# HG changeset patch
# User ebi-gxa
# Date 1571407854 14400
# Node ID 247b439a78f7858e16f22c2a96ee180afebe741f
# Parent  040d4b3a19d56203e274362043b670562557311f
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552

diff -r 040d4b3a19d5 -r 247b439a78f7 gtf2featureAnnotation.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf2featureAnnotation.R	Fri Oct 18 10:10:54 2019 -0400
@@ -0,0 +1,195 @@
+#!/usr/bin/env Rscript
+
+# This script parses the GTF file to create a feature-wise annotation file with
+# mitochondrial features flagged, to assist in annotation and QC of single-cell
+# expression data analysis.
+
+suppressPackageStartupMessages(require(rtracklayer))
+suppressPackageStartupMessages(require(optparse))
+
+ucfirst <- function (str) {
+  paste(toupper(substring(str, 1, 1)), tolower(substring(str, 2)), sep = "")
+}
+
+die <- function(message){
+  write(message, stderr())
+  q(status = 1)
+}
+
+cleanlist <- function(str){
+  tolower(unlist(strsplit(str, ',')))
+}
+
+cl <- commandArgs(trailingOnly = TRUE)
+
+option_list = list(
+  make_option(
+    c("-g", "--gtf-file"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = "Path to a valid GTF file"
+  ),
+  make_option(
+    c("-t", "--feature-type"),
+    action = "store",
+    default = 'gene',
+    type = 'character',
+    help = 'Feature type to use (default: gene)'
+  ),
+  make_option(
+    c("-f", "--first-field"),
+    action = "store",
+    default = 'gene_id',
+    type = 'character',
+    help = 'Field to place first in output table (default: gene_id)'
+  ),
+  make_option(
+    c("-r", "--no-header"),
+    action = "store_false",
+    default = TRUE,
+    type = 'logical',
+    help = 'Suppress header on output'
+  ),
+  make_option(
+    c("-l", "--fields"),
+    action = "store",
+    default = NULL,
+    type = 'character',
+    help = 'Comma-separated list of output fields to retain (default: all)'
+  ),
+  make_option(
+    c("-m", "--mito"),
+    action = "store_true",
+    default = FALSE,
+    type = 'character',
+    help = 'Mark mitochondrial elements with reference to chromsomes and biotypes'
+  ),
+  make_option(
+    c("-n", "--mito-chr"),
+    action = "store",
+    default = 'mt,mitochondrion_genome,mito,m,chrM,chrMt',
+    type = 'character',
+    help = 'If specified, marks in a column called "mito" features on the specified chromosomes (case insensitive)'
+  ),
+  make_option(
+    c("-p", "--mito-biotypes"),
+    action = "store",
+    default = 'mt_trna,mt_rrna,mt_trna_pseudogene',
+    type = 'character',
+    help = 'If specified,  marks in a column called "mito" features with the specified biotypes (case insensitve)'
+  ),
+  make_option(
+    c("-c", "--filter-cdnas"),
+    action = "store",
+    default = NULL,
+    type = 'character',
+    help = 'If specified, sequences in the provided FASTA-format cDNAs file will be filtered to remove entries not present in the annotation'
+  ),
+  make_option(
+    c("-d", "--filter-cdnas-field"),
+    action = "store",
+    default = 'transcript_id',
+    type = 'character',
+    help = 'Where --filter-cdnas is specified, what field should be used to compare to identfiers from the FASTA?'
+  ),
+  make_option(
+    c("-e", "--filter-cdnas-output"),
+    action = "store",
+    default = 'filtered.fa.gz',
+    type = 'character',
+    help = 'Where --filter-cdnas is specified, what file should the filtered sequences be output to?'
+  ),
+  make_option(
+    c("-u", "--version-transcripts"),
+    action = "store_true",
+    default = FALSE,
+    type = 'logical',
+    help = 'Where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes.'
+  ),
+  make_option(
+    c("-o", "--output-file"),
+    action = "store",
+    default = NA,
+    type = 'character',
+    help = 'Output file path'
+  )
+)
+
+opt <- parse_args(OptionParser(option_list = option_list), convert_hyphens_to_underscores = TRUE)
+
+if (is.na(opt$gtf_file)){
+  die('ERROR: No input GTF file specified')
+}
+
+if (is.na(opt$output_file)){
+  die('ERROR: No output file specified')
+}
+
+# Import the GTF
+
+print(paste('Reading', opt$gtf_file, 'elements of type', opt$feature_type))
+gtf <- import(opt$gtf_file, feature.type = opt$feature_type )
+
+# Combine basic info (chromosomes, coordinates) with annotation found in GTF attributes
+
+anno <- cbind(chromosome = seqnames(gtf), as.data.frame(ranges(gtf)), elementMetadata(gtf))
+print(paste('Found', nrow(anno), 'features'))
+
+# Mark mitochondrial features
+
+if (opt$mito){
+  anno$mito <- ucfirst(as.character(tolower(anno$gene_biotype) %in% cleanlist(opt$mito_biotypes) | tolower(anno$chromosome) %in% cleanlist(opt$mito_chr)))
+}
+
+# If specified, put the desired field first
+
+if (! is.na(opt$first_field)){
+  if (! opt$first_field %in% colnames(anno)){
+    die(paste(first_field, 'is not a valid field'))
+  }
+  anno <- anno[,c(opt$first_field, colnames(anno)[colnames(anno) != opt$first_field])]
+}
+
+# Version transcripts
+
+if ( opt$feature_type == 'transcript' && opt$version_transcripts && all(c('transcript_id', 'transcript_version') %in% colnames(anno) )){
+  anno$transcript_id <- paste(anno$transcript_id, anno$transcript_version, sep='.')
+}
+
+# If specified, filter down a provided cDNA FASTA file
+
+if (! is.null(opt$filter_cdnas)){
+  
+  print(paste("Filtering", opt$filter_cdnas, "to match the GTF"))
+  
+  suppressPackageStartupMessages(require(Biostrings))
+  
+  cdna <- readDNAStringSet(opt$filter_cdnas)
+  cdna_transcript_names <- unlist(lapply(names(cdna), function(x) unlist(strsplit(x, ' '))[1]  ))
+  
+  # Filter out cDNAs without matching transcript entries in the GTF
+  
+  if (! any(cdna_transcript_names %in% anno[[opt$filter_cdnas_field]])){
+    die(paste("ERROR: None of the input sequences have matching", opt$filter_cdnas_field, 'values in the GTF file'))
+  }
+  
+  cdna <- cdna[which(cdna_transcript_names %in% anno[[opt$filter_cdnas_field]])]
+  
+  print(paste('Storing filtered seqeunces to', opt$filter_cdnas_output))
+  writeXStringSet(x = cdna, filepath = opt$filter_cdnas_output, compress = 'gzip')
+}
+
+# If specified, subset to desired fields
+
+if (! is.null(opt$fields) && opt$fields != ''){
+  fields <- unlist(strsplit(opt$fields, ','))
+  if (any(! fields %in% colnames(anno))){
+    die(paste('ERROR:', fields, 'contains invalid field(s)'))
+  }
+  anno <- anno[,fields, drop = FALSE]
+  anno <- anno[apply(anno, 1, function(x) all(! is.na(x))), ]
+}
+
+print(paste('Storing output to', opt$output_file))
+write.table(anno, file = opt$output_file, sep = "\t", quote=FALSE, row.names = FALSE, col.names = opt$no_header)
diff -r 040d4b3a19d5 -r 247b439a78f7 gtf2featureAnnotation.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf2featureAnnotation.xml	Fri Oct 18 10:10:54 2019 -0400
@@ -0,0 +1,96 @@
+<tool id="_ensembl_gtf2gene_list" name="GTF2GeneAnnotationTable" version="1.42.1+galaxy1">
+    <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description>
+    <requirements>
+      <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
+      <requirement type="package">bioconductor-biostrings</requirement>
+      <requirement type="package">r-optparse</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+       ln -s '$gtf_input' input.gtf;
+       $__tool_directory__/gtf2featureAnnotation.R --gtf-file input.gtf
+#if $noheader
+--no-header
+#end if
+#if $version_transcripts
+--version-transcripts
+#end if
+#if $mito.mark_mito
+--mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}" 
+#end if
+#if $cdnas.filter_cdnas
+--filter-cdnas "${cdnas.fasta_input}" --filter-cdnas-field "${cdnas.cdnas_field}" --filter-cdnas-output "${fasta_output}"
+#end if
+--feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}"
+	    ]]></command>
+
+    <inputs>
+        <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" />
+        <param name="feature_type" type="text" optional='true' value="gene" label="Feature type for which to derive annotation"/>
+        <param name="first_field" type="text" optional='true' value="gene_id" label="Field to place first in output table"/>
+        <param name="noheader" type="boolean" checked="false" label="Suppress header line in output?"/>
+        <param name="fields" type="text" optional='true' value="" label="Comma-separated list of field names to extract from the GTF (default: use all fields)"/>
+        <param name="version_transcripts" type="boolean" checked="false" label="Append version to transcript identifiers?" help="For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes"/>
+        <conditional name="mito">
+          <param name="mark_mito" type="boolean" checked="true" label="Flag mitochondrial features?"/>
+          <when value="true">
+            <param name="mito_chr" type="text" optional='true' value="mt,mitochondrion_genome,mito,m,chrM,chrMt" label="Comma-separated list of possible mitochondrial chromosome names (case insensitive)"/>
+            <param name="mito_biotypes" type="text" optional='true' value="mt_trna,mt_rrna,mt_trna_pseudogene" label="Comma-separated list of possible mitochondrial biotypes (case insensitive)"/>
+          </when>
+          <when value="false" />
+        </conditional>
+        <conditional name="cdnas">
+          <param name="filter_cdnas" type="boolean" checked="false" label="Filter a FASTA-format cDNA file to match annotations?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/>
+          <when value="true">
+            <param name="fasta_input" type="data" format="fasta" label="FASTA-format cDNA/ transcript file" />
+            <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field to match with sequences."/>
+          </when>
+          <when value="false" />
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="feature_annotation" format="tsv" from_work_dir="annotation.txt" label="${tool.name} on ${on_string}: annotation table"/>
+        <data name="fasta_output" format="fasta" from_work_dir="filtered.fa.gz" label="${tool.name} on ${on_string}: annotation-matched sequences">
+          <filter>filter_cdnas</filter>
+        </data>
+    </outputs>
+    <tests>
+      <test>
+        <param name="gtf_input" ftype="gtf" value="test.gtf"/>
+        <output name="feature_annotation" file="annotation.txt"/>
+      </test>
+    </tests>
+
+
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged.
+
+You can also supply a fasta-format file of sequences, which will be filtered by identifier to match annotation. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation).
+
+
+**Inputs**
+
+    * Ensembl GTF file
+
+-----
+
+**Outputs**
+
+    * Gene annotations in tsv.
+]]></help>
+<citations>
+  <citation type="bibtex">
+@misc{github-hinxton-single-cell,
+author = {Jonathan Manning, EBI Gene Expression Team},
+year = {2019},
+title = {Hinxton Single Cell Anlysis Environment},
+publisher = {GitHub},
+journal = {GitHub repository},
+url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
+  }</citation>
+</citations>
+</tool>
diff -r 040d4b3a19d5 -r 247b439a78f7 gtf2gene.R
--- a/gtf2gene.R	Wed Apr 03 12:05:26 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-#!/usr/bin/env Rscript
-
-suppressPackageStartupMessages(require(rtracklayer))
-args <- commandArgs(TRUE)
-
-annotation <- elementMetadata(import( args[1] ))
-genes <- unique(annotation[['gene_id']])
-writeLines(genes[ ! is.na(genes)], con = 'genes.txt')
diff -r 040d4b3a19d5 -r 247b439a78f7 gtf2gene_list.xml
--- a/gtf2gene_list.xml	Wed Apr 03 12:05:26 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy0">
-    <description>extracts gene ids from Ensembl GTF using rtracklayer</description>
-    <requirements>
-      <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-       ln -s '$gtf_input' input.gtf;
-       Rscript $__tool_directory__/gtf2gene.R input.gtf
-	    ]]></command>
-
-    <inputs>
-        <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" />
-    </inputs>
-
-    <outputs>
-        <data name="gene_list" format="tsv" from_work_dir="genes.txt" label="${tool.name} on ${on_string}"/>
-    </outputs>
-    <tests>
-      <test>
-        <param name="gtf_input" ftype="data" value="short_ensembl_gtf.gtf"/>
-        <output name="gene_list" ftype="data" value="genes.txt" compare="sim_size"/>
-      </test>
-    </tests>
-
-
-    <help><![CDATA[
-.. class:: infomark
-
-**What it does**
-
-Given an Ensembl GTF file, it will extract the list of all gene identifiers in the GTF to a simple tsv file.
-
-**Inputs**
-
-    * Ensembl GTF file
-
------
-
-**Outputs**
-
-    * Gene identifier list in tsv.
-]]></help>
-<citations>
-  <citation type="bibtex">
-@misc{github-hinxton-single-cell,
-author = {Pablo Moreno, EBI Gene Expression Team},
-year = {2019},
-title = {Hinxton Single Cell Anlysis Environment},
-publisher = {GitHub},
-journal = {GitHub repository},
-url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary},
-  }</citation>
-</citations>
-</tool>
diff -r 040d4b3a19d5 -r 247b439a78f7 test-data/annotation.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation.txt	Fri Oct 18 10:10:54 2019 -0400
@@ -0,0 +1,11 @@
+gene_id	chromosome	start	end	width	source	type	score	phase	gene_version	gene_name	gene_source	gene_biotype	mito
+ENSG00000223972	1	11869	14409	2541	havana	gene	NA	NA	5	DDX11L1	havana	transcribed_unprocessed_pseudogene	False
+ENSG00000227232	1	14404	29570	15167	havana	gene	NA	NA	5	WASH7P	havana	unprocessed_pseudogene	False
+ENSG00000278267	1	17369	17436	68	mirbase	gene	NA	NA	1	MIR6859-1	mirbase	miRNA	False
+ENSG00000243485	1	29554	31109	1556	havana	gene	NA	NA	5	MIR1302-2HG	havana	lncRNA	False
+ENSG00000284332	1	30366	30503	138	mirbase	gene	NA	NA	1	MIR1302-2	mirbase	miRNA	False
+ENSG00000237613	1	34554	36081	1528	havana	gene	NA	NA	2	FAM138A	havana	lncRNA	False
+ENSG00000268020	1	52473	53312	840	havana	gene	NA	NA	3	OR4G4P	havana	unprocessed_pseudogene	False
+ENSG00000240361	1	57598	64116	6519	havana	gene	NA	NA	2	OR4G11P	havana	transcribed_unprocessed_pseudogene	False
+ENSG00000186092	1	65419	71585	6167	ensembl_havana	gene	NA	NA	6	OR4F5	ensembl_havana	protein_coding	False
+ENSG00000238009	1	89295	133723	44429	ensembl_havana	gene	NA	NA	6	AL627309.1	ensembl_havana	lncRNA	False
diff -r 040d4b3a19d5 -r 247b439a78f7 test-data/test.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.gtf	Fri Oct 18 10:10:54 2019 -0400
@@ -0,0 +1,100 @@
+#!genome-build GRCh38.p13
+#!genome-version GRCh38
+#!genome-date 2013-12
+#!genome-build-accession NCBI:GCA_000001405.28
+#!genebuild-last-updated 2019-06
+1	havana	gene	11869	14409	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
+1	havana	transcript	11869	14409	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "1";
+1	havana	exon	11869	12227	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	12613	12721	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	13221	14409	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	transcript	12010	13670	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12010	12057	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12179	12227	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12613	12697	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12975	13052	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	13221	13374	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	13453	13670	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "6"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001863096"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	14404	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1	havana	transcript	14404	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	29534	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001890219"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	24738	24891	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "2"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003507205"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	18268	18366	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "3"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003477500"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17915	18061	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "4"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003565697"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17606	17742	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003475637"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17233	17368	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "6"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003502542"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	16858	17055	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "7"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003553898"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	16607	16765	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "8"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003621279"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	15796	15947	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "9"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00002030414"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	15005	15038	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "10"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001935574"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	14404	14501	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "11"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001843071"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	mirbase	gene	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; gene_name "MIR6859-1"; gene_source "mirbase"; gene_biotype "miRNA";
+1	mirbase	transcript	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; transcript_id "ENST00000619216"; transcript_version "1"; gene_name "MIR6859-1"; gene_source "mirbase"; gene_biotype "miRNA"; transcript_name "MIR6859-1-201"; transcript_source "mirbase"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA";
+1	mirbase	exon	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; transcript_id "ENST00000619216"; transcript_version "1"; exon_number "1"; gene_name "MIR6859-1"; gene_source "mirbase"; gene_biotype "miRNA"; transcript_name "MIR6859-1-201"; transcript_source "mirbase"; transcript_biotype "miRNA"; exon_id "ENSE00003746039"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	29554	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "5"; gene_name "MIR1302-2HG"; gene_source "havana"; gene_biotype "lncRNA";
+1	havana	transcript	29554	31097	.	+	.	gene_id "ENSG00000243485"; gene_version "5"; transcript_id "ENST00000473358"; transcript_version "1"; gene_name "MIR1302-2HG"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "MIR1302-2HG-202"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "5";
+1	havana	exon	29554	30039	.	+	.	gene_id "ENSG00000243485"; gene_version "5"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "1"; gene_name "MIR1302-2HG"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "MIR1302-2HG-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001947070"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	30564	30667	.	+	.	gene_id "ENSG00000243485"; gene_version "5"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "2"; gene_name "MIR1302-2HG"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "MIR1302-2HG-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001922571"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	30976	31097	.	+	.	gene_id "ENSG00000243485"; gene_version "5"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "3"; gene_name "MIR1302-2HG"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "MIR1302-2HG-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001827679"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	transcript	30267	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "5"; transcript_id "ENST00000469289"; transcript_version "1"; gene_name "MIR1302-2HG"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "MIR1302-2HG-201"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "5";
+1	havana	exon	30267	30667	.	+	.	gene_id "ENSG00000243485"; gene_version "5"; transcript_id "ENST00000469289"; transcript_version "1"; exon_number "1"; gene_name "MIR1302-2HG"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "MIR1302-2HG-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001841699"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	30976	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "5"; transcript_id "ENST00000469289"; transcript_version "1"; exon_number "2"; gene_name "MIR1302-2HG"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "MIR1302-2HG-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001890064"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	mirbase	gene	30366	30503	.	+	.	gene_id "ENSG00000284332"; gene_version "1"; gene_name "MIR1302-2"; gene_source "mirbase"; gene_biotype "miRNA";
+1	mirbase	transcript	30366	30503	.	+	.	gene_id "ENSG00000284332"; gene_version "1"; transcript_id "ENST00000607096"; transcript_version "1"; gene_name "MIR1302-2"; gene_source "mirbase"; gene_biotype "miRNA"; transcript_name "MIR1302-2-201"; transcript_source "mirbase"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA";
+1	mirbase	exon	30366	30503	.	+	.	gene_id "ENSG00000284332"; gene_version "1"; transcript_id "ENST00000607096"; transcript_version "1"; exon_number "1"; gene_name "MIR1302-2"; gene_source "mirbase"; gene_biotype "miRNA"; transcript_name "MIR1302-2-201"; transcript_source "mirbase"; transcript_biotype "miRNA"; exon_id "ENSE00003695741"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	34554	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lncRNA";
+1	havana	transcript	34554	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FAM138A-201"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "1";
+1	havana	exon	35721	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FAM138A-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001656588"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	35277	35481	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FAM138A-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001669267"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	34554	35174	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "3"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FAM138A-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001727627"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	transcript	35245	36073	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FAM138A-202"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "3";
+1	havana	exon	35721	36073	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; exon_number "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FAM138A-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001618781"; exon_version "2"; transcript_support_level "3";
+1	havana	exon	35245	35481	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; exon_number "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "FAM138A-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001874421"; exon_version "1"; transcript_support_level "3";
+1	havana	gene	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1	havana	transcript	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; transcript_id "ENST00000606857"; transcript_version "1"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G4P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; transcript_id "ENST00000606857"; transcript_version "1"; exon_number "1"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G4P-201"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003698237"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	57598	64116	.	+	.	gene_id "ENSG00000240361"; gene_version "2"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
+1	havana	transcript	57598	64116	.	+	.	gene_id "ENSG00000240361"; gene_version "2"; transcript_id "ENST00000642116"; transcript_version "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "OR4G11P-202"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic";
+1	havana	exon	57598	57653	.	+	.	gene_id "ENSG00000240361"; gene_version "2"; transcript_id "ENST00000642116"; transcript_version "1"; exon_number "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "OR4G11P-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003812686"; exon_version "1"; tag "basic";
+1	havana	exon	58700	58856	.	+	.	gene_id "ENSG00000240361"; gene_version "2"; transcript_id "ENST00000642116"; transcript_version "1"; exon_number "2"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "OR4G11P-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003812505"; exon_version "1"; tag "basic";
+1	havana	exon	62916	64116	.	+	.	gene_id "ENSG00000240361"; gene_version "2"; transcript_id "ENST00000642116"; transcript_version "1"; exon_number "3"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "OR4G11P-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003811818"; exon_version "1"; tag "basic";
+1	havana	transcript	62949	63887	.	+	.	gene_id "ENSG00000240361"; gene_version "2"; transcript_id "ENST00000492842"; transcript_version "2"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "OR4G11P-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA (assigned to previous version 1)";
+1	havana	exon	62949	63887	.	+	.	gene_id "ENSG00000240361"; gene_version "2"; transcript_id "ENST00000492842"; transcript_version "2"; exon_number "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "OR4G11P-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001830178"; exon_version "2"; tag "basic"; transcript_support_level "NA (assigned to previous version 1)";
+1	ensembl_havana	gene	65419	71585	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
+1	havana	transcript	65419	71585	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "basic";
+1	havana	exon	65419	65433	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003812156"; exon_version "1"; tag "basic";
+1	havana	exon	65520	65573	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; exon_number "2"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003813641"; exon_version "1"; tag "basic";
+1	havana	CDS	65565	65573	.	+	0	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; exon_number "2"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSP00000493376"; protein_version "2"; tag "basic";
+1	havana	start_codon	65565	65567	.	+	0	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; exon_number "2"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "basic";
+1	havana	exon	69037	71585	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; exon_number "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003813949"; exon_version "1"; tag "basic";
+1	havana	CDS	69037	70005	.	+	0	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; exon_number "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSP00000493376"; protein_version "2"; tag "basic";
+1	havana	stop_codon	70006	70008	.	+	0	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; exon_number "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "basic";
+1	havana	five_prime_utr	65419	65433	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "basic";
+1	havana	five_prime_utr	65520	65564	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "basic";
+1	havana	three_prime_utr	70009	71585	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000641515"; transcript_version "2"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "basic";
+1	ensembl	transcript	69055	70108	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000335137"; transcript_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA (assigned to previous version 3)";
+1	ensembl	exon	69055	70108	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000335137"; transcript_version "4"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; exon_id "ENSE00002319515"; exon_version "2"; tag "basic"; transcript_support_level "NA (assigned to previous version 3)";
+1	ensembl	CDS	69091	70005	.	+	0	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000335137"; transcript_version "4"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA (assigned to previous version 3)";
+1	ensembl	start_codon	69091	69093	.	+	0	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000335137"; transcript_version "4"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA (assigned to previous version 3)";
+1	ensembl	stop_codon	70006	70008	.	+	0	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000335137"; transcript_version "4"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA (assigned to previous version 3)";
+1	ensembl	five_prime_utr	69055	69090	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000335137"; transcript_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA (assigned to previous version 3)";
+1	ensembl	three_prime_utr	70009	70108	.	+	.	gene_id "ENSG00000186092"; gene_version "6"; transcript_id "ENST00000335137"; transcript_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA (assigned to previous version 3)";
+1	ensembl_havana	gene	89295	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA";
+1	havana	transcript	89295	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000466430"; transcript_version "5"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-201"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "5";
+1	havana	exon	120775	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000466430"; transcript_version "5"; exon_number "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001606755"; exon_version "2"; tag "basic"; transcript_support_level "5";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000466430"; transcript_version "5"; exon_number "2"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001957285"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	92091	92240	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000466430"; transcript_version "5"; exon_number "3"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001944529"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	89295	91629	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000466430"; transcript_version "5"; exon_number "4"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-201"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001846804"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	transcript	92230	129217	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000477740"; transcript_version "5"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "5";
+1	havana	exon	129055	129217	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000477740"; transcript_version "5"; exon_number "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001919246"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	120721	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000477740"; transcript_version "5"; exon_number "2"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001171005"; exon_version "3"; transcript_support_level "5";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000477740"; transcript_version "5"; exon_number "3"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001957285"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	92230	92240	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000477740"; transcript_version "5"; exon_number "4"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001896976"; exon_version "1"; transcript_support_level "5";
+1	havana	transcript	110953	129173	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000471248"; transcript_version "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-203"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "5";
+1	havana	exon	129055	129173	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-203"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001934975"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "2"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-203"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001957285"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	110953	111357	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "3"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-203"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001879696"; exon_version "1"; transcript_support_level "5";
+1	ensembl	transcript	120725	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000610542"; transcript_version "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-205"; transcript_source "ensembl"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "5";
+1	ensembl	exon	133374	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-205"; transcript_source "ensembl"; transcript_biotype "lncRNA"; exon_id "ENSE00003748456"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	ensembl	exon	129055	129223	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "2"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-205"; transcript_source "ensembl"; transcript_biotype "lncRNA"; exon_id "ENSE00003734824"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	ensembl	exon	120874	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "3"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-205"; transcript_source "ensembl"; transcript_biotype "lncRNA"; exon_id "ENSE00003740919"; exon_version "1"; tag "basic"; transcript_support_level "5";