5; -1 araport11 CDS 197775 197904 . + 1 ID=CDS:AT1G01540.2;Parent=transcript:AT1G01540.2;protein_id=AT1G01540.2 -1 araport11 exon 197974 198183 . + . Name=AT1G01540.2.exon6;Parent=transcript:AT1G01540.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01540.2.exon6;rank=6; -1 araport11 CDS 197974 198183 . + 0 ID=CDS:AT1G01540.2;Parent=transcript:AT1G01540.2;protein_id=AT1G01540.2 -1 araport11 CDS 198267 198383 . + 0 ID=CDS:AT1G01540.2;Parent=transcript:AT1G01540.2;protein_id=AT1G01540.2 -1 araport11 exon 198267 198787 . + . Name=AT1G01540.2.exon7;Parent=transcript:AT1G01540.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01540.2.exon7;rank=7; -1 araport11 three_prime_UTR 198384 198787 . + . Parent=transcript:AT1G01540.2; -1 araport11 mRNA 195812 198635 . + . ID=transcript:AT1G01540.1;biotype=protein_coding;Parent=gene:AT1G01540;transcript_id=AT1G01540.1; -1 araport11 five_prime_UTR 195812 195979 . + . Parent=transcript:AT1G01540.1; -1 araport11 exon 195812 196542 . + . Name=AT1G01540.1.exon1;Parent=transcript:AT1G01540.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01540.1.exon1;rank=1; -1 araport11 CDS 195980 196542 . + 0 ID=CDS:AT1G01540.1;Parent=transcript:AT1G01540.1;protein_id=AT1G01540.1 -1 araport11 exon 197115 197219 . + . Name=AT1G01540.2.exon2;Parent=transcript:AT1G01540.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01540.2.exon2;rank=2; -1 araport11 CDS 197115 197219 . + 1 ID=CDS:AT1G01540.1;Parent=transcript:AT1G01540.1;protein_id=AT1G01540.1 -1 araport11 exon 197300 197422 . + . Name=AT1G01540.2.exon3;Parent=transcript:AT1G01540.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01540.2.exon3;rank=3; -1 araport11 CDS 197300 197422 . + 1 ID=CDS:AT1G01540.1;Parent=transcript:AT1G01540.1;protein_id=AT1G01540.1 -1 araport11 exon 197501 197671 . + . Name=AT1G01540.2.exon4;Parent=transcript:AT1G01540.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01540.2.exon4;rank=4; -1 araport11 CDS 197501 197671 . + 1 ID=CDS:AT1G01540.1;Parent=transcript:AT1G01540.1;protein_id=AT1G01540.1 -1 araport11 CDS 197775 197973 . + 1 ID=CDS:AT1G01540.1;Parent=transcript:AT1G01540.1;protein_id=AT1G01540.1 -1 araport11 exon 197775 198183 . + . Name=AT1G01540.1.exon5;Parent=transcript:AT1G01540.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01540.1.exon5;rank=5; -1 araport11 three_prime_UTR 197974 198183 . + . Parent=transcript:AT1G01540.1; -1 araport11 exon 198267 198635 . + . Name=AT1G01540.1.exon6;Parent=transcript:AT1G01540.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01540.1.exon6;rank=6; -1 araport11 three_prime_UTR 198267 198635 . + . Parent=transcript:AT1G01540.1; -1 araport11 gene 199527 201775 . + . ID=gene:AT1G01550;Name=BPS1;biotype=protein_coding;description=Protein BPS1%2c chloroplastic [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LMM6];gene_id=AT1G01550;logic_name=araport11; -1 araport11 mRNA 199527 201775 . + . ID=transcript:AT1G01550.1;biotype=protein_coding;Parent=gene:AT1G01550;transcript_id=AT1G01550.1; -1 araport11 exon 199527 199763 . + . Name=AT1G01550.1.exon1;Parent=transcript:AT1G01550.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01550.1.exon1;rank=1; -1 araport11 five_prime_UTR 199527 199763 . + . Parent=transcript:AT1G01550.1; -1 araport11 exon 199890 199959 . + . Name=AT1G01550.1.exon2;Parent=transcript:AT1G01550.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01550.1.exon2;rank=2; -1 araport11 five_prime_UTR 199890 199959 . + . Parent=transcript:AT1G01550.1; -1 araport11 five_prime_UTR 200511 200525 . + . Parent=transcript:AT1G01550.1; -1 araport11 exon 200511 201775 . + . Name=AT1G01550.2.exon2;Parent=transcript:AT1G01550.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01550.2.exon2;rank=3; -1 araport11 CDS 200526 201575 . + 0 ID=CDS:AT1G01550.1;Parent=transcript:AT1G01550.1;protein_id=AT1G01550.1 -1 araport11 three_prime_UTR 201576 201775 . + . Parent=transcript:AT1G01550.1; -1 araport11 mRNA 199630 201775 . + . ID=transcript:AT1G01550.2;biotype=protein_coding;Parent=gene:AT1G01550;transcript_id=AT1G01550.2; -1 araport11 exon 199630 199959 . + . Name=AT1G01550.2.exon1;Parent=transcript:AT1G01550.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01550.2.exon1;rank=1; -1 araport11 five_prime_UTR 199630 199959 . + . Parent=transcript:AT1G01550.2; -1 araport11 five_prime_UTR 200511 200525 . + . Parent=transcript:AT1G01550.2; -1 araport11 exon 200511 201775 . + . Name=AT1G01550.2.exon2;Parent=transcript:AT1G01550.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01550.2.exon2;rank=2; -1 araport11 CDS 200526 201575 . + 0 ID=CDS:AT1G01550.2;Parent=transcript:AT1G01550.2;protein_id=AT1G01550.2 -1 araport11 three_prime_UTR 201576 201775 . + . Parent=transcript:AT1G01550.2; -1 araport11 gene 202103 204440 . + . ID=gene:AT1G01560;Name=MPK11;biotype=protein_coding;description=Mitogen-activated protein kinase 11 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LMM5];gene_id=AT1G01560;logic_name=araport11; -1 araport11 mRNA 202103 204388 . + . ID=transcript:AT1G01560.3;biotype=protein_coding;Parent=gene:AT1G01560;transcript_id=AT1G01560.3; -1 araport11 five_prime_UTR 202103 202344 . + . Parent=transcript:AT1G01560.3; -1 araport11 exon 202103 202508 . + . Name=AT1G01560.3.exon1;Parent=transcript:AT1G01560.3;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01560.3.exon1;rank=1; -1 araport11 CDS 202345 202508 . + 0 ID=CDS:AT1G01560.3;Parent=transcript:AT1G01560.3;protein_id=AT1G01560.3 -1 araport11 exon 202782 202911 . + . Name=AT1G01560.1.exon2;Parent=transcript:AT1G01560.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01560.1.exon2;rank=2; -1 araport11 CDS 202782 202911 . + 1 ID=CDS:AT1G01560.3;Parent=transcript:AT1G01560.3;protein_id=AT1G01560.3 -1 araport11 exon 202991 203128 . + . Name=AT1G01560.1.exon3;Parent=transcript:AT1G01560.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01560.1.exon3;rank=3; -1 araport11 CDS 202991 203128 . + 0 ID=CDS:AT1G01560.3;Parent=transcript:AT1G01560.3;protein_id=AT1G01560.3 -1 araport11 exon 203267 203599 . + . Name=AT1G01560.3.exon4;Parent=transcript:AT1G01560.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01560.3.exon4;rank=4; -1 araport11 CDS 203267 203599 . + 0 ID=CDS:AT1G01560.3;Parent=transcript:AT1G01560.3;protein_id=AT1G01560.3 -1 araport11 CDS 203760 204035 . + 0 ID=CDS:AT1G01560.3;Parent=transcript:AT1G01560.3;protein_id=AT1G01560.3 -1 araport11 exon 203760 204388 . + . Name=AT1G01560.3.exon5;Parent=transcript:AT1G01560.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01560.3.exon5;rank=5; -1 araport11 three_prime_UTR 204036 204388 . + . Parent=transcript:AT1G01560.3; -1 araport11 mRNA 202111 204440 . + . ID=transcript:AT1G01560.2;biotype=protein_coding;Parent=gene:AT1G01560;transcript_id=AT1G01560.2; -1 araport11 five_prime_UTR 202111 202344 . + . Parent=transcript:AT1G01560.2; -1 araport11 exon 202111 202508 . + . Name=AT1G01560.2.exon1;Parent=transcript:AT1G01560.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01560.2.exon1;rank=1; -1 araport11 CDS 202345 202508 . + 0 ID=CDS:AT1G01560.2;Parent=transcript:AT1G01560.2;protein_id=AT1G01560.2 -1 araport11 exon 202782 202911 . + . Name=AT1G01560.1.exon2;Parent=transcript:AT1G01560.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01560.1.exon2;rank=2; -1 araport11 CDS 202782 202911 . + 1 ID=CDS:AT1G01560.2;Parent=transcript:AT1G01560.2;protein_id=AT1G01560.2 -1 araport11 exon 202991 203128 . + . Name=AT1G01560.1.exon3;Parent=transcript:AT1G01560.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01560.1.exon3;rank=3; -1 araport11 CDS 202991 203128 . + 0 ID=CDS:AT1G01560.2;Parent=transcript:AT1G01560.2;protein_id=AT1G01560.2 -1 araport11 exon 203267 203599 . + . Name=AT1G01560.3.exon4;Parent=transcript:AT1G01560.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01560.3.exon4;rank=4; -1 araport11 CDS 203267 203599 . + 0 ID=CDS:AT1G01560.2;Parent=transcript:AT1G01560.2;protein_id=AT1G01560.2 -1 araport11 exon 203760 203943 . + . Name=AT1G01560.2.exon5;Parent=transcript:AT1G01560.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01560.2.exon5;rank=5; -1 araport11 CDS 203760 203943 . + 0 ID=CDS:AT1G01560.2;Parent=transcript:AT1G01560.2;protein_id=AT1G01560.2 -1 araport11 CDS 204029 204189 . + 2 ID=CDS:AT1G01560.2;Parent=transcript:AT1G01560.2;protein_id=AT1G01560.2 -1 araport11 exon 204029 204440 . + . Name=AT1G01560.2.exon6;Parent=transcript:AT1G01560.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01560.2.exon6;rank=6; -1 araport11 three_prime_UTR 204190 204440 . + . Parent=transcript:AT1G01560.2; -1 araport11 mRNA 202136 204335 . + . ID=transcript:AT1G01560.4;biotype=protein_coding;Parent=gene:AT1G01560;transcript_id=AT1G01560.4; -1 araport11 five_prime_UTR 202136 202344 . + . Parent=transcript:AT1G01560.4; -1 araport11 exon 202136 202508 . + . Name=AT1G01560.1.exon1;Parent=transcript:AT1G01560.4;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01560.1.exon1;rank=1; -1 araport11 CDS 202345 202508 . + 0 ID=CDS:AT1G01560.4;Parent=transcript:AT1G01560.4;protein_id=AT1G01560.4 -1 araport11 exon 202782 202911 . + . Name=AT1G01560.1.exon2;Parent=transcript:AT1G01560.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01560.1.exon2;rank=2; -1 araport11 CDS 202782 202911 . + 1 ID=CDS:AT1G01560.4;Parent=transcript:AT1G01560.4;protein_id=AT1G01560.4 -1 araport11 exon 202991 203128 . + . Name=AT1G01560.1.exon3;Parent=transcript:AT1G01560.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01560.1.exon3;rank=3; -1 araport11 CDS 202991 203128 . + 0 ID=CDS:AT1G01560.4;Parent=transcript:AT1G01560.4;protein_id=AT1G01560.4 -1 araport11 CDS 203267 203662 . + 0 ID=CDS:AT1G01560.4;Parent=transcript:AT1G01560.4;protein_id=AT1G01560.4 -1 araport11 exon 203267 203943 . + . Name=AT1G01560.4.exon4;Parent=transcript:AT1G01560.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01560.4.exon4;rank=4; -1 araport11 three_prime_UTR 203663 203943 . + . Parent=transcript:AT1G01560.4; -1 araport11 exon 204029 204335 . + . Name=AT1G01560.4.exon5;Parent=transcript:AT1G01560.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01560.4.exon5;rank=5; -1 araport11 three_prime_UTR 204029 204335 . + . Parent=transcript:AT1G01560.4; -1 araport11 mRNA 202136 204335 . + . ID=transcript:AT1G01560.1;biotype=protein_coding;Parent=gene:AT1G01560;transcript_id=AT1G01560.1; -1 araport11 five_prime_UTR 202136 202344 . + . Parent=transcript:AT1G01560.1; -1 araport11 exon 202136 202508 . + . Name=AT1G01560.1.exon1;Parent=transcript:AT1G01560.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01560.1.exon1;rank=1; -1 araport11 CDS 202345 202508 . + 0 ID=CDS:AT1G01560.1;Parent=transcript:AT1G01560.1;protein_id=AT1G01560.1 -1 araport11 exon 202782 202911 . + . Name=AT1G01560.1.exon2;Parent=transcript:AT1G01560.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01560.1.exon2;rank=2; -1 araport11 CDS 202782 202911 . + 1 ID=CDS:AT1G01560.1;Parent=transcript:AT1G01560.1;protein_id=AT1G01560.1 -1 araport11 exon 202991 203128 . + . Name=AT1G01560.1.exon3;Parent=transcript:AT1G01560.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01560.1.exon3;rank=3; -1 araport11 CDS 202991 203128 . + 0 ID=CDS:AT1G01560.1;Parent=transcript:AT1G01560.1;protein_id=AT1G01560.1 -1 araport11 CDS 203267 203662 . + 0 ID=CDS:AT1G01560.1;Parent=transcript:AT1G01560.1;protein_id=AT1G01560.1 -1 araport11 exon 203267 204335 . + . Name=AT1G01560.1.exon4;Parent=transcript:AT1G01560.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01560.1.exon4;rank=4; -1 araport11 three_prime_UTR 203663 204335 . + . Parent=transcript:AT1G01560.1; -1 araport11 gene 204935 207642 . + . ID=gene:AT1G01570;biotype=protein_coding;description=F22L4.11 protein [Source:UniProtKB/TrEMBL%3bAcc:Q9LMM4];gene_id=AT1G01570;logic_name=araport11; -1 araport11 mRNA 204935 207642 . + . ID=transcript:AT1G01570.2;biotype=protein_coding;Parent=gene:AT1G01570;transcript_id=AT1G01570.2; -1 araport11 five_prime_UTR 204935 205082 . + . Parent=transcript:AT1G01570.2; -1 araport11 exon 204935 205949 . + . Name=AT1G01570.2.exon1;Parent=transcript:AT1G01570.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01570.2.exon1;rank=1; -1 araport11 CDS 205083 205949 . + 0 ID=CDS:AT1G01570.2;Parent=transcript:AT1G01570.2;protein_id=AT1G01570.2 -1 araport11 exon 206692 207243 . + . Name=AT1G01570.1.exon2;Parent=transcript:AT1G01570.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01570.1.exon2;rank=2; -1 araport11 CDS 206692 207243 . + 0 ID=CDS:AT1G01570.2;Parent=transcript:AT1G01570.2;protein_id=AT1G01570.2 -1 araport11 CDS 207325 207435 . + 0 ID=CDS:AT1G01570.2;Parent=transcript:AT1G01570.2;protein_id=AT1G01570.2 -1 araport11 exon 207325 207642 . + . Name=AT1G01570.2.exon3;Parent=transcript:AT1G01570.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01570.2.exon3;rank=3; -1 araport11 three_prime_UTR 207436 207642 . + . Parent=transcript:AT1G01570.2; -1 araport11 mRNA 205176 207435 . + . ID=transcript:AT1G01570.1;biotype=protein_coding;Parent=gene:AT1G01570;transcript_id=AT1G01570.1; -1 araport11 exon 205176 205949 . + . Name=AT1G01570.1.exon1;Parent=transcript:AT1G01570.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01570.1.exon1;rank=1; -1 araport11 CDS 205176 205949 . + 0 ID=CDS:AT1G01570.1;Parent=transcript:AT1G01570.1;protein_id=AT1G01570.1 -1 araport11 exon 206692 207243 . + . Name=AT1G01570.1.exon2;Parent=transcript:AT1G01570.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01570.1.exon2;rank=2; -1 araport11 CDS 206692 207243 . + 0 ID=CDS:AT1G01570.1;Parent=transcript:AT1G01570.1;protein_id=AT1G01570.1 -1 araport11 exon 207325 207435 . + . Name=AT1G01570.1.exon3;Parent=transcript:AT1G01570.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01570.1.exon3;rank=3; -1 araport11 CDS 207325 207435 . + 0 ID=CDS:AT1G01570.1;Parent=transcript:AT1G01570.1;protein_id=AT1G01570.1 -1 araport11 gene 208995 213082 . + . ID=gene:AT1G01580;Name=FRO2;biotype=protein_coding;description=ferric reduction oxidase 2 [Source:TAIR%3bAcc:AT1G01580];gene_id=AT1G01580;logic_name=araport11; -1 araport11 mRNA 208995 213082 . + . ID=transcript:AT1G01580.2;biotype=protein_coding;Parent=gene:AT1G01580;transcript_id=AT1G01580.2; -1 araport11 five_prime_UTR 208995 209160 . + . Parent=transcript:AT1G01580.2; -1 araport11 exon 208995 209608 . + . Name=AT1G01580.2.exon1;Parent=transcript:AT1G01580.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01580.2.exon1;rank=1; -1 araport11 CDS 209161 209608 . + 0 ID=CDS:AT1G01580.2;Parent=transcript:AT1G01580.2;protein_id=AT1G01580.2 -1 araport11 exon 209764 209866 . + . Name=AT1G01580.2.exon2;Parent=transcript:AT1G01580.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01580.2.exon2;rank=2; -1 araport11 CDS 209764 209866 . + 2 ID=CDS:AT1G01580.2;Parent=transcript:AT1G01580.2;protein_id=AT1G01580.2 -1 araport11 exon 209950 210144 . + . Name=AT1G01580.2.exon3;Parent=transcript:AT1G01580.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01580.2.exon3;rank=3; -1 araport11 CDS 209950 210144 . + 1 ID=CDS:AT1G01580.2;Parent=transcript:AT1G01580.2;protein_id=AT1G01580.2 -1 araport11 exon 210385 210619 . + . Name=AT1G01580.2.exon4;Parent=transcript:AT1G01580.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01580.2.exon4;rank=4; -1 araport11 CDS 210385 210619 . + 1 ID=CDS:AT1G01580.2;Parent=transcript:AT1G01580.2;protein_id=AT1G01580.2 -1 araport11 exon 211052 211379 . + . Name=AT1G01580.2.exon5;Parent=transcript:AT1G01580.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01580.2.exon5;rank=5; -1 araport11 CDS 211052 211379 . + 0 ID=CDS:AT1G01580.2;Parent=transcript:AT1G01580.2;protein_id=AT1G01580.2 -1 araport11 exon 211474 211717 . + . Name=AT1G01580.2.exon6;Parent=transcript:AT1G01580.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01580.2.exon6;rank=6; -1 araport11 CDS 211474 211717 . + 2 ID=CDS:AT1G01580.2;Parent=transcript:AT1G01580.2;protein_id=AT1G01580.2 -1 araport11 exon 211855 212573 . + . Name=AT1G01580.2.exon7;Parent=transcript:AT1G01580.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01580.2.exon7;rank=7; -1 araport11 CDS 211855 212573 . + 1 ID=CDS:AT1G01580.2;Parent=transcript:AT1G01580.2;protein_id=AT1G01580.2 -1 araport11 CDS 212671 212810 . + 2 ID=CDS:AT1G01580.2;Parent=transcript:AT1G01580.2;protein_id=AT1G01580.2 -1 araport11 exon 212671 213082 . + . Name=AT1G01580.2.exon8;Parent=transcript:AT1G01580.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01580.2.exon8;rank=8; -1 araport11 three_prime_UTR 212811 213082 . + . Parent=transcript:AT1G01580.2; -1 araport11 mRNA 209208 213080 . + . ID=transcript:AT1G01580.1;biotype=protein_coding;Parent=gene:AT1G01580;transcript_id=AT1G01580.1; -1 araport11 five_prime_UTR 209208 209394 . + . Parent=transcript:AT1G01580.1; -1 araport11 exon 209208 209608 . + . Name=AT1G01580.1.exon1;Parent=transcript:AT1G01580.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01580.1.exon1;rank=1; -1 araport11 CDS 209395 209608 . + 0 ID=CDS:AT1G01580.1;Parent=transcript:AT1G01580.1;protein_id=AT1G01580.1 -1 araport11 exon 209764 209866 . + . Name=AT1G01580.2.exon2;Parent=transcript:AT1G01580.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01580.2.exon2;rank=2; -1 araport11 CDS 209764 209866 . + 2 ID=CDS:AT1G01580.1;Parent=transcript:AT1G01580.1;protein_id=AT1G01580.1 -1 araport11 exon 209950 210144 . + . Name=AT1G01580.2.exon3;Parent=transcript:AT1G01580.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01580.2.exon3;rank=3; -1 araport11 CDS 209950 210144 . + 1 ID=CDS:AT1G01580.1;Parent=transcript:AT1G01580.1;protein_id=AT1G01580.1 -1 araport11 exon 210385 210619 . + . Name=AT1G01580.2.exon4;Parent=transcript:AT1G01580.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01580.2.exon4;rank=4; -1 araport11 CDS 210385 210619 . + 1 ID=CDS:AT1G01580.1;Parent=transcript:AT1G01580.1;protein_id=AT1G01580.1 -1 araport11 exon 211052 211379 . + . Name=AT1G01580.2.exon5;Parent=transcript:AT1G01580.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01580.2.exon5;rank=5; -1 araport11 CDS 211052 211379 . + 0 ID=CDS:AT1G01580.1;Parent=transcript:AT1G01580.1;protein_id=AT1G01580.1 -1 araport11 exon 211474 211717 . + . Name=AT1G01580.2.exon6;Parent=transcript:AT1G01580.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01580.2.exon6;rank=6; -1 araport11 CDS 211474 211717 . + 2 ID=CDS:AT1G01580.1;Parent=transcript:AT1G01580.1;protein_id=AT1G01580.1 -1 araport11 exon 211855 212573 . + . Name=AT1G01580.2.exon7;Parent=transcript:AT1G01580.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01580.2.exon7;rank=7; -1 araport11 CDS 211855 212573 . + 1 ID=CDS:AT1G01580.1;Parent=transcript:AT1G01580.1;protein_id=AT1G01580.1 -1 araport11 CDS 212671 212810 . + 2 ID=CDS:AT1G01580.1;Parent=transcript:AT1G01580.1;protein_id=AT1G01580.1 -1 araport11 exon 212671 213080 . + . Name=AT1G01580.1.exon8;Parent=transcript:AT1G01580.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01580.1.exon8;rank=8; -1 araport11 three_prime_UTR 212811 213080 . + . Parent=transcript:AT1G01580.1; -1 araport11 gene 214150 217734 . + . ID=gene:AT1G01590;Name=FRO1;biotype=protein_coding;description=Probable ferric reduction oxidase 1 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LMM2];gene_id=AT1G01590;logic_name=araport11; -1 araport11 mRNA 214150 217734 . + . ID=transcript:AT1G01590.1;biotype=protein_coding;Parent=gene:AT1G01590;transcript_id=AT1G01590.1; -1 araport11 five_prime_UTR 214150 214228 . + . Parent=transcript:AT1G01590.1; -1 araport11 exon 214150 214406 . + . Name=AT1G01590.1.exon1;Parent=transcript:AT1G01590.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01590.1.exon1;rank=1; -1 araport11 CDS 214229 214406 . + 0 ID=CDS:AT1G01590.1;Parent=transcript:AT1G01590.1;protein_id=AT1G01590.1 -1 araport11 exon 214480 214582 . + . Name=AT1G01590.1.exon2;Parent=transcript:AT1G01590.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01590.1.exon2;rank=2; -1 araport11 CDS 214480 214582 . + 2 ID=CDS:AT1G01590.1;Parent=transcript:AT1G01590.1;protein_id=AT1G01590.1 -1 araport11 exon 214697 214897 . + . Name=AT1G01590.1.exon3;Parent=transcript:AT1G01590.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01590.1.exon3;rank=3; -1 araport11 CDS 214697 214897 . + 1 ID=CDS:AT1G01590.1;Parent=transcript:AT1G01590.1;protein_id=AT1G01590.1 -1 araport11 exon 215317 215554 . + . Name=AT1G01590.1.exon4;Parent=transcript:AT1G01590.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01590.1.exon4;rank=4; -1 araport11 CDS 215317 215554 . + 1 ID=CDS:AT1G01590.1;Parent=transcript:AT1G01590.1;protein_id=AT1G01590.1 -1 araport11 exon 215633 215960 . + . Name=AT1G01590.1.exon5;Parent=transcript:AT1G01590.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01590.1.exon5;rank=5; -1 araport11 CDS 215633 215960 . + 0 ID=CDS:AT1G01590.1;Parent=transcript:AT1G01590.1;protein_id=AT1G01590.1 -1 araport11 exon 216044 216293 . + . Name=AT1G01590.1.exon6;Parent=transcript:AT1G01590.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;exon_id=AT1G01590.1.exon6;rank=6; -1 araport11 CDS 216044 216293 . + 2 ID=CDS:AT1G01590.1;Parent=transcript:AT1G01590.1;protein_id=AT1G01590.1 -1 araport11 exon 216414 217090 . + . Name=AT1G01590.1.exon7;Parent=transcript:AT1G01590.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01590.1.exon7;rank=7; -1 araport11 CDS 216414 217090 . + 1 ID=CDS:AT1G01590.1;Parent=transcript:AT1G01590.1;protein_id=AT1G01590.1 -1 araport11 CDS 217165 217304 . + 2 ID=CDS:AT1G01590.1;Parent=transcript:AT1G01590.1;protein_id=AT1G01590.1 -1 araport11 exon 217165 217734 . + . Name=AT1G01590.1.exon8;Parent=transcript:AT1G01590.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01590.1.exon8;rank=8; -1 araport11 three_prime_UTR 217305 217734 . + . Parent=transcript:AT1G01590.1; -1 araport11 gene 218834 221286 . + . ID=gene:AT1G01600;Name=CYP86A4;biotype=protein_coding;description=Cytochrome P450 86A4 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LMM1];gene_id=AT1G01600;logic_name=araport11; -1 araport11 mRNA 218834 221286 . + . ID=transcript:AT1G01600.1;biotype=protein_coding;Parent=gene:AT1G01600;transcript_id=AT1G01600.1; -1 araport11 five_prime_UTR 218834 219199 . + . Parent=transcript:AT1G01600.1; -1 araport11 exon 218834 219621 . + . Name=AT1G01600.1.exon1;Parent=transcript:AT1G01600.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01600.1.exon1;rank=1; -1 araport11 CDS 219200 219621 . + 0 ID=CDS:AT1G01600.1;Parent=transcript:AT1G01600.1;protein_id=AT1G01600.1 -1 araport11 CDS 219752 220994 . + 1 ID=CDS:AT1G01600.1;Parent=transcript:AT1G01600.1;protein_id=AT1G01600.1 -1 araport11 exon 219752 221286 . + . Name=AT1G01600.1.exon2;Parent=transcript:AT1G01600.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01600.1.exon2;rank=2; -1 araport11 three_prime_UTR 220995 221286 . + . Parent=transcript:AT1G01600.1; -1 araport11 gene 221642 224351 . - . ID=gene:AT1G01610;Name=GPAT4;biotype=protein_coding;description=GPAT4 [Source:UniProtKB/TrEMBL%3bAcc:A0A178W9F8];gene_id=AT1G01610;logic_name=araport11; -1 araport11 mRNA 221642 224351 . - . ID=transcript:AT1G01610.1;biotype=protein_coding;Parent=gene:AT1G01610;transcript_id=AT1G01610.1; -1 araport11 three_prime_UTR 221642 221949 . - . Parent=transcript:AT1G01610.1; -1 araport11 exon 221642 222359 . - . Name=AT1G01610.1.exon4;Parent=transcript:AT1G01610.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01610.1.exon4;rank=4; -1 araport11 CDS 221950 222359 . - 2 ID=CDS:AT1G01610.1;Parent=transcript:AT1G01610.1;protein_id=AT1G01610.1 -1 araport11 exon 222622 223096 . - . Name=AT1G01610.1.exon3;Parent=transcript:AT1G01610.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01610.1.exon3;rank=3; -1 araport11 CDS 222622 223096 . - 0 ID=CDS:AT1G01610.1;Parent=transcript:AT1G01610.1;protein_id=AT1G01610.1 -1 araport11 exon 223551 223866 . - . Name=AT1G01610.1.exon2;Parent=transcript:AT1G01610.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01610.1.exon2;rank=2; -1 araport11 CDS 223551 223866 . - 1 ID=CDS:AT1G01610.1;Parent=transcript:AT1G01610.1;protein_id=AT1G01610.1 -1 araport11 CDS 223945 224255 . - 0 ID=CDS:AT1G01610.1;Parent=transcript:AT1G01610.1;protein_id=AT1G01610.1 -1 araport11 exon 223945 224351 . - . Name=AT1G01610.1.exon1;Parent=transcript:AT1G01610.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01610.1.exon1;rank=1; -1 araport11 five_prime_UTR 224256 224351 . - . Parent=transcript:AT1G01610.1; -1 araport11 gene 225665 227543 . - . ID=gene:AT1G01620;Name=PIP1-3;biotype=protein_coding;description=TMP-B [Source:UniProtKB/TrEMBL%3bAcc:A0A178WIA6];gene_id=AT1G01620;logic_name=araport11; -1 araport11 mRNA 225665 227302 . - . ID=transcript:AT1G01620.2;biotype=protein_coding;Parent=gene:AT1G01620;transcript_id=AT1G01620.2; -1 araport11 three_prime_UTR 225665 225985 . - . Parent=transcript:AT1G01620.2; -1 araport11 exon 225665 226081 . - . Name=AT1G01620.1.exon4;Parent=transcript:AT1G01620.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01620.1.exon4;rank=5; -1 araport11 CDS 225986 226081 . - 0 ID=CDS:AT1G01620.2;Parent=transcript:AT1G01620.2;protein_id=AT1G01620.2 -1 araport11 exon 226171 226311 . - . Name=AT1G01620.1.exon3;Parent=transcript:AT1G01620.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01620.1.exon3;rank=4; -1 araport11 CDS 226171 226311 . - 0 ID=CDS:AT1G01620.2;Parent=transcript:AT1G01620.2;protein_id=AT1G01620.2 -1 araport11 exon 226396 226691 . - . Name=AT1G01620.1.exon2;Parent=transcript:AT1G01620.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01620.1.exon2;rank=3; -1 araport11 CDS 226396 226691 . - 2 ID=CDS:AT1G01620.2;Parent=transcript:AT1G01620.2;protein_id=AT1G01620.2 -1 araport11 CDS 226849 226960 . - 0 ID=CDS:AT1G01620.2;Parent=transcript:AT1G01620.2;protein_id=AT1G01620.2 -1 araport11 exon 226849 227049 . - . Name=AT1G01620.2.exon2;Parent=transcript:AT1G01620.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01620.2.exon2;rank=2; -1 araport11 five_prime_UTR 226961 227049 . - . Parent=transcript:AT1G01620.2; -1 araport11 exon 227079 227302 . - . Name=AT1G01620.2.exon1;Parent=transcript:AT1G01620.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01620.2.exon1;rank=1; -1 araport11 five_prime_UTR 227079 227302 . - . Parent=transcript:AT1G01620.2; -1 araport11 mRNA 225665 227543 . - . ID=transcript:AT1G01620.1;biotype=protein_coding;Parent=gene:AT1G01620;transcript_id=AT1G01620.1; -1 araport11 three_prime_UTR 225665 225985 . - . Parent=transcript:AT1G01620.1; -1 araport11 exon 225665 226081 . - . Name=AT1G01620.1.exon4;Parent=transcript:AT1G01620.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01620.1.exon4;rank=4; -1 araport11 CDS 225986 226081 . - 0 ID=CDS:AT1G01620.1;Parent=transcript:AT1G01620.1;protein_id=AT1G01620.1 -1 araport11 exon 226171 226311 . - . Name=AT1G01620.1.exon3;Parent=transcript:AT1G01620.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01620.1.exon3;rank=3; -1 araport11 CDS 226171 226311 . - 0 ID=CDS:AT1G01620.1;Parent=transcript:AT1G01620.1;protein_id=AT1G01620.1 -1 araport11 exon 226396 226691 . - . Name=AT1G01620.1.exon2;Parent=transcript:AT1G01620.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01620.1.exon2;rank=2; -1 araport11 CDS 226396 226691 . - 2 ID=CDS:AT1G01620.1;Parent=transcript:AT1G01620.1;protein_id=AT1G01620.1 -1 araport11 CDS 226849 227176 . - 0 ID=CDS:AT1G01620.1;Parent=transcript:AT1G01620.1;protein_id=AT1G01620.1 -1 araport11 exon 226849 227543 . - . Name=AT1G01620.1.exon1;Parent=transcript:AT1G01620.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01620.1.exon1;rank=1; -1 araport11 five_prime_UTR 227177 227543 . - . Parent=transcript:AT1G01620.1; -1 araport11 gene 228799 230979 . + . ID=gene:AT1G01630;biotype=protein_coding;description=Polyphosphoinositide binding protein%2c putative [Source:UniProtKB/TrEMBL%3bAcc:Q9LQ96];gene_id=AT1G01630;logic_name=araport11; -1 araport11 mRNA 228799 230979 . + . ID=transcript:AT1G01630.1;biotype=protein_coding;Parent=gene:AT1G01630;transcript_id=AT1G01630.1; -1 araport11 five_prime_UTR 228799 229205 . + . Parent=transcript:AT1G01630.1; -1 araport11 exon 228799 229343 . + . Name=AT1G01630.1.exon1;Parent=transcript:AT1G01630.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01630.1.exon1;rank=1; -1 araport11 CDS 229206 229343 . + 0 ID=CDS:AT1G01630.1;Parent=transcript:AT1G01630.1;protein_id=AT1G01630.1 -1 araport11 exon 229429 229724 . + . Name=AT1G01630.1.exon2;Parent=transcript:AT1G01630.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01630.1.exon2;rank=2; -1 araport11 CDS 229429 229724 . + 0 ID=CDS:AT1G01630.1;Parent=transcript:AT1G01630.1;protein_id=AT1G01630.1 -1 araport11 exon 229829 229934 . + . Name=AT1G01630.1.exon3;Parent=transcript:AT1G01630.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01630.1.exon3;rank=3; -1 araport11 CDS 229829 229934 . + 1 ID=CDS:AT1G01630.1;Parent=transcript:AT1G01630.1;protein_id=AT1G01630.1 -1 araport11 exon 230349 230459 . + . Name=AT1G01630.1.exon4;Parent=transcript:AT1G01630.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01630.1.exon4;rank=4; -1 araport11 CDS 230349 230459 . + 0 ID=CDS:AT1G01630.1;Parent=transcript:AT1G01630.1;protein_id=AT1G01630.1 -1 araport11 CDS 230559 230675 . + 0 ID=CDS:AT1G01630.1;Parent=transcript:AT1G01630.1;protein_id=AT1G01630.1 -1 araport11 exon 230559 230979 . + . Name=AT1G01630.1.exon5;Parent=transcript:AT1G01630.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01630.1.exon5;rank=5; -1 araport11 three_prime_UTR 230676 230979 . + . Parent=transcript:AT1G01630.1; -1 araport11 gene 230908 232630 . - . ID=gene:AT1G01640;biotype=protein_coding;description=BTB/POZ domain-containing protein At1g01640 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LQ95];gene_id=AT1G01640;logic_name=araport11; -1 araport11 mRNA 230908 232630 . - . ID=transcript:AT1G01640.1;biotype=protein_coding;Parent=gene:AT1G01640;transcript_id=AT1G01640.1; -1 araport11 three_prime_UTR 230908 231163 . - . Parent=transcript:AT1G01640.1; -1 araport11 exon 230908 231655 . - . Name=AT1G01640.2.exon3;Parent=transcript:AT1G01640.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01640.2.exon3;rank=3; -1 araport11 CDS 231164 231655 . - 0 ID=CDS:AT1G01640.1;Parent=transcript:AT1G01640.1;protein_id=AT1G01640.1 -1 araport11 CDS 231784 231915 . - 0 ID=CDS:AT1G01640.1;Parent=transcript:AT1G01640.1;protein_id=AT1G01640.1 -1 araport11 exon 231784 231928 . - . Name=AT1G01640.1.exon2;Parent=transcript:AT1G01640.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01640.1.exon2;rank=2; -1 araport11 five_prime_UTR 231916 231928 . - . Parent=transcript:AT1G01640.1; -1 araport11 exon 232398 232630 . - . Name=AT1G01640.2.exon1;Parent=transcript:AT1G01640.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01640.2.exon1;rank=1; -1 araport11 five_prime_UTR 232398 232630 . - . Parent=transcript:AT1G01640.1; -1 araport11 mRNA 230908 232630 . - . ID=transcript:AT1G01640.2;biotype=protein_coding;Parent=gene:AT1G01640;transcript_id=AT1G01640.2; -1 araport11 three_prime_UTR 230908 231163 . - . Parent=transcript:AT1G01640.2; -1 araport11 exon 230908 231655 . - . Name=AT1G01640.2.exon3;Parent=transcript:AT1G01640.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01640.2.exon3;rank=3; -1 araport11 CDS 231164 231655 . - 0 ID=CDS:AT1G01640.2;Parent=transcript:AT1G01640.2;protein_id=AT1G01640.2 -1 araport11 CDS 231784 231852 . - 0 ID=CDS:AT1G01640.2;Parent=transcript:AT1G01640.2;protein_id=AT1G01640.2 -1 araport11 exon 231784 231908 . - . Name=AT1G01640.2.exon2;Parent=transcript:AT1G01640.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01640.2.exon2;rank=2; -1 araport11 five_prime_UTR 231853 231908 . - . Parent=transcript:AT1G01640.2; -1 araport11 exon 232398 232630 . - . Name=AT1G01640.2.exon1;Parent=transcript:AT1G01640.2;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01640.2.exon1;rank=1; -1 araport11 five_prime_UTR 232398 232630 . - . Parent=transcript:AT1G01640.2; -1 araport11 gene 232840 237905 . - . ID=gene:AT1G01650;Name=SPPL4;biotype=protein_coding;description=Signal peptide peptidase-like 4 [Source:UniProtKB/Swiss-Prot%3bAcc:Q0WMJ8];gene_id=AT1G01650;logic_name=araport11; -1 araport11 mRNA 232840 237905 . - . ID=transcript:AT1G01650.1;biotype=protein_coding;Parent=gene:AT1G01650;transcript_id=AT1G01650.1; -1 araport11 three_prime_UTR 232840 233187 . - . Parent=transcript:AT1G01650.1; -1 araport11 exon 232840 233297 . - . Name=AT1G01650.1.exon14;Parent=transcript:AT1G01650.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01650.1.exon14;rank=14; -1 araport11 CDS 233188 233297 . - 2 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 233387 233470 . - . Name=AT1G01650.2.exon12;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01650.2.exon12;rank=13; -1 araport11 CDS 233387 233470 . - 2 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 233548 233618 . - . Name=AT1G01650.2.exon11;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01650.2.exon11;rank=12; -1 araport11 CDS 233548 233618 . - 1 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 234250 234392 . - . Name=AT1G01650.2.exon10;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01650.2.exon10;rank=11; -1 araport11 CDS 234250 234392 . - 0 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 234529 234621 . - . Name=AT1G01650.2.exon9;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon9;rank=10; -1 araport11 CDS 234529 234621 . - 0 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 234935 234988 . - . Name=AT1G01650.2.exon8;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon8;rank=9; -1 araport11 CDS 234935 234988 . - 0 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 235198 235360 . - . Name=AT1G01650.2.exon7;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01650.2.exon7;rank=8; -1 araport11 CDS 235198 235360 . - 1 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 235718 235752 . - . Name=AT1G01650.2.exon6;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01650.2.exon6;rank=7; -1 araport11 CDS 235718 235752 . - 0 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 235845 236027 . - . Name=AT1G01650.2.exon5;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon5;rank=6; -1 araport11 CDS 235845 236027 . - 0 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 236145 236296 . - . Name=AT1G01650.2.exon4;Parent=transcript:AT1G01650.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01650.2.exon4;rank=5; -1 araport11 CDS 236145 236296 . - 2 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 236429 236548 . - . Name=AT1G01650.1.exon4;Parent=transcript:AT1G01650.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01650.1.exon4;rank=4; -1 araport11 CDS 236429 236548 . - 2 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 236673 236784 . - . Name=AT1G01650.1.exon3;Parent=transcript:AT1G01650.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01650.1.exon3;rank=3; -1 araport11 CDS 236673 236784 . - 0 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 236865 237023 . - . Name=AT1G01650.1.exon2;Parent=transcript:AT1G01650.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.1.exon2;rank=2; -1 araport11 CDS 236865 237023 . - 0 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 CDS 237504 237647 . - 0 ID=CDS:AT1G01650.1;Parent=transcript:AT1G01650.1;protein_id=AT1G01650.1 -1 araport11 exon 237504 237905 . - . Name=AT1G01650.1.exon1;Parent=transcript:AT1G01650.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01650.1.exon1;rank=1; -1 araport11 five_prime_UTR 237648 237905 . - . Parent=transcript:AT1G01650.1; -1 araport11 mRNA 232841 237817 . - . ID=transcript:AT1G01650.3;biotype=protein_coding;Parent=gene:AT1G01650;transcript_id=AT1G01650.3; -1 araport11 three_prime_UTR 232841 233187 . - . Parent=transcript:AT1G01650.3; -1 araport11 exon 232841 233297 . - . Name=AT1G01650.2.exon13;Parent=transcript:AT1G01650.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01650.2.exon13;rank=13; -1 araport11 CDS 233188 233297 . - 2 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 233387 233470 . - . Name=AT1G01650.2.exon12;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01650.2.exon12;rank=12; -1 araport11 CDS 233387 233470 . - 2 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 233548 233618 . - . Name=AT1G01650.2.exon11;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01650.2.exon11;rank=11; -1 araport11 CDS 233548 233618 . - 1 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 234250 234392 . - . Name=AT1G01650.2.exon10;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01650.2.exon10;rank=10; -1 araport11 CDS 234250 234392 . - 0 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 234529 234621 . - . Name=AT1G01650.2.exon9;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon9;rank=9; -1 araport11 CDS 234529 234621 . - 0 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 234935 234988 . - . Name=AT1G01650.2.exon8;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon8;rank=8; -1 araport11 CDS 234935 234988 . - 0 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 235198 235360 . - . Name=AT1G01650.2.exon7;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01650.2.exon7;rank=7; -1 araport11 CDS 235198 235360 . - 1 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 235718 235752 . - . Name=AT1G01650.2.exon6;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01650.2.exon6;rank=6; -1 araport11 CDS 235718 235752 . - 0 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 235845 236027 . - . Name=AT1G01650.2.exon5;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon5;rank=5; -1 araport11 CDS 235845 236027 . - 0 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 236145 236296 . - . Name=AT1G01650.2.exon4;Parent=transcript:AT1G01650.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01650.2.exon4;rank=4; -1 araport11 CDS 236145 236296 . - 2 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 CDS 236429 236537 . - 0 ID=CDS:AT1G01650.3;Parent=transcript:AT1G01650.3;protein_id=AT1G01650.3 -1 araport11 exon 236429 236548 . - . Name=AT1G01650.2.exon3;Parent=transcript:AT1G01650.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01650.2.exon3;rank=3; -1 araport11 five_prime_UTR 236538 236548 . - . Parent=transcript:AT1G01650.3; -1 araport11 exon 236673 237023 . - . Name=AT1G01650.4.exon2;Parent=transcript:AT1G01650.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01650.4.exon2;rank=2; -1 araport11 five_prime_UTR 236673 237023 . - . Parent=transcript:AT1G01650.3; -1 araport11 exon 237220 237817 . - . Name=AT1G01650.3.exon1;Parent=transcript:AT1G01650.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01650.3.exon1;rank=1; -1 araport11 five_prime_UTR 237220 237817 . - . Parent=transcript:AT1G01650.3; -1 araport11 mRNA 232841 237817 . - . ID=transcript:AT1G01650.4;biotype=protein_coding;Parent=gene:AT1G01650;transcript_id=AT1G01650.4; -1 araport11 three_prime_UTR 232841 233187 . - . Parent=transcript:AT1G01650.4; -1 araport11 exon 232841 233297 . - . Name=AT1G01650.2.exon13;Parent=transcript:AT1G01650.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01650.2.exon13;rank=13; -1 araport11 CDS 233188 233297 . - 2 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 233387 233470 . - . Name=AT1G01650.2.exon12;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01650.2.exon12;rank=12; -1 araport11 CDS 233387 233470 . - 2 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 233548 233618 . - . Name=AT1G01650.2.exon11;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01650.2.exon11;rank=11; -1 araport11 CDS 233548 233618 . - 1 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 234250 234392 . - . Name=AT1G01650.2.exon10;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01650.2.exon10;rank=10; -1 araport11 CDS 234250 234392 . - 0 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 234529 234621 . - . Name=AT1G01650.2.exon9;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon9;rank=9; -1 araport11 CDS 234529 234621 . - 0 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 234935 234988 . - . Name=AT1G01650.2.exon8;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon8;rank=8; -1 araport11 CDS 234935 234988 . - 0 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 235198 235360 . - . Name=AT1G01650.2.exon7;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01650.2.exon7;rank=7; -1 araport11 CDS 235198 235360 . - 1 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 235718 235752 . - . Name=AT1G01650.2.exon6;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01650.2.exon6;rank=6; -1 araport11 CDS 235718 235752 . - 0 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 235845 236027 . - . Name=AT1G01650.2.exon5;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon5;rank=5; -1 araport11 CDS 235845 236027 . - 0 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 236145 236296 . - . Name=AT1G01650.2.exon4;Parent=transcript:AT1G01650.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01650.2.exon4;rank=4; -1 araport11 CDS 236145 236296 . - 2 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 CDS 236429 236537 . - 0 ID=CDS:AT1G01650.4;Parent=transcript:AT1G01650.4;protein_id=AT1G01650.4 -1 araport11 exon 236429 236548 . - . Name=AT1G01650.2.exon3;Parent=transcript:AT1G01650.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01650.2.exon3;rank=3; -1 araport11 five_prime_UTR 236538 236548 . - . Parent=transcript:AT1G01650.4; -1 araport11 exon 236673 237023 . - . Name=AT1G01650.4.exon2;Parent=transcript:AT1G01650.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01650.4.exon2;rank=2; -1 araport11 five_prime_UTR 236673 237023 . - . Parent=transcript:AT1G01650.4; -1 araport11 exon 237504 237817 . - . Name=AT1G01650.2.exon1;Parent=transcript:AT1G01650.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01650.2.exon1;rank=1; -1 araport11 five_prime_UTR 237504 237817 . - . Parent=transcript:AT1G01650.4; -1 araport11 mRNA 232841 237817 . - . ID=transcript:AT1G01650.2;biotype=protein_coding;Parent=gene:AT1G01650;transcript_id=AT1G01650.2; -1 araport11 three_prime_UTR 232841 233187 . - . Parent=transcript:AT1G01650.2; -1 araport11 exon 232841 233297 . - . Name=AT1G01650.2.exon13;Parent=transcript:AT1G01650.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01650.2.exon13;rank=13; -1 araport11 CDS 233188 233297 . - 2 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 233387 233470 . - . Name=AT1G01650.2.exon12;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01650.2.exon12;rank=12; -1 araport11 CDS 233387 233470 . - 2 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 233548 233618 . - . Name=AT1G01650.2.exon11;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;exon_id=AT1G01650.2.exon11;rank=11; -1 araport11 CDS 233548 233618 . - 1 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 234250 234392 . - . Name=AT1G01650.2.exon10;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01650.2.exon10;rank=10; -1 araport11 CDS 234250 234392 . - 0 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 234529 234621 . - . Name=AT1G01650.2.exon9;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon9;rank=9; -1 araport11 CDS 234529 234621 . - 0 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 234935 234988 . - . Name=AT1G01650.2.exon8;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon8;rank=8; -1 araport11 CDS 234935 234988 . - 0 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 235198 235360 . - . Name=AT1G01650.2.exon7;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01650.2.exon7;rank=7; -1 araport11 CDS 235198 235360 . - 1 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 235718 235752 . - . Name=AT1G01650.2.exon6;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01650.2.exon6;rank=6; -1 araport11 CDS 235718 235752 . - 0 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 235845 236027 . - . Name=AT1G01650.2.exon5;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01650.2.exon5;rank=5; -1 araport11 CDS 235845 236027 . - 0 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 236145 236296 . - . Name=AT1G01650.2.exon4;Parent=transcript:AT1G01650.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01650.2.exon4;rank=4; -1 araport11 CDS 236145 236296 . - 2 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 CDS 236429 236537 . - 0 ID=CDS:AT1G01650.2;Parent=transcript:AT1G01650.2;protein_id=AT1G01650.2 -1 araport11 exon 236429 236548 . - . Name=AT1G01650.2.exon3;Parent=transcript:AT1G01650.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01650.2.exon3;rank=3; -1 araport11 five_prime_UTR 236538 236548 . - . Parent=transcript:AT1G01650.2; -1 araport11 exon 236673 237303 . - . Name=AT1G01650.2.exon2;Parent=transcript:AT1G01650.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01650.2.exon2;rank=2; -1 araport11 five_prime_UTR 236673 237303 . - . Parent=transcript:AT1G01650.2; -1 araport11 exon 237504 237817 . - . Name=AT1G01650.2.exon1;Parent=transcript:AT1G01650.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01650.2.exon1;rank=1; -1 araport11 five_prime_UTR 237504 237817 . - . Parent=transcript:AT1G01650.2; -1 araport11 ncRNA_gene 234006 234159 . - . ID=gene:AT1G04027;biotype=miRNA;gene_id=AT1G04027;logic_name=araport11; -1 araport11 miRNA 234006 234159 . - . ID=transcript:at1g04027;biotype=miRNA;Parent=gene:AT1G04027;transcript_id=at1g04027; -1 araport11 exon 234006 234159 . - . Name=at1g04027.exon;Parent=transcript:at1g04027;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=at1g04027.exon;rank=1; -1 araport11 gene 239841 242703 . - . ID=gene:AT1G01660;biotype=protein_coding;description=RING/U-box superfamily protein [Source:TAIR%3bAcc:AT1G01660];gene_id=AT1G01660;logic_name=araport11; -1 araport11 mRNA 239841 242703 . - . ID=transcript:AT1G01660.2;biotype=protein_coding;Parent=gene:AT1G01660;transcript_id=AT1G01660.2; -1 araport11 three_prime_UTR 239841 240056 . - . Parent=transcript:AT1G01660.2; -1 araport11 exon 239841 240242 . - . Name=AT1G01660.2.exon10;Parent=transcript:AT1G01660.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01660.2.exon10;rank=10; -1 araport11 CDS 240057 240242 . - 0 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 240352 240672 . - . Name=AT1G01660.1.exon9;Parent=transcript:AT1G01660.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01660.1.exon9;rank=9; -1 araport11 CDS 240352 240672 . - 0 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 240744 240892 . - . Name=AT1G01660.2.exon8;Parent=transcript:AT1G01660.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01660.2.exon8;rank=8; -1 araport11 CDS 240744 240892 . - 2 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 240965 241226 . - . Name=AT1G01660.2.exon7;Parent=transcript:AT1G01660.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01660.2.exon7;rank=7; -1 araport11 CDS 240965 241226 . - 0 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 241306 241443 . - . Name=AT1G01660.1.exon6;Parent=transcript:AT1G01660.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01660.1.exon6;rank=6; -1 araport11 CDS 241306 241443 . - 0 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 241539 241719 . - . Name=AT1G01660.1.exon5;Parent=transcript:AT1G01660.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01660.1.exon5;rank=5; -1 araport11 CDS 241539 241719 . - 1 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 241805 241909 . - . Name=AT1G01660.1.exon4;Parent=transcript:AT1G01660.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01660.1.exon4;rank=4; -1 araport11 CDS 241805 241909 . - 1 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 241983 242113 . - . Name=AT1G01660.1.exon3;Parent=transcript:AT1G01660.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01660.1.exon3;rank=3; -1 araport11 CDS 241983 242113 . - 0 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 242214 242290 . - . Name=AT1G01660.1.exon2;Parent=transcript:AT1G01660.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01660.1.exon2;rank=2; -1 araport11 CDS 242214 242290 . - 2 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 CDS 242449 242608 . - 0 ID=CDS:AT1G01660.2;Parent=transcript:AT1G01660.2;protein_id=AT1G01660.2 -1 araport11 exon 242449 242703 . - . Name=AT1G01660.2.exon1;Parent=transcript:AT1G01660.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01660.2.exon1;rank=1; -1 araport11 five_prime_UTR 242609 242703 . - . Parent=transcript:AT1G01660.2; -1 araport11 mRNA 240057 242608 . - . ID=transcript:AT1G01660.1;biotype=protein_coding;Parent=gene:AT1G01660;transcript_id=AT1G01660.1; -1 araport11 exon 240057 240242 . - . Name=AT1G01660.1.exon10;Parent=transcript:AT1G01660.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01660.1.exon10;rank=10; -1 araport11 CDS 240057 240242 . - 0 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 240352 240672 . - . Name=AT1G01660.1.exon9;Parent=transcript:AT1G01660.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01660.1.exon9;rank=9; -1 araport11 CDS 240352 240672 . - 0 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 240744 240884 . - . Name=AT1G01660.1.exon8;Parent=transcript:AT1G01660.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01660.1.exon8;rank=8; -1 araport11 CDS 240744 240884 . - 0 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 240960 241226 . - . Name=AT1G01660.1.exon7;Parent=transcript:AT1G01660.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01660.1.exon7;rank=7; -1 araport11 CDS 240960 241226 . - 0 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 241306 241443 . - . Name=AT1G01660.1.exon6;Parent=transcript:AT1G01660.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01660.1.exon6;rank=6; -1 araport11 CDS 241306 241443 . - 0 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 241539 241719 . - . Name=AT1G01660.1.exon5;Parent=transcript:AT1G01660.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01660.1.exon5;rank=5; -1 araport11 CDS 241539 241719 . - 1 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 241805 241909 . - . Name=AT1G01660.1.exon4;Parent=transcript:AT1G01660.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01660.1.exon4;rank=4; -1 araport11 CDS 241805 241909 . - 1 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 241983 242113 . - . Name=AT1G01660.1.exon3;Parent=transcript:AT1G01660.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01660.1.exon3;rank=3; -1 araport11 CDS 241983 242113 . - 0 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 242214 242290 . - . Name=AT1G01660.1.exon2;Parent=transcript:AT1G01660.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01660.1.exon2;rank=2; -1 araport11 CDS 242214 242290 . - 2 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 exon 242449 242608 . - . Name=AT1G01660.1.exon1;Parent=transcript:AT1G01660.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01660.1.exon1;rank=1; -1 araport11 CDS 242449 242608 . - 0 ID=CDS:AT1G01660.1;Parent=transcript:AT1G01660.1;protein_id=AT1G01660.1 -1 araport11 gene 242713 246054 . - . ID=gene:AT1G01670;Name=PUB56;biotype=protein_coding;description=U-box domain-containing protein 56 [Source:UniProtKB/Swiss-Prot%3bAcc:Q8GXQ7];gene_id=AT1G01670;logic_name=araport11; -1 araport11 mRNA 242713 246054 . - . ID=transcript:AT1G01670.1;biotype=protein_coding;Parent=gene:AT1G01670;transcript_id=AT1G01670.1; -1 araport11 three_prime_UTR 242713 242942 . - . Parent=transcript:AT1G01670.1; -1 araport11 exon 242713 243128 . - . Name=AT1G01670.1.exon8;Parent=transcript:AT1G01670.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01670.1.exon8;rank=8; -1 araport11 CDS 242943 243128 . - 0 ID=CDS:AT1G01670.1;Parent=transcript:AT1G01670.1;protein_id=AT1G01670.1 -1 araport11 exon 243336 243746 . - . Name=AT1G01670.1.exon7;Parent=transcript:AT1G01670.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01670.1.exon7;rank=7; -1 araport11 CDS 243336 243746 . - 0 ID=CDS:AT1G01670.1;Parent=transcript:AT1G01670.1;protein_id=AT1G01670.1 -1 araport11 exon 244035 244182 . - . Name=AT1G01670.1.exon6;Parent=transcript:AT1G01670.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01670.1.exon6;rank=6; -1 araport11 CDS 244035 244182 . - 1 ID=CDS:AT1G01670.1;Parent=transcript:AT1G01670.1;protein_id=AT1G01670.1 -1 araport11 exon 244257 244361 . - . Name=AT1G01670.1.exon5;Parent=transcript:AT1G01670.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01670.1.exon5;rank=5; -1 araport11 CDS 244257 244361 . - 1 ID=CDS:AT1G01670.1;Parent=transcript:AT1G01670.1;protein_id=AT1G01670.1 -1 araport11 exon 244505 244635 . - . Name=AT1G01670.1.exon4;Parent=transcript:AT1G01670.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01670.1.exon4;rank=4; -1 araport11 CDS 244505 244635 . - 0 ID=CDS:AT1G01670.1;Parent=transcript:AT1G01670.1;protein_id=AT1G01670.1 -1 araport11 exon 244770 244873 . - . Name=AT1G01670.1.exon3;Parent=transcript:AT1G01670.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01670.1.exon3;rank=3; -1 araport11 CDS 244770 244873 . - 2 ID=CDS:AT1G01670.1;Parent=transcript:AT1G01670.1;protein_id=AT1G01670.1 -1 araport11 CDS 245151 245163 . - 0 ID=CDS:AT1G01670.1;Parent=transcript:AT1G01670.1;protein_id=AT1G01670.1 -1 araport11 exon 245151 245264 . - . Name=AT1G01670.1.exon2;Parent=transcript:AT1G01670.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01670.1.exon2;rank=2; -1 araport11 five_prime_UTR 245164 245264 . - . Parent=transcript:AT1G01670.1; -1 araport11 exon 245877 246054 . - . Name=AT1G01670.1.exon1;Parent=transcript:AT1G01670.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01670.1.exon1;rank=1; -1 araport11 five_prime_UTR 245877 246054 . - . Parent=transcript:AT1G01670.1; -1 araport11 mRNA 242837 245676 . - . ID=transcript:AT1G01670.2;biotype=protein_coding;Parent=gene:AT1G01670;transcript_id=AT1G01670.2; -1 araport11 three_prime_UTR 242837 242942 . - . Parent=transcript:AT1G01670.2; -1 araport11 exon 242837 243128 . - . Name=AT1G01670.2.exon8;Parent=transcript:AT1G01670.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01670.2.exon8;rank=8; -1 araport11 CDS 242943 243128 . - 0 ID=CDS:AT1G01670.2;Parent=transcript:AT1G01670.2;protein_id=AT1G01670.2 -1 araport11 exon 243336 243746 . - . Name=AT1G01670.1.exon7;Parent=transcript:AT1G01670.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01670.1.exon7;rank=7; -1 araport11 CDS 243336 243746 . - 0 ID=CDS:AT1G01670.2;Parent=transcript:AT1G01670.2;protein_id=AT1G01670.2 -1 araport11 exon 244035 244182 . - . Name=AT1G01670.1.exon6;Parent=transcript:AT1G01670.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01670.1.exon6;rank=6; -1 araport11 CDS 244035 244182 . - 1 ID=CDS:AT1G01670.2;Parent=transcript:AT1G01670.2;protein_id=AT1G01670.2 -1 araport11 exon 244257 244361 . - . Name=AT1G01670.1.exon5;Parent=transcript:AT1G01670.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01670.1.exon5;rank=5; -1 araport11 CDS 244257 244361 . - 1 ID=CDS:AT1G01670.2;Parent=transcript:AT1G01670.2;protein_id=AT1G01670.2 -1 araport11 exon 244505 244635 . - . Name=AT1G01670.1.exon4;Parent=transcript:AT1G01670.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01670.1.exon4;rank=4; -1 araport11 CDS 244505 244635 . - 0 ID=CDS:AT1G01670.2;Parent=transcript:AT1G01670.2;protein_id=AT1G01670.2 -1 araport11 exon 244770 244873 . - . Name=AT1G01670.1.exon3;Parent=transcript:AT1G01670.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01670.1.exon3;rank=3; -1 araport11 CDS 244770 244873 . - 2 ID=CDS:AT1G01670.2;Parent=transcript:AT1G01670.2;protein_id=AT1G01670.2 -1 araport11 CDS 245151 245163 . - 0 ID=CDS:AT1G01670.2;Parent=transcript:AT1G01670.2;protein_id=AT1G01670.2 -1 araport11 exon 245151 245264 . - . Name=AT1G01670.1.exon2;Parent=transcript:AT1G01670.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01670.1.exon2;rank=2; -1 araport11 five_prime_UTR 245164 245264 . - . Parent=transcript:AT1G01670.2; -1 araport11 exon 245630 245676 . - . Name=AT1G01670.2.exon1;Parent=transcript:AT1G01670.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01670.2.exon1;rank=1; -1 araport11 five_prime_UTR 245630 245676 . - . Parent=transcript:AT1G01670.2; -1 araport11 mRNA 242843 244400 . - . ID=transcript:AT1G01670.3;biotype=protein_coding;Parent=gene:AT1G01670;transcript_id=AT1G01670.3; -1 araport11 three_prime_UTR 242843 242942 . - . Parent=transcript:AT1G01670.3; -1 araport11 exon 242843 243128 . - . Name=AT1G01670.3.exon4;Parent=transcript:AT1G01670.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01670.3.exon4;rank=4; -1 araport11 CDS 242943 243128 . - 0 ID=CDS:AT1G01670.3;Parent=transcript:AT1G01670.3;protein_id=AT1G01670.3 -1 araport11 exon 243336 243746 . - . Name=AT1G01670.1.exon7;Parent=transcript:AT1G01670.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01670.1.exon7;rank=3; -1 araport11 CDS 243336 243746 . - 0 ID=CDS:AT1G01670.3;Parent=transcript:AT1G01670.3;protein_id=AT1G01670.3 -1 araport11 exon 244035 244182 . - . Name=AT1G01670.1.exon6;Parent=transcript:AT1G01670.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01670.1.exon6;rank=2; -1 araport11 CDS 244035 244182 . - 1 ID=CDS:AT1G01670.3;Parent=transcript:AT1G01670.3;protein_id=AT1G01670.3 -1 araport11 CDS 244257 244357 . - 0 ID=CDS:AT1G01670.3;Parent=transcript:AT1G01670.3;protein_id=AT1G01670.3 -1 araport11 exon 244257 244400 . - . Name=AT1G01670.3.exon1;Parent=transcript:AT1G01670.3;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01670.3.exon1;rank=1; -1 araport11 five_prime_UTR 244358 244400 . - . Parent=transcript:AT1G01670.3; -1 araport11 gene 246262 248440 . - . ID=gene:AT1G01680;Name=PUB54;biotype=protein_coding;description=U-box domain-containing protein 54 [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LQ92];gene_id=AT1G01680;logic_name=araport11; -1 araport11 mRNA 246262 248440 . - . ID=transcript:AT1G01680.1;biotype=protein_coding;Parent=gene:AT1G01680;transcript_id=AT1G01680.1; -1 araport11 three_prime_UTR 246262 246410 . - . Parent=transcript:AT1G01680.1; -1 araport11 exon 246262 246608 . - . Name=AT1G01680.1.exon7;Parent=transcript:AT1G01680.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01680.1.exon7;rank=7; -1 araport11 CDS 246411 246608 . - 0 ID=CDS:AT1G01680.1;Parent=transcript:AT1G01680.1;protein_id=AT1G01680.1 -1 araport11 exon 246731 246853 . - . Name=AT1G01680.1.exon6;Parent=transcript:AT1G01680.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01680.1.exon6;rank=6; -1 araport11 CDS 246731 246853 . - 0 ID=CDS:AT1G01680.1;Parent=transcript:AT1G01680.1;protein_id=AT1G01680.1 -1 araport11 exon 246949 247078 . - . Name=AT1G01680.1.exon5;Parent=transcript:AT1G01680.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01680.1.exon5;rank=5; -1 araport11 CDS 246949 247078 . - 1 ID=CDS:AT1G01680.1;Parent=transcript:AT1G01680.1;protein_id=AT1G01680.1 -1 araport11 exon 247167 247268 . - . Name=AT1G01680.1.exon4;Parent=transcript:AT1G01680.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01680.1.exon4;rank=4; -1 araport11 CDS 247167 247268 . - 1 ID=CDS:AT1G01680.1;Parent=transcript:AT1G01680.1;protein_id=AT1G01680.1 -1 araport11 exon 247362 247492 . - . Name=AT1G01680.1.exon3;Parent=transcript:AT1G01680.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01680.1.exon3;rank=3; -1 araport11 CDS 247362 247492 . - 0 ID=CDS:AT1G01680.1;Parent=transcript:AT1G01680.1;protein_id=AT1G01680.1 -1 araport11 exon 247577 247680 . - . Name=AT1G01680.1.exon2;Parent=transcript:AT1G01680.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01680.1.exon2;rank=2; -1 araport11 CDS 247577 247680 . - 2 ID=CDS:AT1G01680.1;Parent=transcript:AT1G01680.1;protein_id=AT1G01680.1 -1 araport11 CDS 248191 248329 . - 0 ID=CDS:AT1G01680.1;Parent=transcript:AT1G01680.1;protein_id=AT1G01680.1 -1 araport11 exon 248191 248440 . - . Name=AT1G01680.1.exon1;Parent=transcript:AT1G01680.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01680.1.exon1;rank=1; -1 araport11 five_prime_UTR 248330 248440 . - . Parent=transcript:AT1G01680.1; -1 araport11 gene 249041 252522 . + . ID=gene:AT1G01690;Name=ATPRD3;biotype=protein_coding;description=Putative recombination initiation defects 3 [Source:UniProtKB/TrEMBL%3bAcc:F4HU48];gene_id=AT1G01690;logic_name=araport11; -1 araport11 mRNA 249041 252522 . + . ID=transcript:AT1G01690.2;biotype=protein_coding;Parent=gene:AT1G01690;transcript_id=AT1G01690.2; -1 araport11 five_prime_UTR 249041 249241 . + . Parent=transcript:AT1G01690.2; -1 araport11 exon 249041 249306 . + . Name=AT1G01690.2.exon1;Parent=transcript:AT1G01690.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01690.2.exon1;rank=1; -1 araport11 CDS 249242 249306 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 249543 249693 . + . Name=AT1G01690.2.exon2;Parent=transcript:AT1G01690.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01690.2.exon2;rank=2; -1 araport11 CDS 249543 249693 . + 1 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 249774 249930 . + . Name=AT1G01690.2.exon3;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01690.2.exon3;rank=3; -1 araport11 CDS 249774 249930 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 250014 250151 . + . Name=AT1G01690.2.exon4;Parent=transcript:AT1G01690.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01690.2.exon4;rank=4; -1 araport11 CDS 250014 250151 . + 2 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 250536 250588 . + . Name=AT1G01690.2.exon5;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01690.2.exon5;rank=5; -1 araport11 CDS 250536 250588 . + 2 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 250669 250863 . + . Name=AT1G01690.2.exon6;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon6;rank=6; -1 araport11 CDS 250669 250863 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 251004 251066 . + . Name=AT1G01690.2.exon7;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon7;rank=7; -1 araport11 CDS 251004 251066 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 251143 251184 . + . Name=AT1G01690.2.exon8;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon8;rank=8; -1 araport11 CDS 251143 251184 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 251260 251316 . + . Name=AT1G01690.2.exon9;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon9;rank=9; -1 araport11 CDS 251260 251316 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 251399 251440 . + . Name=AT1G01690.2.exon10;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon10;rank=10; -1 araport11 CDS 251399 251440 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 251539 251594 . + . Name=AT1G01690.2.exon11;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01690.2.exon11;rank=11; -1 araport11 CDS 251539 251594 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 251680 251827 . + . Name=AT1G01690.2.exon12;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01690.2.exon12;rank=12; -1 araport11 CDS 251680 251827 . + 1 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 251922 252006 . + . Name=AT1G01690.2.exon13;Parent=transcript:AT1G01690.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01690.2.exon13;rank=13; -1 araport11 CDS 251922 252006 . + 0 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 CDS 252121 252221 . + 2 ID=CDS:AT1G01690.2;Parent=transcript:AT1G01690.2;protein_id=AT1G01690.2 -1 araport11 exon 252121 252522 . + . Name=AT1G01690.2.exon14;Parent=transcript:AT1G01690.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01690.2.exon14;rank=14; -1 araport11 three_prime_UTR 252222 252522 . + . Parent=transcript:AT1G01690.2; -1 araport11 mRNA 249081 252462 . + . ID=transcript:AT1G01690.1;biotype=protein_coding;Parent=gene:AT1G01690;transcript_id=AT1G01690.1; -1 araport11 five_prime_UTR 249081 249241 . + . Parent=transcript:AT1G01690.1; -1 araport11 exon 249081 249306 . + . Name=AT1G01690.1.exon1;Parent=transcript:AT1G01690.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01690.1.exon1;rank=1; -1 araport11 CDS 249242 249306 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 249540 249693 . + . Name=AT1G01690.3.exon2;Parent=transcript:AT1G01690.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01690.3.exon2;rank=2; -1 araport11 CDS 249540 249693 . + 1 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 249774 249930 . + . Name=AT1G01690.2.exon3;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01690.2.exon3;rank=3; -1 araport11 CDS 249774 249930 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 250014 250151 . + . Name=AT1G01690.2.exon4;Parent=transcript:AT1G01690.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01690.2.exon4;rank=4; -1 araport11 CDS 250014 250151 . + 2 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 250536 250588 . + . Name=AT1G01690.2.exon5;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01690.2.exon5;rank=5; -1 araport11 CDS 250536 250588 . + 2 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 250669 250863 . + . Name=AT1G01690.2.exon6;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon6;rank=6; -1 araport11 CDS 250669 250863 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 251004 251066 . + . Name=AT1G01690.2.exon7;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon7;rank=7; -1 araport11 CDS 251004 251066 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 251143 251184 . + . Name=AT1G01690.2.exon8;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon8;rank=8; -1 araport11 CDS 251143 251184 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 251260 251316 . + . Name=AT1G01690.2.exon9;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon9;rank=9; -1 araport11 CDS 251260 251316 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 251399 251440 . + . Name=AT1G01690.2.exon10;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon10;rank=10; -1 araport11 CDS 251399 251440 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 251539 251594 . + . Name=AT1G01690.2.exon11;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01690.2.exon11;rank=11; -1 araport11 CDS 251539 251594 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 251680 251827 . + . Name=AT1G01690.2.exon12;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01690.2.exon12;rank=12; -1 araport11 CDS 251680 251827 . + 1 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 251922 252006 . + . Name=AT1G01690.2.exon13;Parent=transcript:AT1G01690.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01690.2.exon13;rank=13; -1 araport11 CDS 251922 252006 . + 0 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 CDS 252121 252221 . + 2 ID=CDS:AT1G01690.1;Parent=transcript:AT1G01690.1;protein_id=AT1G01690.1 -1 araport11 exon 252121 252462 . + . Name=AT1G01690.3.exon14;Parent=transcript:AT1G01690.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01690.3.exon14;rank=14; -1 araport11 three_prime_UTR 252222 252462 . + . Parent=transcript:AT1G01690.1; -1 araport11 mRNA 249141 252462 . + . ID=transcript:AT1G01690.3;biotype=protein_coding;Parent=gene:AT1G01690;transcript_id=AT1G01690.3; -1 araport11 five_prime_UTR 249141 249241 . + . Parent=transcript:AT1G01690.3; -1 araport11 exon 249141 249306 . + . Name=AT1G01690.3.exon1;Parent=transcript:AT1G01690.3;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01690.3.exon1;rank=1; -1 araport11 CDS 249242 249306 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 249540 249693 . + . Name=AT1G01690.3.exon2;Parent=transcript:AT1G01690.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01690.3.exon2;rank=2; -1 araport11 CDS 249540 249693 . + 1 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 249774 249930 . + . Name=AT1G01690.2.exon3;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01690.2.exon3;rank=3; -1 araport11 CDS 249774 249930 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 250017 250151 . + . Name=AT1G01690.3.exon4;Parent=transcript:AT1G01690.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01690.3.exon4;rank=4; -1 araport11 CDS 250017 250151 . + 2 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 250536 250588 . + . Name=AT1G01690.2.exon5;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01690.2.exon5;rank=5; -1 araport11 CDS 250536 250588 . + 2 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 250669 250863 . + . Name=AT1G01690.2.exon6;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon6;rank=6; -1 araport11 CDS 250669 250863 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 251004 251066 . + . Name=AT1G01690.2.exon7;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon7;rank=7; -1 araport11 CDS 251004 251066 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 251143 251184 . + . Name=AT1G01690.2.exon8;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon8;rank=8; -1 araport11 CDS 251143 251184 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 251260 251316 . + . Name=AT1G01690.2.exon9;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon9;rank=9; -1 araport11 CDS 251260 251316 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 251399 251440 . + . Name=AT1G01690.2.exon10;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01690.2.exon10;rank=10; -1 araport11 CDS 251399 251440 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 251539 251594 . + . Name=AT1G01690.2.exon11;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01690.2.exon11;rank=11; -1 araport11 CDS 251539 251594 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 251680 251827 . + . Name=AT1G01690.2.exon12;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01690.2.exon12;rank=12; -1 araport11 CDS 251680 251827 . + 1 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 251922 252006 . + . Name=AT1G01690.2.exon13;Parent=transcript:AT1G01690.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01690.2.exon13;rank=13; -1 araport11 CDS 251922 252006 . + 0 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 CDS 252121 252221 . + 2 ID=CDS:AT1G01690.3;Parent=transcript:AT1G01690.3;protein_id=AT1G01690.3 -1 araport11 exon 252121 252462 . + . Name=AT1G01690.3.exon14;Parent=transcript:AT1G01690.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01690.3.exon14;rank=14; -1 araport11 three_prime_UTR 252222 252462 . + . Parent=transcript:AT1G01690.3; -1 araport11 gene 252626 254530 . + . ID=gene:AT1G01695;biotype=protein_coding;description=TRM33 [Source:UniProtKB/TrEMBL%3bAcc:A0A178WAP9];gene_id=AT1G01695;logic_name=araport11; -1 araport11 mRNA 252626 254530 . + . ID=transcript:AT1G01695.1;biotype=protein_coding;Parent=gene:AT1G01695;transcript_id=AT1G01695.1; -1 araport11 five_prime_UTR 252626 252946 . + . Parent=transcript:AT1G01695.1; -1 araport11 exon 252626 253457 . + . Name=AT1G01695.1.exon1;Parent=transcript:AT1G01695.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01695.1.exon1;rank=1; -1 araport11 CDS 252947 253457 . + 0 ID=CDS:AT1G01695.1;Parent=transcript:AT1G01695.1;protein_id=AT1G01695.1 -1 araport11 exon 253531 253679 . + . Name=AT1G01695.1.exon2;Parent=transcript:AT1G01695.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01695.1.exon2;rank=2; -1 araport11 CDS 253531 253679 . + 2 ID=CDS:AT1G01695.1;Parent=transcript:AT1G01695.1;protein_id=AT1G01695.1 -1 araport11 exon 253775 253874 . + . Name=AT1G01695.1.exon3;Parent=transcript:AT1G01695.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01695.1.exon3;rank=3; -1 araport11 CDS 253775 253874 . + 0 ID=CDS:AT1G01695.1;Parent=transcript:AT1G01695.1;protein_id=AT1G01695.1 -1 araport11 CDS 253954 254495 . + 2 ID=CDS:AT1G01695.1;Parent=transcript:AT1G01695.1;protein_id=AT1G01695.1 -1 araport11 exon 253954 254530 . + . Name=AT1G01695.1.exon4;Parent=transcript:AT1G01695.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01695.1.exon4;rank=4; -1 araport11 three_prime_UTR 254496 254530 . + . Parent=transcript:AT1G01695.1; -1 araport11 ncRNA_gene 255022 255384 . + . ID=gene:AT1G04033;biotype=lncRNA;gene_id=AT1G04033;logic_name=araport11; -1 araport11 lnc_RNA 255022 255384 . + . ID=transcript:AT1G04033.1;biotype=lncRNA;Parent=gene:AT1G04033;transcript_id=AT1G04033.1; -1 araport11 exon 255022 255384 . + . Name=AT1G04033.1.exon1;Parent=transcript:AT1G04033.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04033.1.exon1;rank=1; -1 araport11 ncRNA_gene 258717 258963 . - . ID=gene:AT1G04037;biotype=lncRNA;gene_id=AT1G04037;logic_name=araport11; -1 araport11 lnc_RNA 258717 258963 . - . ID=transcript:AT1G04037.1;biotype=lncRNA;Parent=gene:AT1G04037;transcript_id=AT1G04037.1; -1 araport11 exon 258717 258963 . - . Name=AT1G04037.1.exon1;Parent=transcript:AT1G04037.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04037.1.exon1;rank=1; -1 araport11 gene 259307 261667 . - . ID=gene:AT1G01700;Name=ATROPGEF2;biotype=protein_coding;description=RHO guanyl-nucleotide exchange factor 2 [Source:TAIR%3bAcc:AT1G01700];gene_id=AT1G01700;logic_name=araport11; -1 araport11 mRNA 259307 261667 . - . ID=transcript:AT1G01700.1;biotype=protein_coding;Parent=gene:AT1G01700;transcript_id=AT1G01700.1; -1 araport11 three_prime_UTR 259307 259494 . - . Parent=transcript:AT1G01700.1; -1 araport11 exon 259307 259614 . - . Name=AT1G01700.1.exon7;Parent=transcript:AT1G01700.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01700.1.exon7;rank=7; -1 araport11 CDS 259495 259614 . - 0 ID=CDS:AT1G01700.1;Parent=transcript:AT1G01700.1;protein_id=AT1G01700.1 -1 araport11 exon 259690 260034 . - . Name=AT1G01700.4.exon5;Parent=transcript:AT1G01700.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.4.exon5;rank=6; -1 araport11 CDS 259690 260034 . - 0 ID=CDS:AT1G01700.1;Parent=transcript:AT1G01700.1;protein_id=AT1G01700.1 -1 araport11 exon 260118 260417 . - . Name=AT1G01700.1.exon5;Parent=transcript:AT1G01700.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.1.exon5;rank=5; -1 araport11 CDS 260118 260417 . - 0 ID=CDS:AT1G01700.1;Parent=transcript:AT1G01700.1;protein_id=AT1G01700.1 -1 araport11 exon 260508 260582 . - . Name=AT1G01700.1.exon4;Parent=transcript:AT1G01700.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.1.exon4;rank=4; -1 araport11 CDS 260508 260582 . - 0 ID=CDS:AT1G01700.1;Parent=transcript:AT1G01700.1;protein_id=AT1G01700.1 -1 araport11 exon 260670 260824 . - . Name=AT1G01700.4.exon3;Parent=transcript:AT1G01700.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01700.4.exon3;rank=3; -1 araport11 CDS 260670 260824 . - 2 ID=CDS:AT1G01700.1;Parent=transcript:AT1G01700.1;protein_id=AT1G01700.1 -1 araport11 exon 260921 261037 . - . Name=AT1G01700.4.exon2;Parent=transcript:AT1G01700.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01700.4.exon2;rank=2; -1 araport11 CDS 260921 261037 . - 2 ID=CDS:AT1G01700.1;Parent=transcript:AT1G01700.1;protein_id=AT1G01700.1 -1 araport11 CDS 261129 261474 . - 0 ID=CDS:AT1G01700.1;Parent=transcript:AT1G01700.1;protein_id=AT1G01700.1 -1 araport11 exon 261129 261667 . - . Name=AT1G01700.1.exon1;Parent=transcript:AT1G01700.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01700.1.exon1;rank=1; -1 araport11 five_prime_UTR 261475 261667 . - . Parent=transcript:AT1G01700.1; -1 araport11 mRNA 259307 261667 . - . ID=transcript:AT1G01700.2;biotype=protein_coding;Parent=gene:AT1G01700;transcript_id=AT1G01700.2; -1 araport11 exon 259307 259614 . - . Name=AT1G01700.2.exon6;Parent=transcript:AT1G01700.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01700.2.exon6;rank=6; -1 araport11 three_prime_UTR 259307 259614 . - . Parent=transcript:AT1G01700.2; -1 araport11 three_prime_UTR 259690 259991 . - . Parent=transcript:AT1G01700.2; -1 araport11 exon 259690 260417 . - . Name=AT1G01700.2.exon5;Parent=transcript:AT1G01700.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01700.2.exon5;rank=5; -1 araport11 CDS 259992 260417 . - 0 ID=CDS:AT1G01700.2;Parent=transcript:AT1G01700.2;protein_id=AT1G01700.2 -1 araport11 exon 260508 260582 . - . Name=AT1G01700.1.exon4;Parent=transcript:AT1G01700.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.1.exon4;rank=4; -1 araport11 CDS 260508 260582 . - 0 ID=CDS:AT1G01700.2;Parent=transcript:AT1G01700.2;protein_id=AT1G01700.2 -1 araport11 exon 260670 260824 . - . Name=AT1G01700.4.exon3;Parent=transcript:AT1G01700.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01700.4.exon3;rank=3; -1 araport11 CDS 260670 260824 . - 2 ID=CDS:AT1G01700.2;Parent=transcript:AT1G01700.2;protein_id=AT1G01700.2 -1 araport11 exon 260921 261037 . - . Name=AT1G01700.4.exon2;Parent=transcript:AT1G01700.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01700.4.exon2;rank=2; -1 araport11 CDS 260921 261037 . - 2 ID=CDS:AT1G01700.2;Parent=transcript:AT1G01700.2;protein_id=AT1G01700.2 -1 araport11 CDS 261129 261474 . - 0 ID=CDS:AT1G01700.2;Parent=transcript:AT1G01700.2;protein_id=AT1G01700.2 -1 araport11 exon 261129 261667 . - . Name=AT1G01700.1.exon1;Parent=transcript:AT1G01700.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01700.1.exon1;rank=1; -1 araport11 five_prime_UTR 261475 261667 . - . Parent=transcript:AT1G01700.2; -1 araport11 mRNA 259486 261474 . - . ID=transcript:AT1G01700.3;biotype=protein_coding;Parent=gene:AT1G01700;transcript_id=AT1G01700.3; -1 araport11 three_prime_UTR 259486 259662 . - . Parent=transcript:AT1G01700.3; -1 araport11 exon 259486 260034 . - . Name=AT1G01700.3.exon6;Parent=transcript:AT1G01700.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01700.3.exon6;rank=6; -1 araport11 CDS 259663 260034 . - 0 ID=CDS:AT1G01700.3;Parent=transcript:AT1G01700.3;protein_id=AT1G01700.3 -1 araport11 exon 260118 260417 . - . Name=AT1G01700.1.exon5;Parent=transcript:AT1G01700.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.1.exon5;rank=5; -1 araport11 CDS 260118 260417 . - 0 ID=CDS:AT1G01700.3;Parent=transcript:AT1G01700.3;protein_id=AT1G01700.3 -1 araport11 exon 260508 260603 . - . Name=AT1G01700.3.exon4;Parent=transcript:AT1G01700.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.3.exon4;rank=4; -1 araport11 CDS 260508 260603 . - 0 ID=CDS:AT1G01700.3;Parent=transcript:AT1G01700.3;protein_id=AT1G01700.3 -1 araport11 exon 260670 260824 . - . Name=AT1G01700.4.exon3;Parent=transcript:AT1G01700.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01700.4.exon3;rank=3; -1 araport11 CDS 260670 260824 . - 2 ID=CDS:AT1G01700.3;Parent=transcript:AT1G01700.3;protein_id=AT1G01700.3 -1 araport11 exon 260921 261037 . - . Name=AT1G01700.4.exon2;Parent=transcript:AT1G01700.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01700.4.exon2;rank=2; -1 araport11 CDS 260921 261037 . - 2 ID=CDS:AT1G01700.3;Parent=transcript:AT1G01700.3;protein_id=AT1G01700.3 -1 araport11 exon 261129 261474 . - . Name=AT1G01700.3.exon1;Parent=transcript:AT1G01700.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01700.3.exon1;rank=1; -1 araport11 CDS 261129 261474 . - 0 ID=CDS:AT1G01700.3;Parent=transcript:AT1G01700.3;protein_id=AT1G01700.3 -1 araport11 mRNA 259495 261615 . - . ID=transcript:AT1G01700.4;biotype=protein_coding;Parent=gene:AT1G01700;transcript_id=AT1G01700.4; -1 araport11 exon 259495 259614 . - . Name=AT1G01700.4.exon6;Parent=transcript:AT1G01700.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.4.exon6;rank=6; -1 araport11 CDS 259495 259614 . - 0 ID=CDS:AT1G01700.4;Parent=transcript:AT1G01700.4;protein_id=AT1G01700.4 -1 araport11 exon 259690 260034 . - . Name=AT1G01700.4.exon5;Parent=transcript:AT1G01700.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.4.exon5;rank=5; -1 araport11 CDS 259690 260034 . - 0 ID=CDS:AT1G01700.4;Parent=transcript:AT1G01700.4;protein_id=AT1G01700.4 -1 araport11 exon 260118 260582 . - . Name=AT1G01700.4.exon4;Parent=transcript:AT1G01700.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.4.exon4;rank=4; -1 araport11 CDS 260118 260582 . - 0 ID=CDS:AT1G01700.4;Parent=transcript:AT1G01700.4;protein_id=AT1G01700.4 -1 araport11 exon 260670 260824 . - . Name=AT1G01700.4.exon3;Parent=transcript:AT1G01700.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01700.4.exon3;rank=3; -1 araport11 CDS 260670 260824 . - 2 ID=CDS:AT1G01700.4;Parent=transcript:AT1G01700.4;protein_id=AT1G01700.4 -1 araport11 exon 260921 261037 . - . Name=AT1G01700.4.exon2;Parent=transcript:AT1G01700.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01700.4.exon2;rank=2; -1 araport11 CDS 260921 261037 . - 2 ID=CDS:AT1G01700.4;Parent=transcript:AT1G01700.4;protein_id=AT1G01700.4 -1 araport11 CDS 261129 261474 . - 0 ID=CDS:AT1G01700.4;Parent=transcript:AT1G01700.4;protein_id=AT1G01700.4 -1 araport11 exon 261129 261615 . - . Name=AT1G01700.4.exon1;Parent=transcript:AT1G01700.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01700.4.exon1;rank=1; -1 araport11 five_prime_UTR 261475 261615 . - . Parent=transcript:AT1G01700.4; -1 araport11 mRNA 259640 261667 . - . ID=transcript:AT1G01700.5;biotype=protein_coding;Parent=gene:AT1G01700;transcript_id=AT1G01700.5; -1 araport11 three_prime_UTR 259640 259991 . - . Parent=transcript:AT1G01700.5; -1 araport11 exon 259640 260417 . - . Name=AT1G01700.5.exon5;Parent=transcript:AT1G01700.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01700.5.exon5;rank=5; -1 araport11 CDS 259992 260417 . - 0 ID=CDS:AT1G01700.5;Parent=transcript:AT1G01700.5;protein_id=AT1G01700.5 -1 araport11 exon 260508 260582 . - . Name=AT1G01700.1.exon4;Parent=transcript:AT1G01700.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01700.1.exon4;rank=4; -1 araport11 CDS 260508 260582 . - 0 ID=CDS:AT1G01700.5;Parent=transcript:AT1G01700.5;protein_id=AT1G01700.5 -1 araport11 exon 260670 260824 . - . Name=AT1G01700.4.exon3;Parent=transcript:AT1G01700.5;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01700.4.exon3;rank=3; -1 araport11 CDS 260670 260824 . - 2 ID=CDS:AT1G01700.5;Parent=transcript:AT1G01700.5;protein_id=AT1G01700.5 -1 araport11 exon 260921 261037 . - . Name=AT1G01700.4.exon2;Parent=transcript:AT1G01700.5;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01700.4.exon2;rank=2; -1 araport11 CDS 260921 261037 . - 2 ID=CDS:AT1G01700.5;Parent=transcript:AT1G01700.5;protein_id=AT1G01700.5 -1 araport11 CDS 261129 261474 . - 0 ID=CDS:AT1G01700.5;Parent=transcript:AT1G01700.5;protein_id=AT1G01700.5 -1 araport11 exon 261129 261667 . - . Name=AT1G01700.1.exon1;Parent=transcript:AT1G01700.5;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01700.1.exon1;rank=1; -1 araport11 five_prime_UTR 261475 261667 . - . Parent=transcript:AT1G01700.5; -1 araport11 gene 262828 266324 . + . ID=gene:AT1G01710;biotype=protein_coding;description=Acyl-CoA thioesterase II [Source:UniProtKB/TrEMBL%3bAcc:F4HU51];gene_id=AT1G01710;logic_name=araport11; -1 araport11 mRNA 262828 266324 . + . ID=transcript:AT1G01710.1;biotype=protein_coding;Parent=gene:AT1G01710;transcript_id=AT1G01710.1; -1 araport11 five_prime_UTR 262828 262949 . + . Parent=transcript:AT1G01710.1; -1 araport11 exon 262828 262965 . + . Name=AT1G01710.1.exon1;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01710.1.exon1;rank=1; -1 araport11 CDS 262950 262965 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 263047 263139 . + . Name=AT1G01710.1.exon2;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01710.1.exon2;rank=2; -1 araport11 CDS 263047 263139 . + 2 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 263232 263299 . + . Name=AT1G01710.1.exon3;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01710.1.exon3;rank=3; -1 araport11 CDS 263232 263299 . + 2 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 263369 263444 . + . Name=AT1G01710.1.exon4;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01710.1.exon4;rank=4; -1 araport11 CDS 263369 263444 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 263526 263572 . + . Name=AT1G01710.1.exon5;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01710.1.exon5;rank=5; -1 araport11 CDS 263526 263572 . + 2 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 263645 263770 . + . Name=AT1G01710.1.exon6;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01710.1.exon6;rank=6; -1 araport11 CDS 263645 263770 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 263857 263934 . + . Name=AT1G01710.1.exon7;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01710.1.exon7;rank=7; -1 araport11 CDS 263857 263934 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 264073 264160 . + . Name=AT1G01710.1.exon8;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01710.1.exon8;rank=8; -1 araport11 CDS 264073 264160 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 264280 264392 . + . Name=AT1G01710.1.exon9;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01710.1.exon9;rank=9; -1 araport11 CDS 264280 264392 . + 2 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 264520 264582 . + . Name=AT1G01710.1.exon10;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01710.1.exon10;rank=10; -1 araport11 CDS 264520 264582 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 264657 264712 . + . Name=AT1G01710.1.exon11;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01710.1.exon11;rank=11; -1 araport11 CDS 264657 264712 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 264797 264901 . + . Name=AT1G01710.1.exon12;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01710.1.exon12;rank=12; -1 araport11 CDS 264797 264901 . + 1 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 265021 265077 . + . Name=AT1G01710.1.exon13;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01710.1.exon13;rank=13; -1 araport11 CDS 265021 265077 . + 1 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 265336 265437 . + . Name=AT1G01710.1.exon14;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01710.1.exon14;rank=14; -1 araport11 CDS 265336 265437 . + 1 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 265578 265626 . + . Name=AT1G01710.1.exon15;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01710.1.exon15;rank=15; -1 araport11 CDS 265578 265626 . + 1 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 265777 265845 . + . Name=AT1G01710.1.exon16;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01710.1.exon16;rank=16; -1 araport11 CDS 265777 265845 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 CDS 265952 266029 . + 0 ID=CDS:AT1G01710.1;Parent=transcript:AT1G01710.1;protein_id=AT1G01710.1 -1 araport11 exon 265952 266324 . + . Name=AT1G01710.1.exon17;Parent=transcript:AT1G01710.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01710.1.exon17;rank=17; -1 araport11 three_prime_UTR 266030 266324 . + . Parent=transcript:AT1G01710.1; -1 araport11 gene 266333 267883 . + . ID=gene:AT1G01715;biotype=protein_coding;gene_id=AT1G01715;logic_name=araport11; -1 araport11 mRNA 266333 267883 . + . ID=transcript:AT1G01715.1;biotype=protein_coding;Parent=gene:AT1G01715;transcript_id=AT1G01715.1; -1 araport11 five_prime_UTR 266333 266516 . + . Parent=transcript:AT1G01715.1; -1 araport11 exon 266333 266724 . + . Name=AT1G01715.1.exon1;Parent=transcript:AT1G01715.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01715.1.exon1;rank=1; -1 araport11 CDS 266517 266724 . + 0 ID=CDS:AT1G01715.1;Parent=transcript:AT1G01715.1;protein_id=AT1G01715.1 -1 araport11 CDS 267293 267504 . + 2 ID=CDS:AT1G01715.1;Parent=transcript:AT1G01715.1;protein_id=AT1G01715.1 -1 araport11 exon 267293 267577 . + . Name=AT1G01715.1.exon2;Parent=transcript:AT1G01715.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01715.1.exon2;rank=2; -1 araport11 three_prime_UTR 267505 267577 . + . Parent=transcript:AT1G01715.1; -1 araport11 exon 267677 267883 . + . Name=AT1G01715.1.exon3;Parent=transcript:AT1G01715.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01715.1.exon3;rank=3; -1 araport11 three_prime_UTR 267677 267883 . + . Parent=transcript:AT1G01715.1; -1 araport11 mRNA 266342 267533 . + . ID=transcript:AT1G01715.2;biotype=protein_coding;Parent=gene:AT1G01715;transcript_id=AT1G01715.2; -1 araport11 five_prime_UTR 266342 266516 . + . Parent=transcript:AT1G01715.2; -1 araport11 exon 266342 266724 . + . Name=AT1G01715.2.exon1;Parent=transcript:AT1G01715.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01715.2.exon1;rank=1; -1 araport11 CDS 266517 266724 . + 0 ID=CDS:AT1G01715.2;Parent=transcript:AT1G01715.2;protein_id=AT1G01715.2 -1 araport11 CDS 267293 267504 . + 2 ID=CDS:AT1G01715.2;Parent=transcript:AT1G01715.2;protein_id=AT1G01715.2 -1 araport11 exon 267293 267533 . + . Name=AT1G01715.2.exon2;Parent=transcript:AT1G01715.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01715.2.exon2;rank=2; -1 araport11 three_prime_UTR 267505 267533 . + . Parent=transcript:AT1G01715.2; -1 araport11 ncRNA_gene 267993 268336 . - . ID=gene:AT1G04043;biotype=lncRNA;gene_id=AT1G04043;logic_name=araport11; -1 araport11 lnc_RNA 267993 268336 . - . ID=transcript:AT1G04043.1;biotype=lncRNA;Parent=gene:AT1G04043;transcript_id=AT1G04043.1; -1 araport11 exon 267993 268336 . - . Name=AT1G04043.1.exon1;Parent=transcript:AT1G04043.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04043.1.exon1;rank=1; -1 araport11 gene 267993 269819 . + . ID=gene:AT1G01720;Name=NAC002;biotype=protein_coding;description=NAC domain-containing protein 2 [Source:UniProtKB/Swiss-Prot%3bAcc:Q39013];gene_id=AT1G01720;logic_name=araport11; -1 araport11 mRNA 267993 269819 . + . ID=transcript:AT1G01720.1;biotype=protein_coding;Parent=gene:AT1G01720;transcript_id=AT1G01720.1; -1 araport11 five_prime_UTR 267993 268470 . + . Parent=transcript:AT1G01720.1; -1 araport11 exon 267993 268630 . + . Name=AT1G01720.1.exon1;Parent=transcript:AT1G01720.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01720.1.exon1;rank=1; -1 araport11 CDS 268471 268630 . + 0 ID=CDS:AT1G01720.1;Parent=transcript:AT1G01720.1;protein_id=AT1G01720.1 -1 araport11 exon 268717 268994 . + . Name=AT1G01720.1.exon2;Parent=transcript:AT1G01720.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01720.1.exon2;rank=2; -1 araport11 CDS 268717 268994 . + 2 ID=CDS:AT1G01720.1;Parent=transcript:AT1G01720.1;protein_id=AT1G01720.1 -1 araport11 CDS 269083 269514 . + 0 ID=CDS:AT1G01720.1;Parent=transcript:AT1G01720.1;protein_id=AT1G01720.1 -1 araport11 exon 269083 269819 . + . Name=AT1G01720.1.exon3;Parent=transcript:AT1G01720.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01720.1.exon3;rank=3; -1 araport11 three_prime_UTR 269515 269819 . + . Parent=transcript:AT1G01720.1; -1 araport11 gene 269792 270859 . - . ID=gene:AT1G01725;biotype=protein_coding;description=Adenylosuccinate synthetase [Source:UniProtKB/TrEMBL%3bAcc:Q9LQ84];gene_id=AT1G01725;logic_name=araport11; -1 araport11 mRNA 269792 270859 . - . ID=transcript:AT1G01725.1;biotype=protein_coding;Parent=gene:AT1G01725;transcript_id=AT1G01725.1; -1 araport11 three_prime_UTR 269792 270015 . - . Parent=transcript:AT1G01725.1; -1 araport11 exon 269792 270090 . - . Name=AT1G01725.1.exon2;Parent=transcript:AT1G01725.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01725.1.exon2;rank=2; -1 araport11 CDS 270016 270090 . - 0 ID=CDS:AT1G01725.1;Parent=transcript:AT1G01725.1;protein_id=AT1G01725.1 -1 araport11 CDS 270622 270735 . - 0 ID=CDS:AT1G01725.1;Parent=transcript:AT1G01725.1;protein_id=AT1G01725.1 -1 araport11 exon 270622 270859 . - . Name=AT1G01725.1.exon1;Parent=transcript:AT1G01725.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01725.1.exon1;rank=1; -1 araport11 five_prime_UTR 270736 270859 . - . Parent=transcript:AT1G01725.1; -1 araport11 ncRNA_gene 270067 270517 . + . ID=gene:AT1G04047;biotype=lncRNA;gene_id=AT1G04047;logic_name=araport11; -1 araport11 lnc_RNA 270067 270517 . + . ID=transcript:AT1G04047.1;biotype=lncRNA;Parent=gene:AT1G04047;transcript_id=AT1G04047.1; -1 araport11 exon 270067 270517 . + . Name=AT1G04047.1.exon1;Parent=transcript:AT1G04047.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04047.1.exon1;rank=1; -1 araport11 gene 270797 272189 . + . ID=gene:AT1G01730;biotype=protein_coding;description=T1N6.14 protein [Source:UniProtKB/TrEMBL%3bAcc:Q9LQ83];gene_id=AT1G01730;logic_name=araport11; -1 araport11 mRNA 270797 272189 . + . ID=transcript:AT1G01730.1;biotype=protein_coding;Parent=gene:AT1G01730;transcript_id=AT1G01730.1; -1 araport11 five_prime_UTR 270797 271001 . + . Parent=transcript:AT1G01730.1; -1 araport11 exon 270797 271289 . + . Name=AT1G01730.1.exon1;Parent=transcript:AT1G01730.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01730.1.exon1;rank=1; -1 araport11 CDS 271002 271289 . + 0 ID=CDS:AT1G01730.1;Parent=transcript:AT1G01730.1;protein_id=AT1G01730.1 -1 araport11 exon 271379 271433 . + . Name=AT1G01730.1.exon2;Parent=transcript:AT1G01730.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01730.1.exon2;rank=2; -1 araport11 CDS 271379 271433 . + 0 ID=CDS:AT1G01730.1;Parent=transcript:AT1G01730.1;protein_id=AT1G01730.1 -1 araport11 CDS 271541 271872 . + 2 ID=CDS:AT1G01730.1;Parent=transcript:AT1G01730.1;protein_id=AT1G01730.1 -1 araport11 exon 271541 272189 . + . Name=AT1G01730.1.exon3;Parent=transcript:AT1G01730.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=1;exon_id=AT1G01730.1.exon3;rank=3; -1 araport11 three_prime_UTR 271873 272189 . + . Parent=transcript:AT1G01730.1; -1 araport11 gene 272111 274930 . - . ID=gene:AT1G01740;Name=BSK4;biotype=protein_coding;description=Serine/threonine-protein kinase BSK4 [Source:UniProtKB/Swiss-Prot%3bAcc:F4HU55];gene_id=AT1G01740;logic_name=araport11; -1 araport11 mRNA 272111 274569 . - . ID=transcript:AT1G01740.4;biotype=protein_coding;Parent=gene:AT1G01740;transcript_id=AT1G01740.4; -1 araport11 exon 272111 272362 . - . Name=AT1G01740.3.exon10;Parent=transcript:AT1G01740.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon10;rank=10; -1 araport11 CDS 272111 272362 . - 0 ID=CDS:AT1G01740.4;Parent=transcript:AT1G01740.4;protein_id=AT1G01740.4 -1 araport11 exon 272445 272555 . - . Name=AT1G01740.3.exon9;Parent=transcript:AT1G01740.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon9;rank=9; -1 araport11 CDS 272445 272555 . - 0 ID=CDS:AT1G01740.4;Parent=transcript:AT1G01740.4;protein_id=AT1G01740.4 -1 araport11 exon 272651 272983 . - . Name=AT1G01740.3.exon8;Parent=transcript:AT1G01740.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon8;rank=8; -1 araport11 CDS 272651 272983 . - 0 ID=CDS:AT1G01740.4;Parent=transcript:AT1G01740.4;protein_id=AT1G01740.4 -1 araport11 exon 273064 273149 . - . Name=AT1G01740.3.exon7;Parent=transcript:AT1G01740.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon7;rank=7; -1 araport11 CDS 273064 273149 . - 2 ID=CDS:AT1G01740.4;Parent=transcript:AT1G01740.4;protein_id=AT1G01740.4 -1 araport11 exon 273234 273339 . - . Name=AT1G01740.3.exon6;Parent=transcript:AT1G01740.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon6;rank=6; -1 araport11 CDS 273234 273339 . - 0 ID=CDS:AT1G01740.4;Parent=transcript:AT1G01740.4;protein_id=AT1G01740.4 -1 araport11 exon 273429 273562 . - . Name=AT1G01740.3.exon5;Parent=transcript:AT1G01740.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon5;rank=5; -1 araport11 CDS 273429 273562 . - 2 ID=CDS:AT1G01740.4;Parent=transcript:AT1G01740.4;protein_id=AT1G01740.4 -1 araport11 exon 273653 273788 . - . Name=AT1G01740.3.exon4;Parent=transcript:AT1G01740.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon4;rank=4; -1 araport11 CDS 273653 273788 . - 0 ID=CDS:AT1G01740.4;Parent=transcript:AT1G01740.4;protein_id=AT1G01740.4 -1 araport11 CDS 273863 273922 . - 0 ID=CDS:AT1G01740.4;Parent=transcript:AT1G01740.4;protein_id=AT1G01740.4 -1 araport11 exon 273863 274083 . - . Name=AT1G01740.3.exon3;Parent=transcript:AT1G01740.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01740.3.exon3;rank=3; -1 araport11 five_prime_UTR 273923 274083 . - . Parent=transcript:AT1G01740.4; -1 araport11 exon 274171 274249 . - . Name=AT1G01740.4.exon2;Parent=transcript:AT1G01740.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01740.4.exon2;rank=2; -1 araport11 five_prime_UTR 274171 274249 . - . Parent=transcript:AT1G01740.4; -1 araport11 exon 274384 274569 . - . Name=AT1G01740.5.exon1;Parent=transcript:AT1G01740.4;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01740.5.exon1;rank=1; -1 araport11 five_prime_UTR 274384 274569 . - . Parent=transcript:AT1G01740.4; -1 araport11 mRNA 272111 274569 . - . ID=transcript:AT1G01740.1;biotype=protein_coding;Parent=gene:AT1G01740;transcript_id=AT1G01740.1; -1 araport11 exon 272111 272362 . - . Name=AT1G01740.3.exon10;Parent=transcript:AT1G01740.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon10;rank=10; -1 araport11 CDS 272111 272362 . - 0 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 exon 272445 272555 . - . Name=AT1G01740.3.exon9;Parent=transcript:AT1G01740.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon9;rank=9; -1 araport11 CDS 272445 272555 . - 0 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 exon 272651 272983 . - . Name=AT1G01740.3.exon8;Parent=transcript:AT1G01740.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon8;rank=8; -1 araport11 CDS 272651 272983 . - 0 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 exon 273064 273149 . - . Name=AT1G01740.3.exon7;Parent=transcript:AT1G01740.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon7;rank=7; -1 araport11 CDS 273064 273149 . - 2 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 exon 273234 273339 . - . Name=AT1G01740.3.exon6;Parent=transcript:AT1G01740.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon6;rank=6; -1 araport11 CDS 273234 273339 . - 0 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 exon 273429 273562 . - . Name=AT1G01740.3.exon5;Parent=transcript:AT1G01740.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon5;rank=5; -1 araport11 CDS 273429 273562 . - 2 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 exon 273653 273788 . - . Name=AT1G01740.3.exon4;Parent=transcript:AT1G01740.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon4;rank=4; -1 araport11 CDS 273653 273788 . - 0 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 exon 273863 274083 . - . Name=AT1G01740.5.exon3;Parent=transcript:AT1G01740.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.5.exon3;rank=3; -1 araport11 CDS 273863 274083 . - 2 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 CDS 274167 274239 . - 0 ID=CDS:AT1G01740.1;Parent=transcript:AT1G01740.1;protein_id=AT1G01740.1 -1 araport11 exon 274167 274249 . - . Name=AT1G01740.5.exon2;Parent=transcript:AT1G01740.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01740.5.exon2;rank=2; -1 araport11 five_prime_UTR 274240 274249 . - . Parent=transcript:AT1G01740.1; -1 araport11 exon 274384 274569 . - . Name=AT1G01740.5.exon1;Parent=transcript:AT1G01740.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01740.5.exon1;rank=1; -1 araport11 five_prime_UTR 274384 274569 . - . Parent=transcript:AT1G01740.1; -1 araport11 mRNA 272111 274569 . - . ID=transcript:AT1G01740.5;biotype=protein_coding;Parent=gene:AT1G01740;transcript_id=AT1G01740.5; -1 araport11 exon 272111 272362 . - . Name=AT1G01740.3.exon10;Parent=transcript:AT1G01740.5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon10;rank=10; -1 araport11 CDS 272111 272362 . - 0 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 exon 272445 272531 . - . Name=AT1G01740.5.exon9;Parent=transcript:AT1G01740.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.5.exon9;rank=9; -1 araport11 CDS 272445 272531 . - 0 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 exon 272651 272983 . - . Name=AT1G01740.3.exon8;Parent=transcript:AT1G01740.5;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon8;rank=8; -1 araport11 CDS 272651 272983 . - 0 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 exon 273064 273149 . - . Name=AT1G01740.3.exon7;Parent=transcript:AT1G01740.5;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon7;rank=7; -1 araport11 CDS 273064 273149 . - 2 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 exon 273234 273339 . - . Name=AT1G01740.3.exon6;Parent=transcript:AT1G01740.5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon6;rank=6; -1 araport11 CDS 273234 273339 . - 0 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 exon 273429 273562 . - . Name=AT1G01740.3.exon5;Parent=transcript:AT1G01740.5;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon5;rank=5; -1 araport11 CDS 273429 273562 . - 2 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 exon 273653 273788 . - . Name=AT1G01740.3.exon4;Parent=transcript:AT1G01740.5;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon4;rank=4; -1 araport11 CDS 273653 273788 . - 0 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 exon 273863 274083 . - . Name=AT1G01740.5.exon3;Parent=transcript:AT1G01740.5;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.5.exon3;rank=3; -1 araport11 CDS 273863 274083 . - 2 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 CDS 274167 274239 . - 0 ID=CDS:AT1G01740.5;Parent=transcript:AT1G01740.5;protein_id=AT1G01740.5 -1 araport11 exon 274167 274249 . - . Name=AT1G01740.5.exon2;Parent=transcript:AT1G01740.5;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01740.5.exon2;rank=2; -1 araport11 five_prime_UTR 274240 274249 . - . Parent=transcript:AT1G01740.5; -1 araport11 exon 274384 274569 . - . Name=AT1G01740.5.exon1;Parent=transcript:AT1G01740.5;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01740.5.exon1;rank=1; -1 araport11 five_prime_UTR 274384 274569 . - . Parent=transcript:AT1G01740.5; -1 araport11 mRNA 272111 274792 . - . ID=transcript:AT1G01740.2;biotype=protein_coding;Parent=gene:AT1G01740;transcript_id=AT1G01740.2; -1 araport11 exon 272111 272362 . - . Name=AT1G01740.3.exon10;Parent=transcript:AT1G01740.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon10;rank=10; -1 araport11 CDS 272111 272362 . - 0 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 exon 272445 272555 . - . Name=AT1G01740.3.exon9;Parent=transcript:AT1G01740.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon9;rank=9; -1 araport11 CDS 272445 272555 . - 0 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 exon 272651 272983 . - . Name=AT1G01740.3.exon8;Parent=transcript:AT1G01740.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon8;rank=8; -1 araport11 CDS 272651 272983 . - 0 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 exon 273064 273149 . - . Name=AT1G01740.3.exon7;Parent=transcript:AT1G01740.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon7;rank=7; -1 araport11 CDS 273064 273149 . - 2 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 exon 273234 273339 . - . Name=AT1G01740.3.exon6;Parent=transcript:AT1G01740.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon6;rank=6; -1 araport11 CDS 273234 273339 . - 0 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 exon 273429 273562 . - . Name=AT1G01740.3.exon5;Parent=transcript:AT1G01740.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon5;rank=5; -1 araport11 CDS 273429 273562 . - 2 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 exon 273653 273788 . - . Name=AT1G01740.3.exon4;Parent=transcript:AT1G01740.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon4;rank=4; -1 araport11 CDS 273653 273788 . - 0 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 exon 273863 274083 . - . Name=AT1G01740.5.exon3;Parent=transcript:AT1G01740.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.5.exon3;rank=3; -1 araport11 CDS 273863 274083 . - 2 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 CDS 274167 274239 . - 0 ID=CDS:AT1G01740.2;Parent=transcript:AT1G01740.2;protein_id=AT1G01740.2 -1 araport11 exon 274167 274289 . - . Name=AT1G01740.2.exon2;Parent=transcript:AT1G01740.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01740.2.exon2;rank=2; -1 araport11 five_prime_UTR 274240 274289 . - . Parent=transcript:AT1G01740.2; -1 araport11 exon 274384 274792 . - . Name=AT1G01740.2.exon1;Parent=transcript:AT1G01740.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01740.2.exon1;rank=1; -1 araport11 five_prime_UTR 274384 274792 . - . Parent=transcript:AT1G01740.2; -1 araport11 mRNA 272111 274930 . - . ID=transcript:AT1G01740.3;biotype=protein_coding;Parent=gene:AT1G01740;transcript_id=AT1G01740.3; -1 araport11 exon 272111 272362 . - . Name=AT1G01740.3.exon10;Parent=transcript:AT1G01740.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon10;rank=10; -1 araport11 CDS 272111 272362 . - 0 ID=CDS:AT1G01740.3;Parent=transcript:AT1G01740.3;protein_id=AT1G01740.3 -1 araport11 exon 272445 272555 . - . Name=AT1G01740.3.exon9;Parent=transcript:AT1G01740.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon9;rank=9; -1 araport11 CDS 272445 272555 . - 0 ID=CDS:AT1G01740.3;Parent=transcript:AT1G01740.3;protein_id=AT1G01740.3 -1 araport11 exon 272651 272983 . - . Name=AT1G01740.3.exon8;Parent=transcript:AT1G01740.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01740.3.exon8;rank=8; -1 araport11 CDS 272651 272983 . - 0 ID=CDS:AT1G01740.3;Parent=transcript:AT1G01740.3;protein_id=AT1G01740.3 -1 araport11 exon 273064 273149 . - . Name=AT1G01740.3.exon7;Parent=transcript:AT1G01740.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon7;rank=7; -1 araport11 CDS 273064 273149 . - 2 ID=CDS:AT1G01740.3;Parent=transcript:AT1G01740.3;protein_id=AT1G01740.3 -1 araport11 exon 273234 273339 . - . Name=AT1G01740.3.exon6;Parent=transcript:AT1G01740.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon6;rank=6; -1 araport11 CDS 273234 273339 . - 0 ID=CDS:AT1G01740.3;Parent=transcript:AT1G01740.3;protein_id=AT1G01740.3 -1 araport11 exon 273429 273562 . - . Name=AT1G01740.3.exon5;Parent=transcript:AT1G01740.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01740.3.exon5;rank=5; -1 araport11 CDS 273429 273562 . - 2 ID=CDS:AT1G01740.3;Parent=transcript:AT1G01740.3;protein_id=AT1G01740.3 -1 araport11 exon 273653 273788 . - . Name=AT1G01740.3.exon4;Parent=transcript:AT1G01740.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01740.3.exon4;rank=4; -1 araport11 CDS 273653 273788 . - 0 ID=CDS:AT1G01740.3;Parent=transcript:AT1G01740.3;protein_id=AT1G01740.3 -1 araport11 CDS 273863 273922 . - 0 ID=CDS:AT1G01740.3;Parent=transcript:AT1G01740.3;protein_id=AT1G01740.3 -1 araport11 exon 273863 274083 . - . Name=AT1G01740.3.exon3;Parent=transcript:AT1G01740.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01740.3.exon3;rank=3; -1 araport11 five_prime_UTR 273923 274083 . - . Parent=transcript:AT1G01740.3; -1 araport11 exon 274171 274289 . - . Name=AT1G01740.3.exon2;Parent=transcript:AT1G01740.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01740.3.exon2;rank=2; -1 araport11 five_prime_UTR 274171 274289 . - . Parent=transcript:AT1G01740.3; -1 araport11 exon 274384 274930 . - . Name=AT1G01740.3.exon1;Parent=transcript:AT1G01740.3;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01740.3.exon1;rank=1; -1 araport11 five_prime_UTR 274384 274930 . - . Parent=transcript:AT1G01740.3; -1 araport11 gene 275188 276310 . + . ID=gene:AT1G01750;Name=ADF11;biotype=protein_coding;description=actin depolymerizing factor 11 [Source:TAIR%3bAcc:AT1G01750];gene_id=AT1G01750;logic_name=araport11; -1 araport11 mRNA 275188 276310 . + . ID=transcript:AT1G01750.1;biotype=protein_coding;Parent=gene:AT1G01750;transcript_id=AT1G01750.1; -1 araport11 five_prime_UTR 275188 275527 . + . Parent=transcript:AT1G01750.1; -1 araport11 exon 275188 275530 . + . Name=AT1G01750.1.exon1;Parent=transcript:AT1G01750.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01750.1.exon1;rank=1; -1 araport11 CDS 275528 275530 . + 0 ID=CDS:AT1G01750.1;Parent=transcript:AT1G01750.1;protein_id=AT1G01750.1 -1 araport11 exon 275632 275897 . + . Name=AT1G01750.1.exon2;Parent=transcript:AT1G01750.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01750.1.exon2;rank=2; -1 araport11 CDS 275632 275897 . + 0 ID=CDS:AT1G01750.1;Parent=transcript:AT1G01750.1;protein_id=AT1G01750.1 -1 araport11 CDS 275973 276126 . + 1 ID=CDS:AT1G01750.1;Parent=transcript:AT1G01750.1;protein_id=AT1G01750.1 -1 araport11 exon 275973 276310 . + . Name=AT1G01750.1.exon3;Parent=transcript:AT1G01750.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01750.1.exon3;rank=3; -1 araport11 three_prime_UTR 276127 276310 . + . Parent=transcript:AT1G01750.1; -1 araport11 mRNA 275331 276126 . + . ID=transcript:AT1G01750.2;biotype=protein_coding;Parent=gene:AT1G01750;transcript_id=AT1G01750.2; -1 araport11 five_prime_UTR 275331 275613 . + . Parent=transcript:AT1G01750.2; -1 araport11 exon 275331 275897 . + . Name=AT1G01750.2.exon1;Parent=transcript:AT1G01750.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01750.2.exon1;rank=1; -1 araport11 CDS 275614 275897 . + 0 ID=CDS:AT1G01750.2;Parent=transcript:AT1G01750.2;protein_id=AT1G01750.2 -1 araport11 exon 275973 276126 . + . Name=AT1G01750.2.exon2;Parent=transcript:AT1G01750.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01750.2.exon2;rank=2; -1 araport11 CDS 275973 276126 . + 1 ID=CDS:AT1G01750.2;Parent=transcript:AT1G01750.2;protein_id=AT1G01750.2 -1 araport11 ncRNA_gene 275473 276319 . - . ID=gene:AT1G04053;biotype=lncRNA;gene_id=AT1G04053;logic_name=araport11; -1 araport11 lnc_RNA 275473 276319 . - . ID=transcript:AT1G04053.1;biotype=lncRNA;Parent=gene:AT1G04053;transcript_id=AT1G04053.1; -1 araport11 exon 275473 275977 . - . Name=AT1G04053.1.exon2;Parent=transcript:AT1G04053.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04053.1.exon2;rank=2; -1 araport11 exon 276247 276319 . - . Name=AT1G04053.1.exon1;Parent=transcript:AT1G04053.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04053.1.exon1;rank=1; -1 araport11 gene 276266 278599 . - . ID=gene:AT1G01760;biotype=protein_coding;description=TAD1 [Source:UniProtKB/TrEMBL%3bAcc:A0A178W782];gene_id=AT1G01760;logic_name=araport11; -1 araport11 mRNA 276266 278448 . - . ID=transcript:AT1G01760.1;biotype=protein_coding;Parent=gene:AT1G01760;transcript_id=AT1G01760.1; -1 araport11 exon 276266 276307 . - . Name=AT1G01760.1.exon10;Parent=transcript:AT1G01760.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01760.1.exon10;rank=10; -1 araport11 three_prime_UTR 276266 276307 . - . Parent=transcript:AT1G01760.1; -1 araport11 three_prime_UTR 276405 276411 . - . Parent=transcript:AT1G01760.1; -1 araport11 exon 276405 276519 . - . Name=AT1G01760.1.exon9;Parent=transcript:AT1G01760.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01760.1.exon9;rank=9; -1 araport11 CDS 276412 276519 . - 0 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 exon 276706 276793 . - . Name=AT1G01760.3.exon8;Parent=transcript:AT1G01760.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01760.3.exon8;rank=8; -1 araport11 CDS 276706 276793 . - 1 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 exon 276870 276989 . - . Name=AT1G01760.3.exon7;Parent=transcript:AT1G01760.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01760.3.exon7;rank=7; -1 araport11 CDS 276870 276989 . - 1 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 exon 277077 277153 . - . Name=AT1G01760.3.exon6;Parent=transcript:AT1G01760.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01760.3.exon6;rank=6; -1 araport11 CDS 277077 277153 . - 0 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 exon 277232 277401 . - . Name=AT1G01760.3.exon5;Parent=transcript:AT1G01760.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01760.3.exon5;rank=5; -1 araport11 CDS 277232 277401 . - 2 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 exon 277493 277606 . - . Name=AT1G01760.3.exon4;Parent=transcript:AT1G01760.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon4;rank=4; -1 araport11 CDS 277493 277606 . - 2 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 exon 277717 277863 . - . Name=AT1G01760.3.exon3;Parent=transcript:AT1G01760.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon3;rank=3; -1 araport11 CDS 277717 277863 . - 2 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 exon 277947 278252 . - . Name=AT1G01760.3.exon2;Parent=transcript:AT1G01760.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon2;rank=2; -1 araport11 CDS 277947 278252 . - 2 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 exon 278316 278448 . - . Name=AT1G01760.1.exon1;Parent=transcript:AT1G01760.1;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01760.1.exon1;rank=1; -1 araport11 CDS 278316 278448 . - 0 ID=CDS:AT1G01760.1;Parent=transcript:AT1G01760.1;protein_id=AT1G01760.1 -1 araport11 mRNA 276368 278599 . - . ID=transcript:AT1G01760.2;biotype=protein_coding;Parent=gene:AT1G01760;transcript_id=AT1G01760.2; -1 araport11 exon 276368 276519 . - . Name=AT1G01760.2.exon9;Parent=transcript:AT1G01760.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01760.2.exon9;rank=9; -1 araport11 three_prime_UTR 276368 276519 . - . Parent=transcript:AT1G01760.2; -1 araport11 three_prime_UTR 276623 276639 . - . Parent=transcript:AT1G01760.2; -1 araport11 exon 276623 276793 . - . Name=AT1G01760.2.exon8;Parent=transcript:AT1G01760.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01760.2.exon8;rank=8; -1 araport11 CDS 276640 276793 . - 1 ID=CDS:AT1G01760.2;Parent=transcript:AT1G01760.2;protein_id=AT1G01760.2 -1 araport11 exon 276870 276989 . - . Name=AT1G01760.3.exon7;Parent=transcript:AT1G01760.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01760.3.exon7;rank=7; -1 araport11 CDS 276870 276989 . - 1 ID=CDS:AT1G01760.2;Parent=transcript:AT1G01760.2;protein_id=AT1G01760.2 -1 araport11 exon 277077 277153 . - . Name=AT1G01760.3.exon6;Parent=transcript:AT1G01760.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01760.3.exon6;rank=6; -1 araport11 CDS 277077 277153 . - 0 ID=CDS:AT1G01760.2;Parent=transcript:AT1G01760.2;protein_id=AT1G01760.2 -1 araport11 exon 277232 277401 . - . Name=AT1G01760.3.exon5;Parent=transcript:AT1G01760.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01760.3.exon5;rank=5; -1 araport11 CDS 277232 277401 . - 2 ID=CDS:AT1G01760.2;Parent=transcript:AT1G01760.2;protein_id=AT1G01760.2 -1 araport11 exon 277493 277606 . - . Name=AT1G01760.3.exon4;Parent=transcript:AT1G01760.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon4;rank=4; -1 araport11 CDS 277493 277606 . - 2 ID=CDS:AT1G01760.2;Parent=transcript:AT1G01760.2;protein_id=AT1G01760.2 -1 araport11 exon 277717 277863 . - . Name=AT1G01760.3.exon3;Parent=transcript:AT1G01760.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon3;rank=3; -1 araport11 CDS 277717 277863 . - 2 ID=CDS:AT1G01760.2;Parent=transcript:AT1G01760.2;protein_id=AT1G01760.2 -1 araport11 exon 277947 278252 . - . Name=AT1G01760.3.exon2;Parent=transcript:AT1G01760.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon2;rank=2; -1 araport11 CDS 277947 278252 . - 2 ID=CDS:AT1G01760.2;Parent=transcript:AT1G01760.2;protein_id=AT1G01760.2 -1 araport11 CDS 278316 278487 . - 0 ID=CDS:AT1G01760.2;Parent=transcript:AT1G01760.2;protein_id=AT1G01760.2 -1 araport11 exon 278316 278599 . - . Name=AT1G01760.3.exon1;Parent=transcript:AT1G01760.2;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01760.3.exon1;rank=1; -1 araport11 five_prime_UTR 278488 278599 . - . Parent=transcript:AT1G01760.2; -1 araport11 mRNA 276412 278448 . - . ID=transcript:AT1G01760.4;biotype=protein_coding;Parent=gene:AT1G01760;transcript_id=AT1G01760.4; -1 araport11 exon 276412 276519 . - . Name=AT1G01760.3.exon9;Parent=transcript:AT1G01760.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01760.3.exon9;rank=9; -1 araport11 CDS 276412 276519 . - 0 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 exon 276706 276793 . - . Name=AT1G01760.3.exon8;Parent=transcript:AT1G01760.4;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01760.3.exon8;rank=8; -1 araport11 CDS 276706 276793 . - 1 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 exon 276870 276989 . - . Name=AT1G01760.3.exon7;Parent=transcript:AT1G01760.4;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01760.3.exon7;rank=7; -1 araport11 CDS 276870 276989 . - 1 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 exon 277077 277153 . - . Name=AT1G01760.3.exon6;Parent=transcript:AT1G01760.4;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01760.3.exon6;rank=6; -1 araport11 CDS 277077 277153 . - 0 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 exon 277232 277401 . - . Name=AT1G01760.3.exon5;Parent=transcript:AT1G01760.4;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01760.3.exon5;rank=5; -1 araport11 CDS 277232 277401 . - 2 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 exon 277493 277606 . - . Name=AT1G01760.3.exon4;Parent=transcript:AT1G01760.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon4;rank=4; -1 araport11 CDS 277493 277606 . - 2 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 exon 277717 277863 . - . Name=AT1G01760.3.exon3;Parent=transcript:AT1G01760.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon3;rank=3; -1 araport11 CDS 277717 277863 . - 2 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 exon 277947 278252 . - . Name=AT1G01760.3.exon2;Parent=transcript:AT1G01760.4;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon2;rank=2; -1 araport11 CDS 277947 278252 . - 2 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 exon 278316 278448 . - . Name=AT1G01760.1.exon1;Parent=transcript:AT1G01760.4;constitutive=0;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01760.1.exon1;rank=1; -1 araport11 CDS 278316 278448 . - 0 ID=CDS:AT1G01760.4;Parent=transcript:AT1G01760.4;protein_id=AT1G01760.4 -1 araport11 mRNA 276412 278599 . - . ID=transcript:AT1G01760.3;biotype=protein_coding;Parent=gene:AT1G01760;transcript_id=AT1G01760.3; -1 araport11 exon 276412 276519 . - . Name=AT1G01760.3.exon9;Parent=transcript:AT1G01760.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01760.3.exon9;rank=9; -1 araport11 CDS 276412 276519 . - 0 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 exon 276706 276793 . - . Name=AT1G01760.3.exon8;Parent=transcript:AT1G01760.3;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01760.3.exon8;rank=8; -1 araport11 CDS 276706 276793 . - 1 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 exon 276870 276989 . - . Name=AT1G01760.3.exon7;Parent=transcript:AT1G01760.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=AT1G01760.3.exon7;rank=7; -1 araport11 CDS 276870 276989 . - 1 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 exon 277077 277153 . - . Name=AT1G01760.3.exon6;Parent=transcript:AT1G01760.3;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01760.3.exon6;rank=6; -1 araport11 CDS 277077 277153 . - 0 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 exon 277232 277401 . - . Name=AT1G01760.3.exon5;Parent=transcript:AT1G01760.3;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01760.3.exon5;rank=5; -1 araport11 CDS 277232 277401 . - 2 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 exon 277493 277606 . - . Name=AT1G01760.3.exon4;Parent=transcript:AT1G01760.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon4;rank=4; -1 araport11 CDS 277493 277606 . - 2 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 exon 277717 277863 . - . Name=AT1G01760.3.exon3;Parent=transcript:AT1G01760.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon3;rank=3; -1 araport11 CDS 277717 277863 . - 2 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 exon 277947 278252 . - . Name=AT1G01760.3.exon2;Parent=transcript:AT1G01760.3;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01760.3.exon2;rank=2; -1 araport11 CDS 277947 278252 . - 2 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 CDS 278316 278487 . - 0 ID=CDS:AT1G01760.3;Parent=transcript:AT1G01760.3;protein_id=AT1G01760.3 -1 araport11 exon 278316 278599 . - . Name=AT1G01760.3.exon1;Parent=transcript:AT1G01760.3;constitutive=0;ensembl_end_phase=1;ensembl_phase=-1;exon_id=AT1G01760.3.exon1;rank=1; -1 araport11 five_prime_UTR 278488 278599 . - . Parent=transcript:AT1G01760.3; -1 araport11 ncRNA_gene 276543 276729 . + . ID=gene:AT1G04057;biotype=ncRNA;gene_id=AT1G04057;logic_name=araport11; -1 araport11 ncRNA 276543 276729 . + . ID=transcript:AT1G04057.1;biotype=ncRNA;Parent=gene:AT1G04057;transcript_id=AT1G04057.1; -1 araport11 exon 276543 276729 . + . Name=AT1G04057.1.exon1;Parent=transcript:AT1G04057.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04057.1.exon1;rank=1; -1 araport11 gene 278600 282891 . + . ID=gene:AT1G01770;biotype=protein_coding;description=Propionyl-CoA carboxylase [Source:UniProtKB/TrEMBL%3bAcc:Q8GZ85];gene_id=AT1G01770;logic_name=araport11; -1 araport11 mRNA 278600 282891 . + . ID=transcript:AT1G01770.1;biotype=protein_coding;Parent=gene:AT1G01770;transcript_id=AT1G01770.1; -1 araport11 five_prime_UTR 278600 278758 . + . Parent=transcript:AT1G01770.1; -1 araport11 exon 278600 278809 . + . Name=AT1G01770.1.exon1;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01770.1.exon1;rank=1; -1 araport11 CDS 278759 278809 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 278887 279088 . + . Name=AT1G01770.1.exon2;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01770.1.exon2;rank=2; -1 araport11 CDS 278887 279088 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 279166 279240 . + . Name=AT1G01770.1.exon3;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01770.1.exon3;rank=3; -1 araport11 CDS 279166 279240 . + 2 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 279327 279425 . + . Name=AT1G01770.1.exon4;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;exon_id=AT1G01770.1.exon4;rank=4; -1 araport11 CDS 279327 279425 . + 2 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 279536 279576 . + . Name=AT1G01770.1.exon5;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01770.1.exon5;rank=5; -1 araport11 CDS 279536 279576 . + 2 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 279797 279910 . + . Name=AT1G01770.1.exon6;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01770.1.exon6;rank=6; -1 araport11 CDS 279797 279910 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 279974 280088 . + . Name=AT1G01770.1.exon7;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01770.1.exon7;rank=7; -1 araport11 CDS 279974 280088 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 280180 280370 . + . Name=AT1G01770.1.exon8;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01770.1.exon8;rank=8; -1 araport11 CDS 280180 280370 . + 2 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 280449 280568 . + . Name=AT1G01770.1.exon9;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01770.1.exon9;rank=9; -1 araport11 CDS 280449 280568 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 280657 280737 . + . Name=AT1G01770.1.exon10;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01770.1.exon10;rank=10; -1 araport11 CDS 280657 280737 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 280889 281121 . + . Name=AT1G01770.1.exon11;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01770.1.exon11;rank=11; -1 araport11 CDS 280889 281121 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 281309 281348 . + . Name=AT1G01770.1.exon12;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01770.1.exon12;rank=12; -1 araport11 CDS 281309 281348 . + 1 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 281438 281536 . + . Name=AT1G01770.1.exon13;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01770.1.exon13;rank=13; -1 araport11 CDS 281438 281536 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 281759 282189 . + . Name=AT1G01770.1.exon14;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01770.1.exon14;rank=14; -1 araport11 CDS 281759 282189 . + 0 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 CDS 282484 282490 . + 1 ID=CDS:AT1G01770.1;Parent=transcript:AT1G01770.1;protein_id=AT1G01770.1 -1 araport11 exon 282484 282766 . + . Name=AT1G01770.1.exon15;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=AT1G01770.1.exon15;rank=15; -1 araport11 three_prime_UTR 282491 282766 . + . Parent=transcript:AT1G01770.1; -1 araport11 exon 282849 282891 . + . Name=AT1G01770.1.exon16;Parent=transcript:AT1G01770.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01770.1.exon16;rank=16; -1 araport11 three_prime_UTR 282849 282891 . + . Parent=transcript:AT1G01770.1; -1 araport11 gene 282761 284245 . + . ID=gene:AT1G01780;Name=PLIM2B;biotype=protein_coding;description=LIM domain-containing protein PLIM2b [Source:UniProtKB/Swiss-Prot%3bAcc:Q1ECF5];gene_id=AT1G01780;logic_name=araport11; -1 araport11 mRNA 282761 284245 . + . ID=transcript:AT1G01780.1;biotype=protein_coding;Parent=gene:AT1G01780;transcript_id=AT1G01780.1; -1 araport11 five_prime_UTR 282761 282918 . + . Parent=transcript:AT1G01780.1; -1 araport11 exon 282761 283053 . + . Name=AT1G01780.1.exon1;Parent=transcript:AT1G01780.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01780.1.exon1;rank=1; -1 araport11 CDS 282919 283053 . + 0 ID=CDS:AT1G01780.1;Parent=transcript:AT1G01780.1;protein_id=AT1G01780.1 -1 araport11 exon 283132 283231 . + . Name=AT1G01780.1.exon2;Parent=transcript:AT1G01780.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01780.1.exon2;rank=2; -1 araport11 CDS 283132 283231 . + 0 ID=CDS:AT1G01780.1;Parent=transcript:AT1G01780.1;protein_id=AT1G01780.1 -1 araport11 exon 283314 283336 . + . Name=AT1G01780.1.exon3;Parent=transcript:AT1G01780.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01780.1.exon3;rank=3; -1 araport11 CDS 283314 283336 . + 2 ID=CDS:AT1G01780.1;Parent=transcript:AT1G01780.1;protein_id=AT1G01780.1 -1 araport11 exon 283444 283533 . + . Name=AT1G01780.1.exon4;Parent=transcript:AT1G01780.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01780.1.exon4;rank=4; -1 araport11 CDS 283444 283533 . + 0 ID=CDS:AT1G01780.1;Parent=transcript:AT1G01780.1;protein_id=AT1G01780.1 -1 araport11 CDS 283813 284082 . + 0 ID=CDS:AT1G01780.1;Parent=transcript:AT1G01780.1;protein_id=AT1G01780.1 -1 araport11 exon 283813 284245 . + . Name=AT1G01780.1.exon5;Parent=transcript:AT1G01780.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01780.1.exon5;rank=5; -1 araport11 three_prime_UTR 284083 284245 . + . Parent=transcript:AT1G01780.1; -1 araport11 gene 284350 291203 . + . ID=gene:AT1G01790;Name=KEA1;biotype=protein_coding;description=K(+) efflux antiporter 1%2c chloroplastic [Source:UniProtKB/Swiss-Prot%3bAcc:Q9ZTZ7];gene_id=AT1G01790;logic_name=araport11; -1 araport11 mRNA 284350 291201 . + . ID=transcript:AT1G01790.1;biotype=protein_coding;Parent=gene:AT1G01790;transcript_id=AT1G01790.1; -1 araport11 exon 284350 284635 . + . Name=AT1G01790.1.exon1;Parent=transcript:AT1G01790.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01790.1.exon1;rank=1; -1 araport11 five_prime_UTR 284350 284635 . + . Parent=transcript:AT1G01790.1; -1 araport11 five_prime_UTR 284722 284780 . + . Parent=transcript:AT1G01790.1; -1 araport11 exon 284722 286351 . + . Name=AT1G01790.1.exon2;Parent=transcript:AT1G01790.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01790.1.exon2;rank=2; -1 araport11 CDS 284781 286351 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 286452 286623 . + . Name=AT1G01790.2.exon2;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01790.2.exon2;rank=3; -1 araport11 CDS 286452 286623 . + 1 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 286717 286807 . + . Name=AT1G01790.2.exon3;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01790.2.exon3;rank=4; -1 araport11 CDS 286717 286807 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 286997 287133 . + . Name=AT1G01790.2.exon4;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01790.2.exon4;rank=5; -1 araport11 CDS 286997 287133 . + 2 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 287221 287280 . + . Name=AT1G01790.2.exon5;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon5;rank=6; -1 araport11 CDS 287221 287280 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 287395 287514 . + . Name=AT1G01790.2.exon6;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon6;rank=7; -1 araport11 CDS 287395 287514 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 287642 287710 . + . Name=AT1G01790.2.exon7;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon7;rank=8; -1 araport11 CDS 287642 287710 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 287789 287854 . + . Name=AT1G01790.2.exon8;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon8;rank=9; -1 araport11 CDS 287789 287854 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 288087 288176 . + . Name=AT1G01790.2.exon9;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon9;rank=10; -1 araport11 CDS 288087 288176 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 288401 288505 . + . Name=AT1G01790.2.exon10;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon10;rank=11; -1 araport11 CDS 288401 288505 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 288593 288721 . + . Name=AT1G01790.2.exon11;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon11;rank=12; -1 araport11 CDS 288593 288721 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 288882 289091 . + . Name=AT1G01790.2.exon12;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon12;rank=13; -1 araport11 CDS 288882 289091 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 289237 289386 . + . Name=AT1G01790.2.exon13;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon13;rank=14; -1 araport11 CDS 289237 289386 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 289539 289592 . + . Name=AT1G01790.2.exon14;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon14;rank=15; -1 araport11 CDS 289539 289592 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 289718 289776 . + . Name=AT1G01790.2.exon15;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01790.2.exon15;rank=16; -1 araport11 CDS 289718 289776 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 290028 290094 . + . Name=AT1G01790.2.exon16;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01790.2.exon16;rank=17; -1 araport11 CDS 290028 290094 . + 1 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 290170 290346 . + . Name=AT1G01790.2.exon17;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon17;rank=18; -1 araport11 CDS 290170 290346 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 290439 290495 . + . Name=AT1G01790.2.exon18;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon18;rank=19; -1 araport11 CDS 290439 290495 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 290578 290652 . + . Name=AT1G01790.2.exon19;Parent=transcript:AT1G01790.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon19;rank=20; -1 araport11 CDS 290578 290652 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 CDS 290747 290869 . + 0 ID=CDS:AT1G01790.1;Parent=transcript:AT1G01790.1;protein_id=AT1G01790.1 -1 araport11 exon 290747 291201 . + . Name=AT1G01790.1.exon21;Parent=transcript:AT1G01790.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01790.1.exon21;rank=21; -1 araport11 three_prime_UTR 290870 291201 . + . Parent=transcript:AT1G01790.1; -1 araport11 mRNA 284460 291203 . + . ID=transcript:AT1G01790.2;biotype=protein_coding;Parent=gene:AT1G01790;transcript_id=AT1G01790.2; -1 araport11 five_prime_UTR 284460 284780 . + . Parent=transcript:AT1G01790.2; -1 araport11 exon 284460 286351 . + . Name=AT1G01790.2.exon1;Parent=transcript:AT1G01790.2;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01790.2.exon1;rank=1; -1 araport11 CDS 284781 286351 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 286452 286623 . + . Name=AT1G01790.2.exon2;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01790.2.exon2;rank=2; -1 araport11 CDS 286452 286623 . + 1 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 286717 286807 . + . Name=AT1G01790.2.exon3;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=1;ensembl_phase=0;exon_id=AT1G01790.2.exon3;rank=3; -1 araport11 CDS 286717 286807 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 286997 287133 . + . Name=AT1G01790.2.exon4;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;exon_id=AT1G01790.2.exon4;rank=4; -1 araport11 CDS 286997 287133 . + 2 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 287221 287280 . + . Name=AT1G01790.2.exon5;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon5;rank=5; -1 araport11 CDS 287221 287280 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 287395 287514 . + . Name=AT1G01790.2.exon6;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon6;rank=6; -1 araport11 CDS 287395 287514 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 287642 287710 . + . Name=AT1G01790.2.exon7;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon7;rank=7; -1 araport11 CDS 287642 287710 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 287789 287854 . + . Name=AT1G01790.2.exon8;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon8;rank=8; -1 araport11 CDS 287789 287854 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 288087 288176 . + . Name=AT1G01790.2.exon9;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon9;rank=9; -1 araport11 CDS 288087 288176 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 288401 288505 . + . Name=AT1G01790.2.exon10;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon10;rank=10; -1 araport11 CDS 288401 288505 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 288593 288721 . + . Name=AT1G01790.2.exon11;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon11;rank=11; -1 araport11 CDS 288593 288721 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 288882 289091 . + . Name=AT1G01790.2.exon12;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon12;rank=12; -1 araport11 CDS 288882 289091 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 289237 289386 . + . Name=AT1G01790.2.exon13;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon13;rank=13; -1 araport11 CDS 289237 289386 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 289539 289592 . + . Name=AT1G01790.2.exon14;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon14;rank=14; -1 araport11 CDS 289539 289592 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 289718 289776 . + . Name=AT1G01790.2.exon15;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=2;ensembl_phase=0;exon_id=AT1G01790.2.exon15;rank=15; -1 araport11 CDS 289718 289776 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 290028 290094 . + . Name=AT1G01790.2.exon16;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01790.2.exon16;rank=16; -1 araport11 CDS 290028 290094 . + 1 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 290170 290346 . + . Name=AT1G01790.2.exon17;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon17;rank=17; -1 araport11 CDS 290170 290346 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 290439 290495 . + . Name=AT1G01790.2.exon18;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon18;rank=18; -1 araport11 CDS 290439 290495 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 290578 290652 . + . Name=AT1G01790.2.exon19;Parent=transcript:AT1G01790.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01790.2.exon19;rank=19; -1 araport11 CDS 290578 290652 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 CDS 290747 290869 . + 0 ID=CDS:AT1G01790.2;Parent=transcript:AT1G01790.2;protein_id=AT1G01790.2 -1 araport11 exon 290747 291203 . + . Name=AT1G01790.2.exon20;Parent=transcript:AT1G01790.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01790.2.exon20;rank=20; -1 araport11 three_prime_UTR 290870 291203 . + . Parent=transcript:AT1G01790.2; -1 araport11 ncRNA_gene 291594 292061 . - . ID=gene:AT1G04063;biotype=lncRNA;gene_id=AT1G04063;logic_name=araport11; -1 araport11 lnc_RNA 291594 292061 . - . ID=transcript:AT1G04063.1;biotype=lncRNA;Parent=gene:AT1G04063;transcript_id=AT1G04063.1; -1 araport11 exon 291594 292061 . - . Name=AT1G04063.1.exon1;Parent=transcript:AT1G04063.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G04063.1.exon1;rank=1; -1 araport11 gene 293246 295086 . + . ID=gene:AT1G01800;biotype=protein_coding;description=AT1G01800 protein [Source:UniProtKB/TrEMBL%3bAcc:Q94K30];gene_id=AT1G01800;logic_name=araport11; -1 araport11 mRNA 293246 295086 . + . ID=transcript:AT1G01800.1;biotype=protein_coding;Parent=gene:AT1G01800;transcript_id=AT1G01800.1; -1 araport11 five_prime_UTR 293246 293395 . + . Parent=transcript:AT1G01800.1; -1 araport11 exon 293246 293409 . + . Name=AT1G01800.1.exon1;Parent=transcript:AT1G01800.1;constitutive=0;ensembl_end_phase=2;ensembl_phase=-1;exon_id=AT1G01800.1.exon1;rank=1; -1 araport11 CDS 293396 293409 . + 0 ID=CDS:AT1G01800.1;Parent=transcript:AT1G01800.1;protein_id=AT1G01800.1 -1 araport11 exon 293500 293752 . + . Name=AT1G01800.1.exon2;Parent=transcript:AT1G01800.1;constitutive=0;ensembl_end_phase=0;ensembl_phase=2;exon_id=AT1G01800.1.exon2;rank=2; -1 araport11 CDS 293500 293752 . + 1 ID=CDS:AT1G01800.1;Parent=transcript:AT1G01800.1;protein_id=AT1G01800.1 -1 araport11 exon 294055 294120 . + . Name=AT1G01800.1.exon3;Parent=transcript:AT1G01800.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01800.1.exon3;rank=3; -1 araport11 CDS 294055 294120 . + 0 ID=CDS:AT1G01800.1;Parent=transcript:AT1G01800.1;protein_id=AT1G01800.1 -1 araport11 exon 294210 294386 . + . Name=AT1G01800.1.exon4;Parent=transcript:AT1G01800.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01800.1.exon4;rank=4; -1 araport11 CDS 294210 294386 . + 0 ID=CDS:AT1G01800.1;Parent=transcript:AT1G01800.1;protein_id=AT1G01800.1 -1 araport11 CDS 294511 294888 . + 0 ID=CDS:AT1G01800.1;Parent=transcript:AT1G01800.1;protein_id=AT1G01800.1 -1 araport11 exon 294511 295086 . + . Name=AT1G01800.1.exon5;Parent=transcript:AT1G01800.1;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01800.1.exon5;rank=5; -1 araport11 three_prime_UTR 294889 295086 . + . Parent=transcript:AT1G01800.1; -1 araport11 mRNA 293342 295040 . + . ID=transcript:AT1G01800.2;biotype=protein_coding;Parent=gene:AT1G01800;transcript_id=AT1G01800.2; -1 araport11 exon 293342 293409 . + . Name=AT1G01800.2.exon1;Parent=transcript:AT1G01800.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01800.2.exon1;rank=1; -1 araport11 five_prime_UTR 293342 293409 . + . Parent=transcript:AT1G01800.2; -1 araport11 five_prime_UTR 293500 293594 . + . Parent=transcript:AT1G01800.2; -1 araport11 exon 293500 293756 . + . Name=AT1G01800.2.exon2;Parent=transcript:AT1G01800.2;constitutive=0;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01800.2.exon2;rank=2; -1 araport11 CDS 293595 293756 . + 0 ID=CDS:AT1G01800.2;Parent=transcript:AT1G01800.2;protein_id=AT1G01800.2 -1 araport11 exon 294055 294120 . + . Name=AT1G01800.1.exon3;Parent=transcript:AT1G01800.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01800.1.exon3;rank=3; -1 araport11 CDS 294055 294120 . + 0 ID=CDS:AT1G01800.2;Parent=transcript:AT1G01800.2;protein_id=AT1G01800.2 -1 araport11 exon 294210 294386 . + . Name=AT1G01800.1.exon4;Parent=transcript:AT1G01800.2;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01800.1.exon4;rank=4; -1 araport11 CDS 294210 294386 . + 0 ID=CDS:AT1G01800.2;Parent=transcript:AT1G01800.2;protein_id=AT1G01800.2 -1 araport11 CDS 294511 294888 . + 0 ID=CDS:AT1G01800.2;Parent=transcript:AT1G01800.2;protein_id=AT1G01800.2 -1 araport11 exon 294511 295040 . + . Name=AT1G01800.2.exon5;Parent=transcript:AT1G01800.2;constitutive=0;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01800.2.exon5;rank=5; -1 araport11 three_prime_UTR 294889 295040 . + . Parent=transcript:AT1G01800.2; -1 araport11 gene 295207 295859 . + . ID=gene:AT1G01810;biotype=protein_coding;description=T1N6.23 [Source:UniProtKB/TrEMBL%3bAcc:Q9LQ74];gene_id=AT1G01810;logic_name=araport11; -1 araport11 mRNA 295207 295859 . + . ID=transcript:AT1G01810.1;biotype=protein_coding;Parent=gene:AT1G01810;transcript_id=AT1G01810.1; -1 araport11 five_prime_UTR 295207 295241 . + . Parent=transcript:AT1G01810.1; -1 araport11 exon 295207 295859 . + . Name=AT1G01810.1.exon1;Parent=transcript:AT1G01810.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01810.1.exon1;rank=1; -1 araport11 CDS 295242 295724 . + 0 ID=CDS:AT1G01810.1;Parent=transcript:AT1G01810.1;protein_id=AT1G01810.1 -1 araport11 three_prime_UTR 295725 295859 . + . Parent=transcript:AT1G01810.1; -1 araport11 gene 296001 298334 . - . ID=gene:AT1G01820;Name=PEX11C;biotype=protein_coding;description=Peroxisomal membrane protein 11C [Source:UniProtKB/Swiss-Prot%3bAcc:Q9LQ73];gene_id=AT1G01820;logic_name=araport11; -1 araport11 mRNA 296001 298334 . - . ID=transcript:AT1G01820.1;biotype=protein_coding;Parent=gene:AT1G01820;transcript_id=AT1G01820.1; -1 araport11 three_prime_UTR 296001 296212 . - . Parent=transcript:AT1G01820.1; -1 araport11 exon 296001 296248 . - . Name=AT1G01820.1.exon8;Parent=transcript:AT1G01820.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;exon_id=AT1G01820.1.exon8;rank=8; -1 araport11 CDS 296213 296248 . - 0 ID=CDS:AT1G01820.1;Parent=transcript:AT1G01820.1;protein_id=AT1G01820.1 -1 araport11 exon 296362 296535 . - . Name=AT1G01820.1.exon7;Parent=transcript:AT1G01820.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01820.1.exon7;rank=7; -1 araport11 CDS 296362 296535 . - 0 ID=CDS:AT1G01820.1;Parent=transcript:AT1G01820.1;protein_id=AT1G01820.1 -1 araport11 exon 296626 296700 . - . Name=AT1G01820.1.exon6;Parent=transcript:AT1G01820.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01820.1.exon6;rank=6; -1 araport11 CDS 296626 296700 . - 0 ID=CDS:AT1G01820.1;Parent=transcript:AT1G01820.1;protein_id=AT1G01820.1 -1 araport11 exon 296782 296862 . - . Name=AT1G01820.1.exon5;Parent=transcript:AT1G01820.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01820.1.exon5;rank=5; -1 araport11 CDS 296782 296862 . - 0 ID=CDS:AT1G01820.1;Parent=transcript:AT1G01820.1;protein_id=AT1G01820.1 -1 araport11 exon 296951 297025 . - . Name=AT1G01820.1.exon4;Parent=transcript:AT1G01820.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01820.1.exon4;rank=4; -1 araport11 CDS 296951 297025 . - 0 ID=CDS:AT1G01820.1;Parent=transcript:AT1G01820.1;protein_id=AT1G01820.1 -1 araport11 exon 297101 297175 . - . Name=AT1G01820.1.exon3;Parent=transcript:AT1G01820.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=AT1G01820.1.exon3;rank=3; -1 araport11 CDS 297101 297175 . - 0 ID=CDS:AT1G01820.1;Parent=transcript:AT1G01820.1;protein_id=AT1G01820.1 -1 araport11 CDS 297532 297723 . - 0 ID=CDS:AT1G01820.1;Parent=transcript:AT1G01820.1;protein_id=AT1G01820.1 -1 araport11 exon 297532 297743 . - . Name=AT1G01820.1.exon2;Parent=transcript:AT1G01820.1;constitutive=1;ensembl_end_phase=0;ensembl_phase=-1;exon_id=AT1G01820.1.exon2;rank=2; -1 araport11 five_prime_UTR 297724 297743 . - . Parent=transcript:AT1G01820.1; -1 araport11 exon 298013 298334 . - . Name=AT1G01820.1.exon1;Parent=transcript:AT1G01820.1;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=AT1G01820.1.exon1;rank=1; -1 araport11 five_prime_UTR 298013 298334 . - . Parent=transcript:AT1G01820.1; -1 araport11 gene 298451 302310 . - . ID=gene:AT1G01830;biotype=protein_coding;description=ARM repeat superfamily protein [Source:UniProtKB/TrEMBL%3bAcc:Q93YW3];gene_id=AT1G01830;logic_name=araport11; -1 araport11 mRNA 298451 300757 . - . ID=transcript:AT1G01830.1;biotype=protein_coding;Parent=gene:AT1G01830;transcript_id=AT1G01830.1; -1 araport11 three_prime_UTR 298451 298716 . - . Parent=transcript:AT1G01830.1; diff --git a/inst/extdata/toyData/methimpute_p1.txt b/inst/extdata/toyData/methimpute_p1.txt index f65380f..ca072a5 100644 --- a/inst/extdata/toyData/methimpute_p1.txt +++ b/inst/extdata/toyData/methimpute_p1.txt @@ -999,79003 +999,3 @@ seqnames,start,strand,context,counts.methylated,counts.total,posteriorMax,status 1,3101,+,CHH,0,25,0.697661974385763,U,0,CAC 1,3103,+,CHH,0,0,0.159743768960945,I,0.618990755826235,CAT 1,3109,+,CHH,0,0,0.292910533125289,I,0.44950035456568,CTA -1,3112,-,CHH,0,0,0.373731096374579,I,0.663134034816176,CTA -1,3115,-,CHH,1,1,0.982004366005769,M,0.867915087705478,CTT -1,3117,+,CHG,0,0,0.148225576367006,I,0.643407718744129,CAG -1,3119,-,CHG,0,0,0.540000853577405,I,0.682099439203739,CTG -1,3123,+,CG,3,3,0.627271620444623,M,1,CGA -1,3124,-,CG,0,0,0.276741738530584,I,0.675498486123979,CGA -1,3126,-,CHH,0,0,0.25954070767086,I,0.65279742013663,CTC -1,3129,-,CHH,0,0,0.344257638656311,I,0.419952272810042,CAA -1,3130,+,CHH,0,0,0.407872313383743,I,0.696011656150222,CTC -1,3132,+,CHH,0,0,0.161212727876157,I,0.461157156247646,CTC -1,3134,+,CHH,1,1,0.903488983010207,M,0.867884539440274,CCT -1,3135,+,CHH,0,7,0.721697849158817,U,0,CTT -1,3139,-,CHH,0,0,0.283132459252849,I,0.45559561913833,CAA -1,3144,-,CHH,0,0,0.132485481311344,I,0.484757240302861,CAA -1,3145,+,CHH,0,0,0.476655802323259,I,0.587839909363538,CTT -1,3149,-,CHH,0,0,0.338458962372281,I,0.437197342980653,CAA -1,3150,-,CHH,0,0,0.463620799460225,I,0.628149664681405,CCA -1,3151,-,CHH,1,1,0.937542485333141,M,1,CCC -1,3153,-,CHH,0,0,0.19498564988073,I,0.424075847771019,CTC -1,3154,-,CHH,0,0,0.11776447713539,I,0.693053276184946,CCT -1,3155,-,CHH,1,1,0.679212165847444,M,0.952334183291532,CCC -1,3157,+,CHH,0,0,0.327211842622384,I,0.433110547717661,CCC -1,3158,+,CHH,0,0,0.394551253045686,I,0.680373879056424,CCA -1,3159,+,CHH,0,0,0.257731753966548,I,0.498235676437616,CAT -1,3167,+,CHG,0,1,0.648138759111236,U,0.0526142101502046,CCG -1,3168,+,CG,14,14,0.713820717308931,M,0.934198770765215,CGC -1,3169,-,CG,0,0,0.302360517305099,I,0.490058626141399,CGG -1,3170,+,CHH,0,0,0.417849163274989,I,0.449774055555463,CCC -1,3171,+,CHH,0,0,0.199069619394615,I,0.626439745072275,CCA -1,3172,+,CHG,0,0,0.53353059709236,I,0.383794897422195,CAG -1,3174,-,CHG,0,0,0.527008888061866,I,0.508901618141681,CTG -1,3175,+,CHG,0,0,0.463474778674319,I,0.663046434335411,CAG -1,3177,-,CHG,0,0,0.429476470436677,I,0.438607586733997,CTG -1,3178,+,CHH,0,0,0.413550997950845,I,0.600164930615574,CTT -1,3181,+,CHH,1,1,0.676347006852776,M,1,CCC -1,3182,+,CHH,0,0,0.168130156683512,I,0.619868785329163,CCA -1,3183,+,CHG,0,0,0.237443953851946,I,0.684544943645597,CAG -1,3185,-,CHG,0,0,0.269521188090332,I,0.450319936685264,CTG -1,3186,+,CHH,0,0,0.42298847365357,I,0.378851641621441,CCT -1,3187,+,CHH,0,0,0.111985830805972,I,0.632089031115174,CTT -1,3190,+,CHH,0,0,0.193462786364146,I,0.655109537392855,CCT 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-1,218590,+,CHH,0,0,0.163420826528929,I,0.481923517864198,CTT -1,218593,-,CHH,0,0,0.279678167292625,I,0.540129550825804,CAA -1,218596,-,CHH,0,0,0.500645481615104,I,0.564666187297553,CTA -1,218597,+,CHG,0,0,0.582339150814116,I,0.520926585886627,CTG -1,218599,-,CHG,0,0,0.499327353068404,I,0.500654857233167,CAG -1,218602,+,CHH,0,0,0.180691392726041,I,0.608345295395702,CCT -1,218603,+,CHH,27,27,0.694172036501505,M,0.855202955962159,CTA -1,218616,-,CHH,0,0,0.326703057141751,I,0.624537375755608,CTA -1,218618,-,CHH,0,0,0.16514583593864,I,0.46804706165567,CTC -1,218619,+,CHH,0,1,0.750562639221083,U,0,CAT -1,218627,+,CHH,0,0,0.406547383388281,I,0.588009461574256,CTA -1,218631,+,CHH,0,0,0.365262902441211,I,0.640789972804487,CTC -1,218633,+,CHH,0,0,0.500844032835923,I,0.597255223616958,CAC -1,218635,+,CHH,0,0,0.348306142358817,I,0.489715758990496,CCA -1,218636,+,CHH,1,1,0.973953603085051,M,0.993688452406786,CAC -1,218638,+,CHG,0,0,0.308797872841135,I,0.688541683647782,CCG -1,218639,+,CG,0,0,0.183310292411372,I,0.459225529804826,CGC -1,218640,-,CG,0,0,0.220037967298888,I,0.357897579390556,CGG -1,218641,+,CHH,0,1,0.790291757853462,U,0,CCA -1,218642,+,CHH,0,0,0.471651376324482,I,0.524061427731067,CAA -1,218646,+,CHH,0,0,0.550716982788183,I,0.570438953209668,CTC -1,218648,+,CHH,0,0,0.38984278820619,I,0.545518779102713,CAA -1,218651,+,CG,0,1,0.635674659271319,U,0.0242406358709559,CGT -1,218652,-,CG,0,0,0.443236302334592,I,0.639297390729189,CGT -1,218654,-,CHH,0,0,0.132207952073552,I,0.362295221444219,CAC -1,218656,-,CHH,0,0,0.543417513353527,I,0.541941994056106,CAC -1,218662,+,CHH,0,1,0.923183138726095,U,0.0777952224947512,CTT -1,218669,+,CHH,0,0,0.138895697409064,I,0.321530976891518,CCC -1,218670,+,CHH,0,0,0.131539725099467,I,0.528410036209971,CCT -1,218671,+,CHH,11,11,0.790413383654617,M,0.956976733449847,CTA -1,218676,+,CHH,0,0,0.474003164779171,I,0.429112166818231,CTT -1,218679,+,CHH,0,0,0.344990192662701,I,0.502529255393893,CTA -1,218694,-,CHH,0,0,0.306301540794559,I,0.564579849876463,CTA -1,218696,+,CG,0,0,0.445940259361416,I,0.347303730994463,CGA -1,218697,-,CG,0,0,0.270930855983645,I,0.307496833708137,CGT -1,218699,+,CHH,0,0,0.227356016036831,I,0.417938547953963,CTT -1,218707,+,CHH,0,0,0.418845697987601,I,0.593983870837838,CTT -1,218714,+,CHH,0,0,0.544342594902739,I,0.506675478629768,CTT -1,218717,+,CHH,0,0,0.228054408898354,I,0.317100988235325,CTT -1,218720,+,CHH,0,0,0.553426745097861,I,0.451159505918622,CTT -1,218723,+,CHH,0,0,0.29902730484657,I,0.339126704260707,CCC -1,218724,+,CHH,0,1,0.781298896727327,U,0.123315376136452,CCC -1,218725,+,CHH,0,0,0.370750074956343,I,0.430941900517792,CCA -1,218726,+,CHH,1,1,0.769916393049869,M,1,CAC -1,218728,+,CHH,0,0,0.514374322590195,I,0.431931543722749,CCA -1,218729,+,CHH,0,0,0.230482554977536,I,0.57352531766519,CAT -1,218732,+,CHH,0,0,0.405550694308952,I,0.30990583030507,CTT -1,218740,-,CHH,0,0,0.418998629885502,I,0.523357870616019,CAA -1,218742,-,CHH,0,0,0.226077388955057,I,0.353944530058652,CAC -1,218743,+,CHH,0,0,0.178326316277273,I,0.313414556439966,CTC -1,218745,+,CHH,0,0,0.508467823366411,I,0.40523320985958,CTA diff --git a/jDMRgrid.Rproj b/jDMRgrid.Rproj deleted file mode 100644 index 497f8bf..0000000 --- a/jDMRgrid.Rproj +++ /dev/null @@ -1,20 +0,0 @@ -Version: 1.0 - -RestoreWorkspace: Default -SaveWorkspace: Default -AlwaysSaveHistory: Default - -EnableCodeIndexing: Yes -UseSpacesForTab: Yes -NumSpacesForTab: 2 -Encoding: UTF-8 - -RnwWeave: Sweave -LaTeX: pdfLaTeX - -AutoAppendNewline: Yes -StripTrailingWhitespace: Yes - -BuildType: Package -PackageUseDevtools: Yes -PackageInstallArgs: --no-multiarch --with-keep.source diff --git a/man/annotateDMRs.Rd b/man/annotateDMRs.Rd index 60e4baf..8735aa1 100644 --- a/man/annotateDMRs.Rd +++ b/man/annotateDMRs.Rd @@ -2,21 +2,25 @@ \alias{annotateDMRs} \title{Annotate DMRs} \usage{ -annotateDMRs(annotation, gff.files, gff3.out, input.dir, out.dir) +annotateDMRs(annotation, gff.files, if.gff3, input.dir, out.dir) } \arguments{ -\item{annotation}{annotation terms used to annotate DMRs} +\item{annotation}{Vector with the annotation terms used to annotate DMRs. +(character)} -\item{gff.files}{multiple gff3 files can be supplied as a vector} +\item{gff.files}{Vector with the multiple gff3 files corresponding to +the annotation terms. (character)} -\item{if.gff3}{a logical specifying whether output annotated files in -gff3 format} +\item{if.gff3}{Logical specifying whether output annotated files in +gff3 format. (logical)} -\item{input.dir}{input directory containing filtered DMR matrix/matrices. -Ideally any file containing 3 columns i.e (chr, start, stop) can be supplied.} +\item{input.dir}{Path to the input directory containing filtered DMR matrices. +Ideally any file containing 3 columns i.e (chr, start, stop) can be supplied. +(character)} -\item{out.dir}{output directory} +\item{out.dir}{Path to the output directory. (character)} } + \value{ output files containing annotated DMRs and DMR counts table. } @@ -25,18 +29,16 @@ This function takes gff3 files as input and outputs annotated DMRs in text and gff3 format. Additionally, a DMR count table is generated. } \examples{ -## Get some toy data -data.dir.pop <- "folder_population/annotate_DMRs" -data.dir.rep <- "folder_replicate/annotate_DMRs" -gff.file_promoters <- system.file( - "extdata/toyData","TAIR10_promoters.gff3", package="jDMRgrid") -gff.file_promoters <- system.file( - "extdata/toyData", "TAIR10_TE.gff3", package="jDMRgrid") -gff.file_genes <- system.file( - "extdata/toyData", "TAIR10.gene.chr1.gff3", package="jDMRgrid") -annotateDMRs(gff.files = c( - gff.file_promoters, gff.file_TE, gff.file_genes), annotation = c( - "promoters", "TE", "gene"), - input.dir = "folder_population/context_DMRs", if.gff3 = FALSE, - out.dir = data.dir.pop) +system2(command = "/bin/mkdir", args = "~/annotation.files") +annotateDMRs( + annotation = c('promoters','TE'), + gff.files = c( + system.file("extdata/toyData","TAIR10_promoters.gff3", + package="jDMRgrid"), + system.file("extdata/toyData","TAIR10_TE.gff3", + package="jDMRgrid")), + if.gff3 = TRUE, + input.dir = system.file( + "extdata", "matrix_CT_replicate", package="jDMRgrid"), + out.dir = "~/annotation.files") } diff --git a/man/context.specific.DMRs.Rd b/man/context.specific.DMRs.Rd new file mode 100644 index 0000000..5f67991 --- /dev/null +++ b/man/context.specific.DMRs.Rd @@ -0,0 +1,45 @@ +\name{context.specific.DMRs} +\alias{context.specific.DMRs} +\title{subset context specific DMRs} +\usage{ +context.specific.DMRs(samplelist, input.dir, output.dir, if.filtered = FALSE) +} +\arguments{ +\item{samplelist}{DataFrame object containing information about +file, sample and replicate. For control/treatment data an +additional column specifying the replicates is required. (DataFrame object)} + +\item{input.dir}{Path to the input directory containing DMR matrix files. +Looks for files with suffix("_StateCalls.txt" and "_rcMethlvl.txt"). +(character)} + +\item{output.dir}{Path to the output directory, which will contain set of DMRs +containing context-specific DMRs, non-CG DMRs and multi-context DMRs. +(character)} + +\item{if.filtered}{Logical to specify if we should use filtered or +non-filtered matrices. By default it is set to FALSE. (logical)} +} + +\value{ +output txt files containing context-specific DMRs for five categories: +-> CG-only, +-> CHG-only, +-> CHH-only, +-> non-CG (occurs for CHG and/or CHH, but not for CG context), +-> multi-context (occurs for CG and CHG and CHH contexts) +} +\description{ +Output context-specific DMRs (only for a given context, nonCG or all context) +} +\examples{ +load(system.file("data", "listFiles2.RData", package="jDMRgrid")) +listFiles2$file <- system.file("extdata", listFiles2$file, package="jDMRgrid") +system2(command = "/bin/mkdir", args = "~/context.specific.DMRs") +context.specific.DMRs( + samplelist = listFiles2, + input.dir = system.file( + "extdata", "matrix_CT_replicate/", package="jDMRgrid"), + output.dir = '~/context.specific.DMRs', + if.filtered = FALSE) +} \ No newline at end of file diff --git a/man/filterDMRmatrix.Rd b/man/filterDMRmatrix.Rd index 08ca19e..afd8965 100644 --- a/man/filterDMRmatrix.Rd +++ b/man/filterDMRmatrix.Rd @@ -3,8 +3,8 @@ \title{filter DMR matrix} \usage{ filterDMRmatrix( - epiMAF.cutoff = NULL, replicate.consensus = NULL, data.dir, samplefiles, - mergingBins = TRUE) + epiMAF.cutoff = NULL, replicate.consensus = NULL, data.dir, samplelist, + if.mergingBins = FALSE) } \arguments{ \item{epiMAF.cutoff}{Numeric threshold to filter for minor epi-allele @@ -20,31 +20,60 @@ Applicable for control/treatment data. By default this option is set to NULL. Looks for files with suffix("_StateCalls.txt" and "_rcMethlvl.txt"). (character)} -\item{samplefiles}{Path to the text file containing path to samples -and sample names. For control/treatment data an -additional column specifying the replicates is required. (character)} +\item{samplelist}{DataFrame object containing information about +file, sample and replicate. For control/treatment data an +additional column specifying the replicates is required. (DataFrame object)} \item{if.mergingBins}{Logical argument if merging consecutive bins having the same stateCalls should be performed. -By default it is set to TRUE. (logical)} +By default it is set to FALSE. (logical)} } \value{ output files containing filtered matrices of state calls, methylation levels and optionally postMax probabilities. } \description{ -Filters non-polymorphic patterns by default. +Filters non-polymorphic patterns by default. User can decide whether: +-> filters non-polymorphic patterns only (epiMAF.cutoff = NULL, +replicate.consensus = NULL, if.mergingBins = FALSE) +-> Set if.mergingBins = TRUE only if the number of samples is relatively small +-> Set epiMAF.cutoff to numeric value if you deal with population-based data +-> Set replicate.consensus to numeric value if you deal with replicate/groups + } \examples{ -## For population-based data use epiMAF cutoff +#------------------------------------------------------------------------------ +# REPLICATE-BASED DATASET; STEP IV +#------------------------------------------------------------------------------ +# Step 1.7: Copy required files and create required directories for outputs +load(system.file("data", "listFiles2.RData", package="jDMRgrid")) +listFiles2$file <- system.file("extdata", listFiles2$file, package="jDMRgrid") +input_file <- system.file("extdata", "matrix_CT_replicate", package="jDMRgrid") +system2( + command = "/bin/cp", + args = paste0("-r ", input_file, " ", "~/")) + +# Step 1.8: filterDMRmatrix for replicate-based data filterDMRmatrix( - epiMAF.cutoff = 0.33, replicate.consensus = NULL, - data.dir = "folder_population/matrix", samplefiles = system.file( - "extdata", "listFiles1.fn", package="jDMRgrid"), if.mergingBins = TRUE) + epiMAF.cutoff = NULL, replicate.consensus = 0.5, + data.dir = "~/matrix_CT_replicate", + samplelist = listFiles2, if.mergingBins = TRUE) -## For treatment-control data use replicate.consensus cutoff +#------------------------------------------------------------------------------ +# POPULATION-BASED DATASET; STEP III +#------------------------------------------------------------------------------ +# Step 2.5: Copy required files and create required directories for outputs +load(system.file("data", "listFiles1.RData", package="jDMRgrid")) +listFiles1$file <- system.file("extdata", listFiles1$file, package="jDMRgrid") +input_file <- system.file("extdata", "matrix_population", package="jDMRgrid") +system2( + command = "/bin/cp", + args = paste0("-r ", input_file, " ", "~/")) + +# Step 2.6: filterDMRmatrix for population-based data filterDMRmatrix( - epiMAF.cutoff = NULL, replicate.consensus = 0.8, - data.dir = "folder_replicate/matrix", samplefiles = system.file( - "extdata", "listFiles2.fn", package="jDMRgrid"), if.mergingBins = TRUE) + epiMAF.cutoff = 0.33, replicate.consensus = NULL, + data.dir = "~/matrix_population", + samplelist = listFiles1, if.mergingBins = TRUE) + } \ No newline at end of file diff --git a/man/filterEpiMAF.Rd b/man/filterEpiMAF.Rd new file mode 100644 index 0000000..e0a08c7 --- /dev/null +++ b/man/filterEpiMAF.Rd @@ -0,0 +1,51 @@ +\name{filterEpiMAF} +\alias{filterEpiMAF} +\title{filter DMR matrix according to the minor epi-allele frequency} +\usage{ +filterEpiMAF(status.collect, rc.methlevel.collect, epiMAF) +} +\arguments{ +\item{status.collect}{Data frame containing state calls for a given sample. +(DataFrame object)} + +\item{rc.methlevel.collect}{Data frame containing methylation levels for +a given sample. (DataFrame object)} + +\item{epiMAF}{Numeric threshold to filter for minor epi-allele +frequency. Applicable for population level data. By default this option is +set to NULL. (NULL or numeric value between 0 and 1)} +} +\value{ +list of data frames for rc-methylation level and state-calls using +minor epi-allele frequency criterion. +} +\description{ +Filter for minor epi-allele frequency in population-based data. +Example: Let's have 4 regions to be filtered having the following frequency of +the state calls among all sample (M = Meth, I = Intermediate, U = Unmeth) +Region 1: 1M, 2I, 7U +Region 2: 3M, 7U +Region 3: 2M 4I 4U +Region 4: 5M 5U + +Let's calculate the frequency of the state call which occurs least often: +Region 1: Meth (10%) +Region 2: Meth (30%) +Region 3: Meth (20%) +Region 4: Meth (50%) + +If the epiMAF cutoff is set to 0.33, region 1 and region 2 would be removed +from the final dataset. +} +\examples{ +list.out <- filterEpiMAF( + status.collect = data.table::fread( + system.file( + "extdata", "matrix_population/CG_StateCalls.txt", + package="jDMRgrid")), + rc.methlevel.collect = data.table::fread( + system.file( + "extdata", "matrix_population/CG_rcMethlvl.txt", + package="jDMRgrid")), + epiMAF = 0.3) +} \ No newline at end of file diff --git a/man/filterReplicateConsensus.Rd b/man/filterReplicateConsensus.Rd new file mode 100644 index 0000000..ab6d6f0 --- /dev/null +++ b/man/filterReplicateConsensus.Rd @@ -0,0 +1,46 @@ +\name{filterReplicateConsensus} +\alias{filterReplicateConsensus} +\title{filter DMR matrix according to the replicate consensus} +\usage{ +filterReplicateConsensus( + status.collect, rc.methlevel.collect, replicate.consensus, diff.ct) +} + +\arguments{ + +\item{status.collect}{Data frame containing state calls for a given sample. +(DataFrame object)} + +\item{rc.methlevel.collect}{Data frame containing methylation levels for +a given sample. (DataFrame object)} + +\item{replicate.consensus}{Numeric threshold as the percentage of concordance +in methylation states among samples with multiple replicates. +Applicable for control/treatment data. (numeric value between 0 and 1)} + +\item{diff.ct}{Allowed difference between control and treatment groups. +In filterDMRmatrix function it is set to 0.5 (numeric value between 0 and 1)} + +} +\value{ +list of data frames for rc-methylation level and state-calls using +replicate consensus criterion.} +\description{ +Filtering of DMR matrices (state-calls and methylation levels) according to the +percentage of concordance in methylation states among samples with multiple +replicates. Applicable for control/treatment data. +} +\examples{ +list.out <- filterReplicateConsensus( + status.collect = data.table::fread( + system.file( + "extdata", "matrix_CT_replicate/CG_WT_mutant1_StateCalls.txt", + package="jDMRgrid")), + rc.methlevel.collect = data.table::fread( + system.file( + "extdata", "matrix_CT_replicate/CG_WT_mutant1_rcMethlvl.txt", + package="jDMRgrid")), + replicate.consensus = 0.5, + diff.ct = 0.5) + +} \ No newline at end of file diff --git a/man/listFiles1.Rd b/man/listFiles1.Rd new file mode 100644 index 0000000..8d1c66b --- /dev/null +++ b/man/listFiles1.Rd @@ -0,0 +1,17 @@ +\docType{data} +\name{listFiles1} +\alias{listFiles1} +\title{samplelist file for population-based data} +\format{A \code{\link[S4Vectors]{DataFrame-class}} object.} +\description{ +A \code{\link[S4Vectors]{DataFrame-class}} object for demonstration purposes in +examples of package jDMRgrid. +The object contains a samplelist file for population-based data +} +\value{ +samplelist file for population-based data +} +\examples{ +data(listFiles1) +print(listFiles1) +} \ No newline at end of file diff --git a/man/listFiles2.Rd b/man/listFiles2.Rd new file mode 100644 index 0000000..ba3cbee --- /dev/null +++ b/man/listFiles2.Rd @@ -0,0 +1,17 @@ +\docType{data} +\name{listFiles2} +\alias{listFiles2} +\title{samplelist file for replicate-based data} +\format{A \code{\link[S4Vectors]{DataFrame-class}} object.} +\description{ +A \code{\link[S4Vectors]{DataFrame-class}} object for demonstration purposes in +examples of package jDMRgrid. +The object contains a samplelist file for replicate-based data +} +\value{ +samplelist file for replicate-based data +} +\examples{ +data(listFiles2) +print(listFiles2) +} \ No newline at end of file diff --git a/man/makeDMRmatrix.Rd b/man/makeDMRmatrix.Rd index 8561ed7..1900dc6 100644 --- a/man/makeDMRmatrix.Rd +++ b/man/makeDMRmatrix.Rd @@ -3,25 +3,34 @@ \title{Builds a DMR matrix for all samples} \usage{ makeDMRmatrix( - contexts = c("CG", "CHG", "CHH"), postMax.out = FALSE, samplefiles, + contexts = c("CG", "CHG", "CHH"), postMax.out = FALSE, samplelist, input.dir, out.dir, include.intermediate = FALSE) } \arguments{ -\item{samplefiles}{file containing full path of base level methylation calls, -sample names and replicates(optional)} +\item{contexts}{Vector of cytosine contexts selected for DMR calling. By +default this option is set for all 3 cytosine contexts CG, CHG and CHH. +(character vector; by default c('CG','CHG','CHH'))} -\item{input.dir}{input directory containing all region level methylome calls} +\item{postMax.out}{(A logical specyfing whether or not to output posterior +probability for the identified state call known as postMax probability. +(optional; logical; by default is FALSE))} -\item{out.dir}{output directory} +\item{samplelist}{DataFrame object containing information about +file, sample and replicate. For control/treatment data an +additional column specifying the replicates is required. (DataFrame object)} + +\item{input.dir}{Path to the input directory containing all region level +methylome calls (character)} + +\item{out.dir}{Path to the output directory (character)} \item{include.intermediate}{A logical specifying whether or not the intermediate component should be included in the HMM model. -By default this option is set as FALSE.} +(optional; logical; be default is FALSE)} -\item{context}{cytosine context} } \value{ -output files containing matrices of state calls, methylation levels and +Output files containing matrices of state calls, methylation levels and optionally postMax probabilities. } \description{ @@ -29,10 +38,39 @@ This function generates a binary matrix, a matrix of recalibrated methylation levels and posterior probabilities for all samples. } \examples{ +#------------------------------------------------------------------------------ +# REPLICATE-BASED DATASET; STEP II +#------------------------------------------------------------------------------ +# Step 1.3: Copy required files and create required directories for outputs +load(system.file("data", "listFiles2.RData", package="jDMRgrid")) +listFiles2$file <- system.file("extdata", listFiles2$file, package="jDMRgrid") +input_file <- system.file("extdata", "grid_replicate", package="jDMRgrid") +system2( + command = "/bin/cp", + args = paste0("-r ", input_file, " ", "~/")) +system2(command = "/bin/mkdir", args = "~/matrix_replicate") + +# Step 1.4: makeDMRmatrix for replicate-based data +makeDMRmatrix( + contexts = c("CG", "CHG", "CHH"), postMax.out = TRUE, + samplelist = listFiles2, input.dir = '~/grid_replicate', + out.dir = '~/matrix_replicate', include.intermediate = FALSE) + +#------------------------------------------------------------------------------ +# POPULATION-BASED DATASET; STEP II +#------------------------------------------------------------------------------ +# Step 1.3: Copy required files and create required directories for outputs +load(system.file("data", "listFiles1.RData", package="jDMRgrid")) +listFiles1$file <- system.file("extdata", listFiles1$file, package="jDMRgrid") +input_file <- system.file("extdata", "grid_population", package="jDMRgrid") +system2( + command = "/bin/cp", + args = paste0("-r ", input_file, " ", "~/")) +system2(command = "/bin/mkdir", args = "~/matrix_population") + +# Step 1.4: makeDMRmatrix for population-based data makeDMRmatrix( contexts = c("CG", "CHG", "CHH"), postMax.out = TRUE, - samplefiles = system.file( - "extdata", "listFiles1.fn", package="jDMRgrid"), - input.dir = 'folder_population/grid', out.dir = 'folder_population/matrix', - include.intermediate = FALSE) + samplelist = listFiles1, input.dir = '~/grid_population', + out.dir = '~/matrix_population', include.intermediate = FALSE) } \ No newline at end of file diff --git a/man/runjDMRgrid.Rd b/man/runjDMRgrid.Rd index 56e80ac..578f4ca 100644 --- a/man/runjDMRgrid.Rd +++ b/man/runjDMRgrid.Rd @@ -1,13 +1,12 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/runjDMR.R \name{runjDMRgrid} \alias{runjDMRgrid} \title{Run jDMR on binned genome} \usage{ runjDMRgrid( - out.dir, window, step, samplefiles, contexts = c("CG", "CHG", "CHH"), + out.dir, window, step, samplelist, contexts = c("CG", "CHG", "CHH"), min.C, mincov = 0, include.intermediate = FALSE, runName = "GridGenome", - numCores = NULL, parallelApply = FALSE + numCores = NULL, parallelApply = FALSE, if.Bismark = FALSE, + FASTA.file = NULL ) } \arguments{ @@ -17,9 +16,9 @@ runjDMRgrid( \item{step}{Step size. (numeric vector)} -\item{samplefiles}{Path to the text file containing path to samples -and sample names. For control/treatment data an additional column -specifying the replicates is required. (character)} +\item{samplelist}{DataFrame object containing information about +file, sample and replicate. For control/treatment data an +additional column specifying the replicates is required. (DataFrame object)} \item{contexts}{Vector of cytosine contexts selected for DMR calling. By default this option is set for all 3 cytosine contexts CG, CHG and CHH. @@ -31,7 +30,7 @@ cytosines across bins. (numeric value between 0 and 100)} \item{mincov}{Minimum read coverage over cytosines. By default this option is set as 0. (numeric value between 0 and 1)} -\item{include.intermediate}{A logical specifying whether or not the +\item{include.intermediate}{Logical specifying whether or not the intermediate component should be included in the HMM model. By default this option is set as FALSE. (logical)} @@ -41,8 +40,15 @@ set to 'GridGenome'. (character)} \item{numCores}{Number of cores to perform parallel operation using foreach loop. Default to NULL. (numeric)} -\item{parallelApply}{A logical specifying if futureapply method should be +\item{parallelApply}{Logical specifying if futureapply method should be performed to use parallel operation. Default to FALSE. (logical)} + +\item{if.Bismark}{Logical if Bismark inputs (CX reports in txt format) +are used. Default as FALSE. (logical)} + +\item{FASTA.file}{Path to the FASTA file; required if Bismark outputs are +used. Please use the same FASTA as in Bismark analysis. +Default as NULL. (char)} } \value{ output files containing matrices of state calls, methylation levels @@ -53,9 +59,61 @@ this function runs a HMM model on a genome binned using a sliding/non-sliding window approach } \examples{ -runjDMRgrid(out.dir = 'folder_replicate/grid', - window = 200, step = 50, samplefiles = system.file( - "extdata", "listFiles2.fn", package="jDMRgrid"), +#------------------------------------------------------------------------------ +# REPLICATE-BASED DATASET; STEP I +#------------------------------------------------------------------------------ +# Step 1.1: Copy required files and create required directories for outputs +load(system.file("data", "listFiles2.RData", package="jDMRgrid")) +listFiles2$file <- system.file("extdata", listFiles2$file, package="jDMRgrid") + +system2(command = "/bin/mkdir", args = "~/folder_replicate") +system2(command = "/bin/mkdir", args = "~/folder_replicate/grid-single") +system2(command = "/bin/mkdir", args = "~/folder_replicate/grid-foreach") +system2(command = "/bin/mkdir", args = "~/folder_replicate/grid-future") + +# Step 1.2.1: runjDMRgrid in single mode +runjDMRgrid(out.dir = '~/folder_replicate/grid-single', + window = 200, step = 50, samplelist = listFiles2, contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, include.intermediate = TRUE, runName = "Arabidopsis") +## Step 1.2.2: runjDMRgrid in for-each mode +#runjDMRgrid(out.dir = '~/folder_replicate/grid-foreach', +# window = 200, step = 50, samplelist = listFiles2,, +# contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, +# include.intermediate = TRUE, runName = "Arabidopsis", numCores = 4) +# Step 1.2.3: runjDMRgrid in future-apply mode +runjDMRgrid(out.dir = '~/folder_replicate/grid-future', + window = 200, step = 50, samplelist = listFiles2,, + contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, + include.intermediate = TRUE, runName = "Arabidopsis", + parallelApply = TRUE) + +#------------------------------------------------------------------------------ +# POPULATION-BASED DATASET; STEP I +#------------------------------------------------------------------------------ +# Step 2.1: Copy required files and create required directories for outputs +load(system.file("data", "listFiles1.RData", package="jDMRgrid")) +listFiles1$file <- system.file("extdata", listFiles1$file, package="jDMRgrid") + +system2(command = "/bin/mkdir", args = "~/folder_population") +system2(command = "/bin/mkdir", args = "~/folder_population/grid-single") +system2(command = "/bin/mkdir", args = "~/folder_population/grid-foreach") +system2(command = "/bin/mkdir", args = "~/folder_population/grid-future") + +# Step 2.2.1: runjDMRgrid in single mode +runjDMRgrid(out.dir = '~/folder_population/grid-single', + window = 200, step = 50, samplelist = listFiles1, + contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, + include.intermediate = TRUE, runName = "Arabidopsis") +## Step 2.2.2: runjDMRgrid in for-each mode +#runjDMRgrid(out.dir = '~/folder_population/grid-foreach', +# window = 200, step = 50, samplelist = listFiles1, +# contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, +# include.intermediate = TRUE, runName = "Arabidopsis", numCores = 4) +# Step 2.2.3: runjDMRgrid in future-apply mode +runjDMRgrid(out.dir = '~/folder_population/grid-future', + window = 200, step = 50, samplelist = listFiles1, + contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, + include.intermediate = TRUE, runName = "Arabidopsis", + parallelApply = TRUE) } \ No newline at end of file diff --git a/man/splitGroups.Rd b/man/splitGroups.Rd new file mode 100644 index 0000000..68dff0a --- /dev/null +++ b/man/splitGroups.Rd @@ -0,0 +1,63 @@ +\name{splitGroups} +\alias{splitGroups} +\title{Split DMR matrix into pairwise groups control/treatment groups} +\usage{ +splitGroups( + samplelist, postMax.out = FALSE, contexts = c("CG", "CHG", "CHH"), + input.dir, out.dir) +} +\arguments{ +\item{samplelist}{ +DataFrame object containing information about +file, sample, and replicate. For control/treatment data, an +additional column specifying the replicates is required. (DataFrame object) +} + +\item{postMax.out}{ +Logical specifying whether or not the +postMax probabilities should be divided into control/treatment groups. +By default, this option is set to FALSE. (logical) +} + +\item{contexts}{ +Vector of cytosine contexts selected for DMR calling. By +default, this option is set for all 3 cytosine contexts CG, CHG, and CHH. +(character vector) +} + +\item{input.dir}{ +Path to the input directory with DMR matrices. (character) +} + +\item{out.dir}{ +Path to the output directory with DMR matrices split by +control/treatment groups. (character) +} +} +\value{ +DMR matrices split by sample/treatment groups, saved in the +output directory with DMR matrices. +} +\description{ +This function splits DMR matrices for state-calls, rc.meth.lvl, and optionally +postMax probabilities by control/treatment groups. +} +\examples{ +#------------------------------------------------------------------------------ +# REPLICATE-BASED DATASET; STEP III +#------------------------------------------------------------------------------ +# Step 1.5: Copy required files and create required directories for outputs +load(system.file("data", "listFiles2.RData", package = "jDMRgrid")) +listFiles2$file <- system.file("extdata", listFiles2$file, package = "jDMRgrid") +system2(command = "/bin/mkdir", args = "~/matrix_CT_replicate") +input_file <- system.file("extdata", "matrix_replicate", package = "jDMRgrid") +system2( + command = "/bin/cp", + args = paste0("-r ", input_file, " ", "~/")) + +# Step 1.6: Split control/treatment for replicate-based data +splitGroups( + samplelist = listFiles2, + postMax.out = TRUE, contexts = c("CG", "CHG", "CHH"), + input.dir = '~/matrix_replicate', out.dir = '~/matrix_CT_replicate') +} \ No newline at end of file diff --git a/vignettes/manual.Rmd b/vignettes/manual.Rmd index 6c21324..c15e800 100644 --- a/vignettes/manual.Rmd +++ b/vignettes/manual.Rmd @@ -1,444 +1,313 @@ --- -title: "jDMRgrid: a heuristic DMR caller for WGBS data using grid approach" -author: 'Robert S. Piecyk, Rashmi R. Hazarika, Yadi Shahryary, Frank Johannes ' -date: "`r Sys.Date()`" +title: 'jDMRgrid: a heuristic DMR caller for WGBS data using grid approach' +author: "Robert S. Piecyk, Rashmi R. Hazarika, Yadi Shahryary, Frank Johannes" +date: "2024-10-31" output: - pdf_document: - fig_caption: yes - number_sections: yes - toc: yes - toc_depth: 4 - word_document: - toc: yes - toc_depth: '4' - html_document: - df_print: paged - toc: yes - toc_depth: '4' -geometry: margin=0.5in -urlcolor: blue -vignette: | - %\VignetteIndexEntry{jDMRgrid} - %\VignetteEngine{knitr::knitr} - %\VignetteEncoding{UTF-8} - %\usepackage[utf8]{inputenc} + pdf_document: + toc: true + toc_depth: 2 + html_document: + toc: true + toc_depth: 2 --- -```{r setup, include = FALSE} -options(width=120) -knitr::opts_chunk$set( - collapse = FALSE, - eval = TRUE, - comment = " ", - tidy.opts =list(width.cutoff=80), - tidy = TRUE, - size="small" -) -``` - -\newpage - -```{r eval=TRUE, include=FALSE} -library(data.table) -library(jDMRgrid) -``` - -\section{Input files} - -For generation of region-level calls, jDMRgrid requires the following inputs. - -## Methimpute files: - -Base-level methylome outputs (generated using the R package "Methimpute") -## A metadata file containing description about samples -For population data-sets without replicates, listfiles.fn should have the -structure below. - -\setlength{\leftskip}{1cm} - -**file**: full PATH of file. +## R Markdown -**sample**: a sample name +This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see . -\setlength{\leftskip}{0pt} +When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. ```{r} -samplefile1 <- system.file("extdata", "listFiles1.fn", package="jDMR") -fread(samplefile1, header = TRUE) +setwd("/jlab/home/ming/rmarkdown") ``` -For pairwise control-treatment data-sets with replicates,additional columns -"replicate" and "group" should be provided. See structure below. -\setlength{\leftskip}{1cm} +## 1 Input files -**file**: full PATH of file +For generation of region-level calls, jDMRgrid requires the following inputs. -**sample**: a sample name +## 1.1 Methimpute files: -**replicate**: label for replicates +Base-level methylome outputs (generated using the R package "Methimpute") -**group**: label for control and treatment groups +## 1.2 A metadata file containing description about samples -\setlength{\leftskip}{0pt} +For population data-sets without replicates, listfiles.fn should have the structure below. ```{r} -samplefile2 <- system.file("extdata", "listFiles2.fn", package="jDMRgrid") -fread(samplefile2, header = TRUE) +load(system.file("data", "listFiles1.RData", package = "jDMRgrid")) +listFiles1$file <- system.file("extdata", listFiles1$file, package = "jDMRgrid") +listFiles1 ``` +For pairwise control-treatment data-sets with replicates,additional columns "replicate" and "group" should be provided. See +structure below. - -```{r eval=TRUE, include=FALSE} -#out.dir <- paste0("/myfolder/results/", Sys.getenv("LOGNAME"),"/") -out.dir.pop <- "/home/robert/jDMRgrid_test/folder_population" -out.dir.rep <- "/home/robert/jDMRgrid_test/folder_replicate" +```{r} +load(system.file("data", "listFiles2.RData", package = "jDMRgrid")) +listFiles2$file <- system.file("extdata", listFiles2$file, package = "jDMRgrid") +listFiles2 ``` \newpage -\section{Step 1: Generate cytosine region calls from genome} -jDMR detects DMRs using two approaches a) finding cytosine clusters in the -genome (section 2.1) b) using a binning approach (section 2.2). -You can use either of the methods to obtain the region calls. -The remaining steps, makeDMRmatrix, filterDMRmatrix, annotateDMRs -are the same for both methods. +## 2 Generate cytosine region calls from genome -## Run jDMRgrid on a binned genome +## 2.1 Run jDMRgrid on a binned genome -This function uses a grid approach to bin the genome into equal sized bins. -User specifies the window and step size as numeric values. +This function uses a grid approach to bin the genome into equal sized bins. User specifies the window and step size as numeric values. -\setlength{\leftskip}{1cm} -**out.dir**: PATH to output directory. +**out.dir:** PATH to output directory. -**window**: NUMERIC VALUE specifying bin size. +**window:** NUMERIC VALUE specifying bin size. -**step**: NUMERIC VALUE specifying step size. If bin and step size are equal, -we are utilizing non-sliding window approach. +**step:** NUMERIC VALUE specifying step size. If bin and step size are equal, we are utilizing non-sliding window approach. -**samplefiles**: PATH to the text file containing path to samples -and sample names. +**samplelist:** DATAFRAME OBJECT containing information about file, sample and replicate. For control/treatment data an additional column specifying the replicates is required. -**contexts**: VECTOR or CHARACTER presenting sequence contexts of the cytosine. -By default this option is set to c("CG", "CHG", "CHH"). If you want to run for -a single context such as CG, set it as "CG". +**contexts:** VECTOR or CHARACTER presenting sequence contexts of the cytosine. By default this option is set to +c("CG", "CHG", "CHH", "CHH"). If you want to run for a single context such as CG, set it as "CG". -**min.C**: NUMERIC VALUE specifying percentile threshold based on empirical -distribution of the cytosines across bins. +**min.C:** NUMERIC VALUE specifying percentile threshold based on empirical distribution of the cytosines across bins. -**mincov**: NUMERIC VALUE specifying minimum read coverage over cytosines. -By default this option is set as 0. +**mincov:** NUMERIC VALUE specifying minimum read coverage over cytosines. By default this option is set as 0. -**include.intermediate**: LOGICAL specifying whether or not the intermediate -component should be included in the HMM model. -By default this option is set as FALSE. +**include.intermediate:** LOGICAL specifying whether or not the intermediate component should be included in the HMM model. By default this option is set as FALSE. -**runName**: CHARACTER as the name of the operation. By default this option -is set to 'GridGenome'. +**runName:** CHARACTER as the name of the operation. By default this option is set to ‘GridGenome’. -**parallelApply**: LOGICAL specifying if future.apply package should be used -to use parallel operation. By default this option is set to FALSE. +**parallelApply:** LOGICAL specifying if future.apply package should be used to use parallel operation. By default this +option is set to FALSE. -**numCores**: NUMERIC VALUE specifying number of cores to perform parallel -operation using foreach loop. By default this option is set to NULL. +**numCores:** NUMERIC VALUE specifying number of cores to perform parallel operation using foreach loop. By default this option is set to NULL. +**if.Bismark:** Logical if Bismark inputs (CX reports in txt format) are used. Default as FALSE. (logical) -\setlength{\leftskip}{0pt} +**FASTA.file:** Path to the FASTA file; required if Bismark outputs are used. Please use the same FASTA as in Bismark analysis. Default as NULL. (char) -```{r eval=FALSE, include=TRUE} +```{r echo = TRUE, message = FALSE, warning=FALSE, results='hide'} library(jDMRgrid) -home_dir <- getwd() -out.dir.pop <- "/home/robert/jDMRgrid_test/folder_population" -out.dir.rep <- "/home/robert/jDMRgrid_test/folder_replicate" -samplefile <- system.file("extdata","listFiles2.fn", package="jDMRgrid") - -runjDMRgrid( - out.dir = paste0(out.dir.pop, '/grid'), window = 200, step = 50, - samplefiles = system.file("extdata", "listFiles1.fn", package="jDMRgrid"), - contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, - include.intermediate = FALSE, runName = "Arabidopsis", - parallelApply = FALSE, #future_apply option enabled - numCores = NULL) #foreach loop option disabled - -runjDMRgrid( - out.dir = paste0(out.dir.rep, '/grid'), window = 200, step = 50, - samplefiles = system.file("extdata", "listFiles2.fn", package="jDMRgrid"), - contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, - include.intermediate = TRUE, #include intermediate calls enabled - runName = "Arabidopsis", parallelApply = FALSE, # future_apply disabled - numCores = NULL) #foreach disabled +runjDMRgrid(out.dir = "./population", + window = 200, step = 50, samplelist = listFiles1, + contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, + include.intermediate = TRUE, + runName = "Arabidopsis") + +runjDMRgrid(out.dir = "./replication", + window = 200, step = 50, samplelist = listFiles2, + contexts = c("CG", "CHG", "CHH"), min.C = 10, mincov = 0, + include.intermediate = TRUE, + runName = "Arabidopsis") ``` -### Output files of jDMR Grid approach - -Region files containing state calls and methylation levels will be generated -for each sample and for each context. - -```{r eval=TRUE, include=FALSE} +## 2.2 Output files of jDMR Grid approach -jDMR.out <- fread(paste0(out.dir.pop, '/grid/methimpute_p1.csv_CG.txt')) -``` +Region files containing state calls, methylation levels and posteriorMax will be generated for each sample and for each context. -```{r echo=FALSE} -head(jDMR.out) +```{r, message=FALSE} +library(data.table) +jDMRgrid.out <- fread("./population/methimpute_p1_CG.txt", header = T) +head(jDMRgrid.out) ``` -\setlength{\leftskip}{1cm} - -**seqnames, start and end**: Chromosome coordinates +**seqnames, start and end:** Chromosome coordinates -**context**: Sequence context of cytosine i.e CG,CHG,CHH +**context:** Sequence context of cytosine i.e CG,CHG,CHH -**posteriorMax**: Posterior value of the methylation state call +**posteriorMax:** Posterior value of the methylation state call -**status** : Methylation status +**status:** Methylation status -**rc.meth.lvl**: Recalibrated methylation level calculated from the posteriors -and fitted parameters - -\setlength{\leftskip}{0pt} +**rc.meth.lvl:** Recalibrated methylation level calculated from the posteriors and fitted parameters \newpage -\section{Step 2: Generate DMR matrix} - -## Run "makeDMRmatrix" -This function generates a DMR matrix of state calls, rc.meth.lvls and posterior -probabilities for all samples in one dataframe. +## 3 Generate DMR matrix -\setlength{\leftskip}{1cm} -**samplefiles**: PATH to file containing description about the samples +## 3.1 Run "makeDMRmatrix" -**input.dir**: PATH to directory containing region files. +This function generates a DMR matrix of state calls, rc.meth.lvls and posterior probabilities for all samples in one dataframe. -**out.dir**: PATH to output directory. +**samplelist:** DATAFRAME OBJECT containing information about file, sample and replicate. For control/treatment data an additional column specifying the replicates is required. -**contexts**: sequence contexts of the cytosine. By default this option is set -to c("CG", "CHG", "CHH"). -If you want to run for a single context such as CG, set it as "CG". +**input.dir:** PATH to directory containing region files. -**postMax.out**: By default this option is set as FALSE. You can set it to TRUE -if you want to output the DMR matrix containing posterior probabilities for -the status call of each region. +**out.dir:** PATH to output directory. -\setlength{\leftskip}{0pt} +**contexts:** sequence contexts of the cytosine. By default this option is set to c("CG", "CHG", "CHH", "CHH"). If you want to run for a single context such as CG, set it as "CG". -```{r eval=FALSE, include=TRUE} +**postMax.out:** By default this option is set as FALSE. You can set it to TRUE if you want to output the DMR matrix containing posterior probabilities for the status call of each region. -makeDMRmatrix( - contexts = c("CG", "CHG", "CHH"), postMax.out = TRUE, - samplefiles = system.file("extdata", "listFiles1.fn", package="jDMRgrid"), - input.dir = paste0(out.dir.pop, '/grid'), - out.dir = paste0(out.dir.pop, '/matrix'), include.intermediate = FALSE) +**include.intermediate:** LOGICAL specifying whether or not the intermediate component should be included in the HMM model. By default this option is set as FALSE. -makeDMRmatrix( - contexts = c("CG", "CHG", "CHH"), postMax.out = TRUE, - samplefiles = system.file("extdata", "listFiles2.fn", package="jDMRgrid"), - input.dir = paste0(out.dir.rep, '/grid'), - out.dir = paste0(out.dir.rep, '/matrix'), include.intermediate = FALSE) +```{r, message=FALSE} +makeDMRmatrix(contexts = c("CG", "CHG", "CHH"), postMax.out = TRUE, + samplelist = listFiles1, + input.dir = "./population", + out.dir = "./population/matrix", + include.intermediate = TRUE) +makeDMRmatrix(contexts = c("CG", "CHG", "CHH"), postMax.out = TRUE, + samplelist = listFiles2, + input.dir = "./replication", + out.dir = "./replication/matrix", + include.intermediate = TRUE) ``` -## Output files of DMRmatrix function -*"CG_StateCalls.txt" has the following structure. "0" in the output matrix* -*denotes "Unmethylated" and "1" stands for "Methylated".* +## 3.2 Output files of makeDMRmatrix function + +"CG_StateCalls.txt" has the following structure. "0" in the output matrix denotes "Unmethylated", "1" stands for "Methylated" and "0.5" stands for "Intermediate". -```{r eval=TRUE, include=TRUE} -statecalls <- fread( - paste0(out.dir.pop, "/matrix/CG_StateCalls.txt" , sep=""), header=TRUE) +```{r} +statecalls <- fread("./population/matrix/CG_StateCalls.txt", header = T) head(statecalls) ``` -*"CG_rcMethlvl.txt" has the following structure. The output matrix contains * -*recalibrated methylation levels for each sample and for the specific region.* +"CG_rcMethlvl.txt" has the following structure. The output matrix contains recalibrated methylation levels for each sample and for the specific region. -```{r eval=TRUE, include=TRUE} -rcmethlvls <- fread( - paste0(out.dir.pop, "/matrix/CG_rcMethlvl.txt" , sep=""), header = TRUE) +```{r} +rcmethlvls <- fread("./population/matrix/CG_rcMethlvl.txt", header = T) head(rcmethlvls) ``` -*"CG_postMax.txt" has the following structure. The output matrix contains* -*posterior probabilities for each sample and for the specific region.* +"CG_postMax.txt" has the following structure. The output matrix contains posterior probabilities for each sample and for the specific region. -```{r eval=TRUE, include=TRUE} -postMax <- fread( - paste0(out.dir.pop, "/matrix/CG_postMax.txt" , sep=""), header = TRUE) +```{r} +postMax <- fread("./population/matrix/CG_postMax.txt", header = T) head(postMax) ``` -## Split DMR matrix into pairwise groups (only applicable for datasets with -## control- treatments) -Ignore this step if you are running jDMR on population data without replicates +## 3.3 Split DMR matrix into pairwise groups -\setlength{\leftskip}{1cm} -**samplefiles**: PATH to file containing description about the samples +Ignore this step if you are running jDMR on population data without replicates. For pairwise control-treatment data-sets with replicates, you need to run this step. This function generates a DMR matrix of state calls, rc.meth.lvls and posterior probabilities for each pairwise control-treatment in one dataframe. For example, if the samplelist includes control, treatment1 and treatment2, this function generates a DMR matrix of state calls, rc.meth.lvls and posterior probabilities for control-treatment1 in one dataframe, and a DMR matrix of state calls, rc.meth.lvls and posterior probabilities for control-treatment2 in one dataframe. -**input.dir**: PATH to directory containing region files. +**samplelist:** DATAFRAME OBJECT containing information about file, sample and replicate. For control/treatment data an additional column specifying the replicates is required. -**out.dir**: PATH to output directory. +**input.dir:** PATH to directory containing region files. -**contexts**: sequence contexts of the cytosine. By default this option is -set to c("CG", "CHG", "CHH"). If you want to run for a single context -such as CG, set it as "CG". +**out.dir:** PATH to output directory. -**postMax.out**: by default this option is set to FALSE. If you want to -output the matrix containing posterior probabilities set it to TRUE. +**contexts:** sequence contexts of the cytosine. By default this option is set to c("CG", "CHG", "CHH"). If you want to run for a single context such as CG, set it as "CG". -\setlength{\leftskip}{0pt} +**postMax.out:** by default this option is set to FALSE. If you want to output the matrix containing posterior probabilities set it to TRUE. -```{r eval=FALSE, include=TRUE} -split.groups( - samplefiles = system.file("extdata", "listFiles2.fn", package="jDMRgrid"), - input.dir = paste0(out.dir.rep, "/matrix"), - out.dir = paste0(out.dir.rep, "/matrix")) +```{r, message=FALSE} +splitGroups(samplelist = listFiles2, postMax.out = TRUE, contexts = c("CG", "CHG", "CHH"), + input.dir = "./replication/matrix", + out.dir = "./replication/matrix") ``` -\newpage -\section{Step 3: Filter DMR matrix} - -## Filter the DMR matrix - -This function filters the DMR matrix for non-polymorphic patterns. - -\setlength{\leftskip}{1cm} - -**data.dir**: PATH to folder containing DMR matrix +## 3.4 Output files of splitGroups function -**epiMAF.cutoff**: Applicable for calling calling population DMRs. -This option can be used to filter for Minor Epi-Allele frequency as -specified by user. By default, this option is set to NULL. +```{r} +statecalls_split <- fread("./replication/matrix/CG_WT_mutant1_StateCalls.txt", header = T) +head(statecalls_split) +``` -**replicate.consensus** : Applicable for control-treatment data-sets -with replicates. Users can specify the percentage of concordance in -methylation states in samples with multiple replicates. -For datasets with just 2 replicates, \textit{replicate.consensus} -should be set as 1 (means 100% concordance). -By default, this option is set to NULL. +\newpage -**samplefiles** : Path to the text file containing path to samples and -sample names. For control/treatment data an additional column specifying -the replicates is required. +## 4 Filter DMR matrix -**mergingBins** : Logical argument if merging consecutive bins having the -same stateCalls should be performed. By default set to TRUE. (logical) +## 4.1 Filter the DMR matrix -\setlength{\leftskip}{0pt} - -```{r eval=FALSE, include=TRUE} +This function filters the DMR matrix for non-polymorphic patterns. -filterDMRmatrix( - epiMAF.cutoff = 0.33, replicate.consensus = NULL, - data.dir = paste0(out.dir.pop, "/matrix"), samplefiles = system.file( - "extdata", "listFiles1.fn", package="jDMRgrid"), mergingBins = FALSE) +For population data-sets without replicates, this function will find the outputs of 'runjDMRgrid' for filtering. For pairwise control-treatment data-sets with replicates, this function will find the outputs of 'splitGroups' for filtering. -filterDMRmatrix( - epiMAF.cutoff = NULL, replicate.consensus = 0.8, - data.dir = paste0(out.dir.rep, "/matrix"), samplefiles = system.file( - "extdata", "listFiles2.fn", package="jDMRgrid"), mergingBins = FALSE) +**data.dir:** PATH to folder containing DMR matrix +**epiMAF.cutoff:** Applicable for calling calling population DMRs. This option can be used to filter for Minor Epi-Allele frequency as specified by user. By default, this option is set to NULL. -``` +**replicate.consensus:** Applicable for control-treatment data-sets with replicates. Users can specify the percentage of concordance in methylation states in samples with multiple replicates. For datasets with just 2 replicates, replicate.consensus should be set as 1 (means 100% concordance). By default, this option is set to NULL. -## Filtered Output +**samplelist:** DATAFRAME OBJECT containing information about file, sample and replicate. For control/treatment data an additional column specifying the replicates is required. -*"CG_StateCalls-filtered.txt" has the following structure.* +**if.mergingBins:** Logical argument if merging consecutive bins having the same stateCalls should be performed. By default set to TRUE. (logical) -```{r eval=TRUE, include=TRUE} -statecallsFiltered <- fread( - paste0(out.dir.pop,"/matrix/CG_StateCalls-filtered.txt",sep=""),header=TRUE) -head(statecallsFiltered) +```{r echo = TRUE, message = FALSE, warning=FALSE, results='hide'} +filterDMRmatrix(epiMAF.cutoff = 0.33, replicate.consensus = NULL, + data.dir = "./population/matrix", + samplelist = listFiles1, if.mergingBins = FALSE) ``` -If "rc.methlvl.out" option is set to TRUE a filtered matrix with averaged -methylation levels in generated. -```{r eval=TRUE, include=TRUE} -rcmethlvlFiltered <- fread( - paste0(out.dir.pop,"/matrix/CG_rcMethlvl-filtered.txt",sep=""),header=TRUE) -head(rcmethlvlFiltered) +```{r echo = TRUE, message = FALSE, warning=FALSE, results='hide'} +filterDMRmatrix(epiMAF.cutoff = NULL, replicate.consensus = 0.5, + data.dir = "./replication/matrix", + samplelist = listFiles2, if.mergingBins = FALSE) ``` -\newpage -\section{Step 4: Search for context-specific and annotate DMRs} -## Output context specific DMRs +## 4.2 Filtered Output -Output DMRs specific for contexts i.e CG-only, CHG-only, CHH-only, -non-CG and multi-context DMRs using the *StateCalls-filtered.txt files -(if variable ifFiltered equals to TRUE) or *StateCalls.txt files -(if variable ifFiltered equals to FALSE, as default). +"CG_StateCalls-filtered.txt" has the following structure. -```{r eval=FALSE, include=TRUE} +```{r} +statecalls_filtered <- fread("./population/matrix/CG_StateCalls-filtered.txt", header = T) +head(statecalls_filtered) -context.specific.DMRs( - samplefiles = system.file("extdata", "listFiles1.fn", package="jDMRgrid"), - output.dir = paste0(out.dir.pop, "/context_DMRs"), - input.dir = paste0(out.dir.pop, "/matrix"), if.filtered = FALSE) +statecalls_filtered <- fread("./replication/matrix/CG_WT_mutant1_StateCalls-filtered.txt", header = T) +head(statecalls_filtered) +``` -context.specific.DMRs( - samplefiles = system.file("extdata", "listFiles2.fn", package="jDMRgrid"), - output.dir = paste0(out.dir.rep, "/context_DMRs"), - input.dir = paste0(out.dir.rep, "/matrix"), if.filtered = FALSE) -``` +\newpage +## 5 Search for context-specific and annotate DMRs -## Annotate DMRs +## 5.1 Output context specific DMR -This function annotates the lists of DMRs. Any file(.txt) containing 3 columns -(chr, start, stop) can be annotated using the annotateDMRs function. -Please move all files to be annotated to a separate folder and set the full -PATH to the "input.dir" option. +Output DMRs specific for contexts i.e CG-only, CHG-only, CHH-only, non-CG and multi-context DMRs using the StateCalls_filtered.txt files (if variable if Filtered equals to TRUE) or StateCalls.txt files (if variable ifFiltered equals to FALSE, as default). -\setlength{\leftskip}{1cm} +```{r, message=FALSE} +context.specific.DMRs(samplelist = listFiles2, + output.dir="./replication/context_DMRs", + input.dir = "./replication/matrix", + if.filtered = TRUE) +``` -**gff.files**: Multiple gff3 annotation files can be supplied as a vector +## 5.2 Annotate DMRs -**annotation**: specify annotation categories +This function annotates the lists of DMRs. Any file(.txt) containing 3 columns (chr, start, end) can be annotated using the annotateDMRs function. Please move all files to be annotated to a separate folder and set the full PATH to the "input.dir" option. -**input.dir**: path to folder containing only files to be annotated. -Any file containing 3 columns (chr, start, stop) can be annotated -using the annotateDMRs function. +**gff.files:** Multiple gff3 annotation files can be supplied as a vector -**gff3.out**: whether to output annotated files in gff3 format +**annotation:** specify annotation categories -**out.dir**: path to output folder +**input.dir:** path to folder containing only files to be annotated. Any file containing 3 columns (chr, start, end) can be annotated using the annotateDMRs function. -\setlength{\leftskip}{0pt} -In the following example, I will annotate the files generated in section 4.3 +**if.gff3:** whether to output annotated files in gff3 format -```{r eval=FALSE, include=TRUE} +**out.dir:** path to output folder -gff.file_promoters <- "~/jDMRgrid/jDMRgrid/toyData/TAIR10_promoters.gff3" -gff.file_TE <- "~/jDMRgrid/jDMRgrid/toyData/TAIR10_TE.gff3" -gff.file_genes <- "Z/jDMRgrid/jDMRgrid/toyData/TAIR10.gene.chr1.gff3" +In the following example, I will annotate the files generated in section 3.1 -annotateDMRs( - gff.files = c(gff.file_promoters, gff.file_TE, gff.file_genes), - annotation = c("promoters", "TE", "gene"), #vec containing annotation types - input.dir = paste0(out.dir.pop, "/context_DMRs"), if.gff3 = FALSE, - out.dir = paste0(out.dir.pop, '/annotate_DMRs')) +```{r, message=FALSE} +gff.file_promoters <- system.file("extdata/toyData", "TAIR10_promoters.gff3", package = "jDMRgrid") +gff.file_TE <- system.file("extdata/toyData", "TAIR10_TE.gff3", package = "jDMRgrid") -annotateDMRs( - gff.files = c(gff.file_promoters, gff.file_TE, gff.file_genes), - annotation = c("promoters", "TE", "gene"), #vec containing annotation types - input.dir = paste0(out.dir.rep, "/context_DMRs"), if.gff3 = FALSE, - out.dir = paste0(out.dir.pop, '/annotate_DMRs')) +annotateDMRs(gff.files = c(gff.file_promoters, gff.file_TE), + annotation = c("promoters", "TE"), + input.dir = "./replication/annotation", + if.gff3 = FALSE, + out.dir = "./replication/annotation") ``` -## Output files after annotation +## 5.3 Output files after annotation -Mapped files are output in .txt and/or .gff3 format. -Addiitonally, a DMR count table is generated. +Mapped files are output in .txt and/or .gff3 format. Addiitonally, a DMR count table is generated. -```{r eval=TRUE, include=TRUE} -DMRcounts <- fread( - paste0(out.dir.pop, "/annotate_DMRs/DMR-counts.txt", sep=""), header=TRUE) -DMRcounts +```{r, message=FALSE} +annotations <- fread("./replication/annotation/CG_WT_mutant1_StateCalls_annotation.txt", + header = T) +head(annotations) + +DMRcounts <- fread("./replication/annotation/DMR-counts.txt", header = T) +head(DMRcounts) ``` \newpage -\section{R session info } + +## 6 R session info ```{r} sessionInfo() ``` + diff --git a/vignettes/manual.pdf b/vignettes/manual.pdf new file mode 100644 index 0000000..f0e2f3d Binary files /dev/null and b/vignettes/manual.pdf differ