# HG changeset patch
# User galaxyp
# Date 1515687411 18000
# Node ID 7e572e148175f706d37c0fd17620e485d5755f7a

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit 321b217382f6be33bd77c7dbb51c8caf5fa50afe

diff -r 000000000000 -r 7e572e148175 gffcompare_to_bed.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gffcompare_to_bed.py	Thu Jan 11 11:16:51 2018 -0500
@@ -0,0 +1,132 @@
+#!/usr/bin/env python
+"""
+#
+#------------------------------------------------------------------------------
+#                         University of Minnesota
+#         Copyright 2017, Regents of the University of Minnesota
+#------------------------------------------------------------------------------
+# Author:
+#
+#  James E Johnson
+#
+#------------------------------------------------------------------------------
+"""
+
+import argparse
+import sys
+
+
+class BedEntry(object):
+    def __init__(self, chrom=None, chromStart=None, chromEnd=None,
+                 name=None, score=None, strand=None,
+                 thickStart=None, thickEnd=None, itemRgb=None,
+                 blockCount=None, blockSizes=None, blockStarts=None):
+        self.chrom = chrom
+        self.chromStart = int(chromStart)
+        self.chromEnd = int(chromEnd)
+        self.name = name
+        self.score = int(score) if score is not None else 0
+        self.strand = '-' if str(strand).startswith('-') else '+'
+        self.thickStart = int(thickStart) if thickStart else self.chromStart
+        self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd
+        self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100'
+        self.blockCount = int(blockCount)
+        if isinstance(blockSizes, str) or isinstance(blockSizes, unicode):
+            self.blockSizes = [int(x) for x in blockSizes.split(',')]
+        elif isinstance(blockSizes, list):
+            self.blockSizes = [int(x) for x in blockSizes]
+        else:
+            self.blockSizes = blockSizes
+        if isinstance(blockStarts, str) or isinstance(blockSizes, unicode):
+            self.blockStarts = [int(x) for x in blockStarts.split(',')]
+        elif isinstance(blockStarts, list):
+            self.blockStarts = [int(x) for x in blockStarts]
+        else:
+            self.blockStarts = blockStarts
+
+    def __str__(self):
+        return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s' % (
+            self.chrom, self.chromStart, self.chromEnd,
+            self.name, self.score, self.strand,
+            self.thickStart, self.thickEnd, str(self.itemRgb), self.blockCount,
+            ','.join([str(x) for x in self.blockSizes]),
+            ','.join([str(x) for x in self.blockStarts]))
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        description='Retrieve Ensembl cDNAs and three frame translate')
+    parser.add_argument(
+        'input',
+        help='GFFCompare annotated GTF file,  (-) for stdin')
+    parser.add_argument(
+        'output',
+        help='BED file,  (-) for stdout')
+    parser.add_argument(
+        '-C', '--class_code', action='append', default=[],
+        help='Restrict output to gffcompare class codes')
+    parser.add_argument('-d', '--debug', action='store_true', help='Debug')
+    args = parser.parse_args()
+
+    # print >> sys.stderr, "args: %s" % args
+    input_rdr = open(args.input, 'r') if args.input != '-' else sys.stdin
+    output_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout
+
+    def write_bed_entry(bed):
+        if bed.blockCount == 0:
+            bed.blockCount = 1
+        output_wtr.write("%s\n" % str(bed))
+
+    class_codes = [c.strip() for codes in args.class_code
+                   for c in codes.split(',')] if args.class_code else None
+    bed = None
+    class_code = None
+    for i, line in enumerate(input_rdr):
+        if line.startswith('#'):
+            continue
+        fields = line.rstrip('\r\n').split('\t')
+        if len(fields) != 9:
+            continue
+        (seqname, source, feature, start, end,
+         score, strand, frame, attributes) = fields
+        attribute = {i[0]: i[1].strip('"') for i in [j.strip().split(' ')
+                     for j in attributes.rstrip(';').split(';')]}
+        if feature == 'transcript':
+            if args.debug:
+                print >> sys.stderr, "%s\t%s"\
+                    % ('\t'.join([seqname, source, feature,
+                                  start, end, score, strand, frame]),
+                        attribute)
+            if bed is not None:
+                write_bed_entry(bed)
+                bed = None
+            class_code = attribute['class_code'].strip('"')\
+                if 'class_code' in attribute else None
+            if class_codes and class_code not in class_codes:
+                continue
+            chromStart = int(start) - 1
+            chromEnd = int(end)
+            cat = '_' + class_code if class_code and class_code != '=' else ''
+            bed = BedEntry(chrom=seqname,
+                           chromStart=chromStart, chromEnd=chromEnd,
+                           name=attribute['transcript_id'] + cat,
+                           strand=strand,
+                           blockCount=0,
+                           blockSizes=[chromEnd - chromStart],
+                           blockStarts=[0])
+        elif feature == 'exon' and bed is not None:
+            chromStart = int(start) - 1
+            chromEnd = int(end)
+            blockSize = chromEnd - chromStart
+            if bed.blockCount == 0:
+                bed.blockSizes = []
+                bed.blockStarts = []
+            bed.blockSizes.append(blockSize)
+            bed.blockStarts.append(chromStart - bed.chromStart)
+            bed.blockCount += 1
+    if bed is not None:
+        write_bed_entry(bed)
+
+
+if __name__ == "__main__":
+    __main__()
diff -r 000000000000 -r 7e572e148175 gffcompare_to_bed.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gffcompare_to_bed.xml	Thu Jan 11 11:16:51 2018 -0500
@@ -0,0 +1,66 @@
+<tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.1.0">
+    <description>for StringTie results</description>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/gffcompare_to_bed.py'  
+        #if $class_codes:
+            --class_code='$class_codes'
+        #end if
+        $input $output
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="gtf" label="GTF annotated by gffCompare"/>
+        <param name="class_codes" type="select" display="checkboxes" multiple="true" optional="true" 
+            label="filter gffCompare class_codes to convert" help="No selection implies no filtering">
+            <option value="=">= : Complete match of intron chain</option>
+            <option value="c">c : Contained</option>
+            <option value="j">j : Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript</option>
+            <option value="e">e : Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.</option>
+            <option value="i">i : A transfrag falling entirely within a reference intron</option>
+            <option value="o">o : Generic exonic overlap with a reference transcript</option>
+            <option value="p">p : Possible polymerase run-on fragment (within 2Kbases of a reference transcript)</option>
+            <option value="r">r : Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case</option>
+            <option value="u">u : Unknown, intergenic transcript</option>
+            <option value="x">x : Exonic overlap with reference on the opposite strand</option>
+            <option value="s">s : An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="bed" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
+            <output name="output" file="gffcompare_output.bed"/>
+        </test>
+        <test>
+            <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
+            <param name="class_codes" value="j"/>
+            <output name="output" file="gffcompare_output_j.bed"/>
+        </test>
+        <test>
+            <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
+            <param name="class_codes" value="j,e,i,p,u,x"/>
+            <output name="output" file="gffcompare_output_jeipux.bed"/>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+Convert a GFFCompare annotated GTF file to BED format.
+
+usage: gffcompare_to_bed.py [-h] [-C CLASS_CODE] [-v] [-d] input output
+
+positional arguments:
+  input                 GFFCompare annotated GTF file, (-) for stdin
+  output                BED file, (-) for stdout
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -C CLASS_CODE, --class_code CLASS_CODE
+                        Restrict output to gffcompare class codes
+  -d, --debug           Debug
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 7e572e148175 test-data/gffcompare_annotated.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gffcompare_annotated.gtf	Thu Jan 11 11:16:51 2018 -0500
@@ -0,0 +1,1024 @@
+1	StringTie	exon	43778515	43778980	.	-	.	transcript_id "STRG.1163.3"; gene_id "STRG.1163"; exon_number "2";
+1	StringTie	transcript	43776567	43778980	.	-	.	transcript_id "STRG.1163.2"; gene_id "STRG.1163"; gene_name "Uxs1"; xloc "XLOC_000439"; cmp_ref "ENSMUST00000126008"; class_code "i"; tss_id "TSS1162";
+1	StringTie	exon	43776567	43777660	.	-	.	transcript_id "STRG.1163.2"; gene_id "STRG.1163"; exon_number "1";
+1	StringTie	exon	43778515	43778758	.	-	.	transcript_id "STRG.1163.2"; gene_id "STRG.1163"; exon_number "2";
+1	StringTie	exon	43778881	43778980	.	-	.	transcript_id "STRG.1163.2"; gene_id "STRG.1163"; exon_number "3";
+1	StringTie	transcript	43776567	43778980	.	-	.	transcript_id "STRG.1163.1"; gene_id "STRG.1163"; gene_name "Uxs1"; xloc "XLOC_000439"; cmp_ref "ENSMUST00000126008"; class_code "i"; tss_id "TSS1162";
+1	StringTie	exon	43776567	43777721	.	-	.	transcript_id "STRG.1163.1"; gene_id "STRG.1163"; exon_number "1";
+1	StringTie	exon	43778454	43778575	.	-	.	transcript_id "STRG.1163.1"; gene_id "STRG.1163"; exon_number "2";
+1	StringTie	exon	43778881	43778980	.	-	.	transcript_id "STRG.1163.1"; gene_id "STRG.1163"; exon_number "3";
+1	StringTie	transcript	45331687	45332998	.	+	.	transcript_id "STRG.1209.1"; gene_id "STRG.1209"; gene_name "Col3a1"; xloc "XLOC_000069"; cmp_ref "ENSMUST00000087883"; class_code "c"; tss_id "TSS174";
+1	StringTie	exon	45331687	45331776	.	+	.	transcript_id "STRG.1209.1"; gene_id "STRG.1209"; exon_number "1";
+1	StringTie	exon	45331973	45332026	.	+	.	transcript_id "STRG.1209.1"; gene_id "STRG.1209"; exon_number "2";
+1	StringTie	exon	45332135	45332242	.	+	.	transcript_id "STRG.1209.1"; gene_id "STRG.1209"; exon_number "3";
+1	StringTie	exon	45332965	45332998	.	+	.	transcript_id "STRG.1209.1"; gene_id "STRG.1209"; exon_number "4";
+1	StringTie	transcript	6453837	6460700	.	+	.	transcript_id "STRG.88.1"; gene_id "STRG.88"; xloc "XLOC_000004"; class_code "u"; tss_id "TSS16";
+1	StringTie	exon	6453837	6453886	.	+	.	transcript_id "STRG.88.1"; gene_id "STRG.88"; exon_number "1";
+1	StringTie	exon	6460545	6460700	.	+	.	transcript_id "STRG.88.1"; gene_id "STRG.88"; exon_number "2";
+1	StringTie	transcript	86703819	87050095	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; gene_name "Dis3l2"; xloc "XLOC_000165"; ref_gene_id "ENSMUSG00000053333"; cmp_ref "ENSMUST00000168237"; class_code "="; tss_id "TSS424"; p_id "P253";
+1	StringTie	exon	86703819	86703871	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "1";
+1	StringTie	exon	86744681	86744828	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "2";
+1	StringTie	exon	86745341	86745498	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "3";
+1	StringTie	exon	86754227	86754280	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "4";
+1	StringTie	exon	86760288	86760389	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "5";
+1	StringTie	exon	86791416	86791457	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "6";
+1	StringTie	exon	86821222	86821450	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "7";
+1	StringTie	exon	86854360	86854460	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "8";
+1	StringTie	exon	86857127	86857374	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "9";
+1	StringTie	exon	86878403	86878576	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "10";
+1	StringTie	exon	86930754	86930833	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "11";
+1	StringTie	exon	86959743	86959855	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "12";
+1	StringTie	exon	86973400	86973507	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "13";
+1	StringTie	exon	86990092	86990325	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "14";
+1	StringTie	exon	87021038	87021117	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "15";
+1	StringTie	exon	87044017	87044200	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "16";
+1	StringTie	exon	87044830	87044916	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "17";
+1	StringTie	exon	87047037	87047184	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "18";
+1	StringTie	exon	87047448	87047578	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "19";
+1	StringTie	exon	87047688	87047792	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "20";
+1	StringTie	exon	87048833	87048934	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "21";
+1	StringTie	exon	87049623	87050095	.	+	.	transcript_id "STRG.2299.1"; gene_id "STRG.2299"; exon_number "22";
+1	StringTie	transcript	86703828	86882439	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; gene_name "Dis3l2"; xloc "XLOC_000165"; ref_gene_id "ENSMUSG00000053333"; cmp_ref "ENSMUST00000189044"; class_code "="; tss_id "TSS424";
+1	StringTie	exon	86703828	86703871	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "1";
+1	StringTie	exon	86744681	86744828	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "2";
+1	StringTie	exon	86745341	86745498	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "3";
+1	StringTie	exon	86754227	86754280	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "4";
+1	StringTie	exon	86760288	86760389	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "5";
+1	StringTie	exon	86791416	86791457	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "6";
+1	StringTie	exon	86812512	86812589	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "7";
+1	StringTie	exon	86821222	86821450	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "8";
+1	StringTie	exon	86854360	86854460	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "9";
+1	StringTie	exon	86857127	86857374	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "10";
+1	StringTie	exon	86878403	86882439	.	+	.	transcript_id "STRG.2299.5"; gene_id "STRG.2299"; exon_number "11";
+1	StringTie	transcript	86703828	87049195	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; gene_name "Dis3l2"; xloc "XLOC_000165"; ref_gene_id "ENSMUSG00000053333"; cmp_ref "ENSMUST00000190618"; class_code "="; tss_id "TSS424"; p_id "P252";
+1	StringTie	exon	86703828	86703871	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "1";
+1	StringTie	exon	86744681	86744828	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "2";
+1	StringTie	exon	86745341	86745498	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "3";
+1	StringTie	exon	86754227	86754280	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "4";
+1	StringTie	exon	86760288	86760389	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "5";
+1	StringTie	exon	86812512	86812589	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "6";
+1	StringTie	exon	86821222	86821450	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "7";
+1	StringTie	exon	86854360	86854460	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "8";
+1	StringTie	exon	86857127	86857374	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "9";
+1	StringTie	exon	86878403	86878576	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "10";
+1	StringTie	exon	86930754	86930833	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "11";
+1	StringTie	exon	86959743	86959855	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "12";
+1	StringTie	exon	86973400	86973507	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "13";
+1	StringTie	exon	86990092	86990325	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "14";
+1	StringTie	exon	87021038	87021117	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "15";
+1	StringTie	exon	87044017	87044200	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "16";
+1	StringTie	exon	87044830	87044916	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "17";
+1	StringTie	exon	87047037	87047184	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "18";
+1	StringTie	exon	87047448	87047578	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "19";
+1	StringTie	exon	87047688	87047792	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "20";
+1	StringTie	exon	87048833	87049195	.	+	.	transcript_id "STRG.2299.3"; gene_id "STRG.2299"; exon_number "21";
+1	StringTie	transcript	86703843	87050092	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; gene_name "Dis3l2"; xloc "XLOC_000165"; cmp_ref "ENSMUST00000168237"; class_code "j"; tss_id "TSS424";
+1	StringTie	exon	86703843	86703871	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "1";
+1	StringTie	exon	86744681	86744828	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "2";
+1	StringTie	exon	86745341	86745498	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "3";
+1	StringTie	exon	86754227	86754280	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "4";
+1	StringTie	exon	86760288	86760389	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "5";
+1	StringTie	exon	86812512	86812589	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "6";
+1	StringTie	exon	86821222	86821450	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "7";
+1	StringTie	exon	86854360	86854460	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "8";
+1	StringTie	exon	86857127	86857374	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "9";
+1	StringTie	exon	86878403	86878576	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "10";
+1	StringTie	exon	86930754	86930833	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "11";
+1	StringTie	exon	86959743	86959855	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "12";
+1	StringTie	exon	86990092	86990325	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "13";
+1	StringTie	exon	87021038	87021117	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "14";
+1	StringTie	exon	87044017	87044200	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "15";
+1	StringTie	exon	87044830	87044916	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "16";
+1	StringTie	exon	87047037	87047184	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "17";
+1	StringTie	exon	87047448	87047578	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "18";
+1	StringTie	exon	87047688	87047792	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "19";
+1	StringTie	exon	87048833	87048934	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "20";
+1	StringTie	exon	87049623	87050092	.	+	.	transcript_id "STRG.2299.4"; gene_id "STRG.2299"; exon_number "21";
+1	StringTie	transcript	86703843	87050092	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; gene_name "Dis3l2"; xloc "XLOC_000165"; ref_gene_id "ENSMUSG00000053333"; cmp_ref "ENSMUST00000065694"; class_code "="; tss_id "TSS424"; p_id "P254";
+1	StringTie	exon	86703843	86703871	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "1";
+1	StringTie	exon	86744681	86744828	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "2";
+1	StringTie	exon	86745341	86745498	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "3";
+1	StringTie	exon	86754227	86754280	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "4";
+1	StringTie	exon	86760288	86760389	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "5";
+1	StringTie	exon	86821222	86821450	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "6";
+1	StringTie	exon	86854360	86854460	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "7";
+1	StringTie	exon	86857127	86857374	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "8";
+1	StringTie	exon	86878403	86878576	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "9";
+1	StringTie	exon	86930754	86930833	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "10";
+1	StringTie	exon	86959743	86959855	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "11";
+1	StringTie	exon	86973400	86973507	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "12";
+1	StringTie	exon	86990092	86990325	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "13";
+1	StringTie	exon	87021038	87021117	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "14";
+1	StringTie	exon	87044017	87044200	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "15";
+1	StringTie	exon	87044830	87044916	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "16";
+1	StringTie	exon	87047037	87047184	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "17";
+1	StringTie	exon	87047448	87047578	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "18";
+1	StringTie	exon	87047688	87047792	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "19";
+1	StringTie	exon	87048833	87048934	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "20";
+1	StringTie	exon	87049623	87050092	.	+	.	transcript_id "STRG.2299.2"; gene_id "STRG.2299"; exon_number "21";
+1	StringTie	transcript	86754159	86767638	.	+	.	transcript_id "STRG.2299.6"; gene_id "STRG.2299"; gene_name "Dis3l2"; xloc "XLOC_000165"; cmp_ref "ENSMUST00000168237"; class_code "j"; tss_id "TSS425";
+1	StringTie	exon	86754159	86754280	.	+	.	transcript_id "STRG.2299.6"; gene_id "STRG.2299"; exon_number "1";
+1	StringTie	exon	86760288	86760389	.	+	.	transcript_id "STRG.2299.6"; gene_id "STRG.2299"; exon_number "2";
+1	StringTie	exon	86767130	86767638	.	+	.	transcript_id "STRG.2299.6"; gene_id "STRG.2299"; exon_number "3";
+1	StringTie	transcript	9941959	9944118	.	-	.	transcript_id "STRG.229.1"; gene_id "STRG.229"; gene_name "Snhg6"; xloc "XLOC_000389"; ref_gene_id "ENSMUSG00000098234"; cmp_ref "ENSMUST00000182580"; class_code "="; tss_id "TSS990";
+1	StringTie	exon	9941959	9942155	.	-	.	transcript_id "STRG.229.1"; gene_id "STRG.229"; exon_number "1";
+1	StringTie	exon	9942323	9942391	.	-	.	transcript_id "STRG.229.1"; gene_id "STRG.229"; exon_number "2";
+1	StringTie	exon	9942610	9942717	.	-	.	transcript_id "STRG.229.1"; gene_id "STRG.229"; exon_number "3";
+1	StringTie	exon	9944020	9944118	.	-	.	transcript_id "STRG.229.1"; gene_id "STRG.229"; exon_number "4";
+1	StringTie	transcript	9942023	9943223	.	-	.	transcript_id "STRG.229.5"; gene_id "STRG.229"; gene_name "Snhg6"; xloc "XLOC_000389"; ref_gene_id "ENSMUSG00000098234"; cmp_ref "ENSMUST00000182819"; class_code "="; tss_id "TSS991";
+1	StringTie	exon	9942023	9942155	.	-	.	transcript_id "STRG.229.5"; gene_id "STRG.229"; exon_number "1";
+1	StringTie	exon	9942323	9942391	.	-	.	transcript_id "STRG.229.5"; gene_id "STRG.229"; exon_number "2";
+1	StringTie	exon	9942610	9943223	.	-	.	transcript_id "STRG.229.5"; gene_id "STRG.229"; exon_number "3";
+1	StringTie	transcript	9942025	9942897	.	-	.	transcript_id "STRG.229.7"; gene_id "STRG.229"; gene_name "Snhg6"; xloc "XLOC_000389"; ref_gene_id "ENSMUSG00000098234"; cmp_ref "ENSMUST00000182043"; class_code "="; tss_id "TSS992";
+1	StringTie	exon	9942025	9942391	.	-	.	transcript_id "STRG.229.7"; gene_id "STRG.229"; exon_number "1";
+1	StringTie	exon	9942610	9942897	.	-	.	transcript_id "STRG.229.7"; gene_id "STRG.229"; exon_number "2";
+1	StringTie	transcript	9942025	9944103	.	-	.	transcript_id "STRG.229.6"; gene_id "STRG.229"; gene_name "Snhg6"; xloc "XLOC_000389"; cmp_ref "ENSMUST00000182580"; class_code "j"; tss_id "TSS990";
+1	StringTie	exon	9942025	9942155	.	-	.	transcript_id "STRG.229.6"; gene_id "STRG.229"; exon_number "1";
+1	StringTie	exon	9942323	9942717	.	-	.	transcript_id "STRG.229.6"; gene_id "STRG.229"; exon_number "2";
+1	StringTie	exon	9944020	9944103	.	-	.	transcript_id "STRG.229.6"; gene_id "STRG.229"; exon_number "3";
+1	StringTie	transcript	9942025	9944103	.	-	.	transcript_id "STRG.229.4"; gene_id "STRG.229"; gene_name "Snhg6"; xloc "XLOC_000389"; ref_gene_id "ENSMUSG00000098234"; cmp_ref "ENSMUST00000182498"; class_code "="; tss_id "TSS990";
+1	StringTie	exon	9942025	9942391	.	-	.	transcript_id "STRG.229.4"; gene_id "STRG.229"; exon_number "1";
+1	StringTie	exon	9942610	9942717	.	-	.	transcript_id "STRG.229.4"; gene_id "STRG.229"; exon_number "2";
+1	StringTie	exon	9944020	9944103	.	-	.	transcript_id "STRG.229.4"; gene_id "STRG.229"; exon_number "3";
+1	StringTie	transcript	9942025	9944103	.	-	.	transcript_id "STRG.229.3"; gene_id "STRG.229"; gene_name "Snhg6"; xloc "XLOC_000389"; cmp_ref "ENSMUST00000182580"; class_code "j"; tss_id "TSS990";
+1	StringTie	exon	9942025	9942155	.	-	.	transcript_id "STRG.229.3"; gene_id "STRG.229"; exon_number "1";
+1	StringTie	exon	9942323	9942384	.	-	.	transcript_id "STRG.229.3"; gene_id "STRG.229"; exon_number "2";
+1	StringTie	exon	9942610	9942717	.	-	.	transcript_id "STRG.229.3"; gene_id "STRG.229"; exon_number "3";
+1	StringTie	exon	9944020	9944103	.	-	.	transcript_id "STRG.229.3"; gene_id "STRG.229"; exon_number "4";
+1	StringTie	transcript	9942025	9944117	.	-	.	transcript_id "STRG.229.2"; gene_id "STRG.229"; gene_name "Snhg6"; xloc "XLOC_000389"; ref_gene_id "ENSMUSG00000098234"; cmp_ref "ENSMUST00000182742"; class_code "="; tss_id "TSS990";
+1	StringTie	exon	9942025	9942149	.	-	.	transcript_id "STRG.229.2"; gene_id "STRG.229"; exon_number "1";
+1	StringTie	exon	9942323	9942391	.	-	.	transcript_id "STRG.229.2"; gene_id "STRG.229"; exon_number "2";
+1	StringTie	exon	9942610	9942717	.	-	.	transcript_id "STRG.229.2"; gene_id "STRG.229"; exon_number "3";
+1	StringTie	exon	9944020	9944117	.	-	.	transcript_id "STRG.229.2"; gene_id "STRG.229"; exon_number "4";
+1	StringTie	transcript	86908793	86909683	.	-	.	transcript_id "STRG.2297.1"; gene_id "STRG.2297"; gene_name "Dis3l2"; xloc "XLOC_000527"; cmp_ref "ENSMUST00000168237"; class_code "i"; tss_id "TSS1418";
+1	StringTie	exon	86908793	86909111	.	-	.	transcript_id "STRG.2297.1"; gene_id "STRG.2297"; exon_number "1";
+1	StringTie	exon	86909399	86909683	.	-	.	transcript_id "STRG.2297.1"; gene_id "STRG.2297"; exon_number "2";
+1	StringTie	transcript	193145391	193173087	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; gene_name "Irf6"; xloc "XLOC_000382"; cmp_ref "ENSMUST00000076521"; class_code "j"; tss_id "TSS969";
+1	StringTie	exon	193145391	193145432	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; exon_number "1";
+1	StringTie	exon	193157216	193157392	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; exon_number "2";
+1	StringTie	exon	193161613	193161817	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; exon_number "3";
+1	StringTie	exon	193162602	193162730	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; exon_number "4";
+1	StringTie	exon	193165766	193165924	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; exon_number "5";
+1	StringTie	exon	193167439	193167831	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; exon_number "6";
+1	StringTie	exon	193168517	193168635	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; exon_number "7";
+1	StringTie	exon	193169282	193173087	.	+	.	transcript_id "STRG.5202.1"; gene_id "STRG.5202"; exon_number "8";
+1	StringTie	transcript	193156669	193164181	.	+	.	transcript_id "STRG.5202.2"; gene_id "STRG.5202"; gene_name "Irf6"; xloc "XLOC_000382"; ref_gene_id "ENSMUSG00000026638"; cmp_ref "ENSMUST00000140066"; class_code "="; tss_id "TSS970";
+1	StringTie	exon	193156669	193157392	.	+	.	transcript_id "STRG.5202.2"; gene_id "STRG.5202"; exon_number "1";
+1	StringTie	exon	193161613	193161817	.	+	.	transcript_id "STRG.5202.2"; gene_id "STRG.5202"; exon_number "2";
+1	StringTie	exon	193162602	193164181	.	+	.	transcript_id "STRG.5202.2"; gene_id "STRG.5202"; exon_number "3";
+1	StringTie	transcript	193167975	193173087	.	+	.	transcript_id "STRG.5202.3"; gene_id "STRG.5202"; gene_name "Irf6"; xloc "XLOC_000382"; cmp_ref "ENSMUST00000076521"; class_code "j"; tss_id "TSS971";
+1	StringTie	exon	193167975	193168131	.	+	.	transcript_id "STRG.5202.3"; gene_id "STRG.5202"; exon_number "1";
+1	StringTie	exon	193168517	193168635	.	+	.	transcript_id "STRG.5202.3"; gene_id "STRG.5202"; exon_number "2";
+1	StringTie	exon	193169282	193173087	.	+	.	transcript_id "STRG.5202.3"; gene_id "STRG.5202"; exon_number "3";
+1	StringTie	transcript	193168503	193169489	.	+	.	transcript_id "STRG.5202.4"; gene_id "STRG.5202"; gene_name "Irf6"; xloc "XLOC_000382"; ref_gene_id "ENSMUSG00000026638"; cmp_ref "ENSMUST00000193772"; class_code "="; tss_id "TSS972";
+1	StringTie	exon	193168503	193168635	.	+	.	transcript_id "STRG.5202.4"; gene_id "STRG.5202"; exon_number "1";
+1	StringTie	exon	193169282	193169489	.	+	.	transcript_id "STRG.5202.4"; gene_id "STRG.5202"; exon_number "2";
+2	StringTie	transcript	119749139	119749844	.	+	.	transcript_id "STRG.8811.1"; gene_id "STRG.8811"; gene_name "Itpka"; xloc "XLOC_006614"; cmp_ref "ENSMUST00000028758"; class_code "j"; tss_id "TSS15414";
+2	StringTie	exon	119749139	119749286	.	+	.	transcript_id "STRG.8811.1"; gene_id "STRG.8811"; exon_number "1";
+2	StringTie	exon	119749362	119749578	.	+	.	transcript_id "STRG.8811.1"; gene_id "STRG.8811"; exon_number "2";
+2	StringTie	exon	119749673	119749844	.	+	.	transcript_id "STRG.8811.1"; gene_id "STRG.8811"; exon_number "3";
+2	StringTie	transcript	119972464	120018974	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; gene_name "Mapkbp1"; xloc "XLOC_006617"; cmp_ref "ENSMUST00000066058"; class_code "j"; tss_id "TSS15426";
+2	StringTie	exon	119972464	119972480	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "1";
+2	StringTie	exon	119972946	119973168	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "2";
+2	StringTie	exon	119998482	119998573	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "3";
+2	StringTie	exon	120010743	120010805	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "4";
+2	StringTie	exon	120011002	120011059	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "5";
+2	StringTie	exon	120011933	120012103	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "6";
+2	StringTie	exon	120012593	120012730	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "7";
+2	StringTie	exon	120012912	120013094	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "8";
+2	StringTie	exon	120013619	120013779	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "9";
+2	StringTie	exon	120014623	120014812	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "10";
+2	StringTie	exon	120015343	120015489	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "11";
+2	StringTie	exon	120015693	120015868	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "12";
+2	StringTie	exon	120016780	120016871	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "13";
+2	StringTie	exon	120017140	120017265	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "14";
+2	StringTie	exon	120017581	120017651	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "15";
+2	StringTie	exon	120017756	120017877	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "16";
+2	StringTie	exon	120018299	120018374	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "17";
+2	StringTie	exon	120018488	120018599	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "18";
+2	StringTie	exon	120018922	120018974	.	+	.	transcript_id "STRG.8821.1"; gene_id "STRG.8821"; exon_number "19";
+2	StringTie	transcript	120011687	120013094	.	+	.	transcript_id "STRG.8821.3"; gene_id "STRG.8821"; gene_name "Mapkbp1"; xloc "XLOC_006617"; ref_gene_id "ENSMUSG00000033902"; cmp_ref "ENSMUST00000137760"; class_code "="; tss_id "TSS15427";
+2	StringTie	exon	120011687	120012103	.	+	.	transcript_id "STRG.8821.3"; gene_id "STRG.8821"; exon_number "1";
+2	StringTie	exon	120012593	120012730	.	+	.	transcript_id "STRG.8821.3"; gene_id "STRG.8821"; exon_number "2";
+2	StringTie	exon	120012912	120013094	.	+	.	transcript_id "STRG.8821.3"; gene_id "STRG.8821"; exon_number "3";
+2	StringTie	transcript	120013043	120015605	.	+	.	transcript_id "STRG.8821.2"; gene_id "STRG.8821"; gene_name "Mapkbp1"; xloc "XLOC_006617"; ref_gene_id "ENSMUSG00000033902"; cmp_ref "ENSMUST00000128077"; class_code "="; tss_id "TSS15428";
+2	StringTie	exon	120013043	120013094	.	+	.	transcript_id "STRG.8821.2"; gene_id "STRG.8821"; exon_number "1";
+2	StringTie	exon	120013619	120013779	.	+	.	transcript_id "STRG.8821.2"; gene_id "STRG.8821"; exon_number "2";
+2	StringTie	exon	120014623	120014812	.	+	.	transcript_id "STRG.8821.2"; gene_id "STRG.8821"; exon_number "3";
+2	StringTie	exon	120015343	120015605	.	+	.	transcript_id "STRG.8821.2"; gene_id "STRG.8821"; exon_number "4";
+2	StringTie	transcript	121008403	121016904	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; gene_name "Ccndbp1"; xloc "XLOC_006626"; ref_gene_id "ENSMUSG00000023572"; cmp_ref "ENSMUST00000060455"; class_code "="; tss_id "TSS15463"; p_id "P8181";
+2	StringTie	exon	121008403	121008609	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "1";
+2	StringTie	exon	121008718	121008777	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "2";
+2	StringTie	exon	121009043	121009122	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "3";
+2	StringTie	exon	121009827	121009908	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "4";
+2	StringTie	exon	121011434	121011530	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "5";
+2	StringTie	exon	121011683	121011756	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "6";
+2	StringTie	exon	121012353	121012429	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "7";
+2	StringTie	exon	121012699	121012976	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "8";
+2	StringTie	exon	121013958	121014018	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "9";
+2	StringTie	exon	121016131	121016177	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "10";
+2	StringTie	exon	121016399	121016904	.	+	.	transcript_id "STRG.8871.1"; gene_id "STRG.8871"; exon_number "11";
+2	StringTie	transcript	121008432	121015120	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; gene_name "Ccndbp1"; xloc "XLOC_006626"; ref_gene_id "ENSMUSG00000023572"; cmp_ref "ENSMUST00000099488"; class_code "="; tss_id "TSS15463"; p_id "P8182";
+2	StringTie	exon	121008432	121008609	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "1";
+2	StringTie	exon	121008718	121008777	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "2";
+2	StringTie	exon	121009043	121009122	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "3";
+2	StringTie	exon	121009827	121009908	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "4";
+2	StringTie	exon	121011434	121011530	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "5";
+2	StringTie	exon	121011683	121011756	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "6";
+2	StringTie	exon	121012353	121012429	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "7";
+2	StringTie	exon	121012699	121012976	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "8";
+2	StringTie	exon	121013958	121014018	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "9";
+2	StringTie	exon	121014513	121015120	.	+	.	transcript_id "STRG.8871.3"; gene_id "STRG.8871"; exon_number "10";
+2	StringTie	transcript	121008448	121016904	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; gene_name "Ccndbp1"; xloc "XLOC_006626"; ref_gene_id "ENSMUSG00000023572"; cmp_ref "ENSMUST00000099489"; class_code "="; tss_id "TSS15463"; p_id "P8183";
+2	StringTie	exon	121008448	121008777	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "1";
+2	StringTie	exon	121009043	121009122	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "2";
+2	StringTie	exon	121009827	121009908	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "3";
+2	StringTie	exon	121011434	121011530	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "4";
+2	StringTie	exon	121011683	121011756	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "5";
+2	StringTie	exon	121012353	121012429	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "6";
+2	StringTie	exon	121012699	121012976	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "7";
+2	StringTie	exon	121013958	121014018	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "8";
+2	StringTie	exon	121016131	121016177	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "9";
+2	StringTie	exon	121016399	121016904	.	+	.	transcript_id "STRG.8871.2"; gene_id "STRG.8871"; exon_number "10";
+2	StringTie	transcript	121008467	121011756	.	+	.	transcript_id "STRG.8871.5"; gene_id "STRG.8871"; gene_name "Ccndbp1"; xloc "XLOC_006626"; cmp_ref "ENSMUST00000060455"; class_code "j"; tss_id "TSS15463";
+2	StringTie	exon	121008467	121008777	.	+	.	transcript_id "STRG.8871.5"; gene_id "STRG.8871"; exon_number "1";
+2	StringTie	exon	121009043	121009122	.	+	.	transcript_id "STRG.8871.5"; gene_id "STRG.8871"; exon_number "2";
+2	StringTie	exon	121009827	121011530	.	+	.	transcript_id "STRG.8871.5"; gene_id "STRG.8871"; exon_number "3";
+2	StringTie	exon	121011683	121011756	.	+	.	transcript_id "STRG.8871.5"; gene_id "STRG.8871"; exon_number "4";
+2	StringTie	transcript	121008467	121012948	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; gene_name "Ccndbp1"; xloc "XLOC_006626"; ref_gene_id "ENSMUSG00000023572"; cmp_ref "ENSMUST00000140468"; class_code "="; tss_id "TSS15463";
+2	StringTie	exon	121008467	121008609	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; exon_number "1";
+2	StringTie	exon	121008718	121008777	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; exon_number "2";
+2	StringTie	exon	121009043	121009122	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; exon_number "3";
+2	StringTie	exon	121009827	121009908	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; exon_number "4";
+2	StringTie	exon	121011434	121011558	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; exon_number "5";
+2	StringTie	exon	121011683	121011756	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; exon_number "6";
+2	StringTie	exon	121012353	121012429	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; exon_number "7";
+2	StringTie	exon	121012699	121012948	.	+	.	transcript_id "STRG.8871.4"; gene_id "STRG.8871"; exon_number "8";
+2	StringTie	transcript	121008704	121010577	.	+	.	transcript_id "STRG.8871.6"; gene_id "STRG.8871"; gene_name "Ccndbp1"; xloc "XLOC_006626"; ref_gene_id "ENSMUSG00000023572"; contained_in "STRG.8871.5"; cmp_ref "ENSMUST00000151532"; class_code "="; tss_id "TSS15464";
+2	StringTie	exon	121008704	121008777	.	+	.	transcript_id "STRG.8871.6"; gene_id "STRG.8871"; exon_number "1";
+2	StringTie	exon	121009043	121009122	.	+	.	transcript_id "STRG.8871.6"; gene_id "STRG.8871"; exon_number "2";
+2	StringTie	exon	121009827	121010577	.	+	.	transcript_id "STRG.8871.6"; gene_id "STRG.8871"; exon_number "3";
+2	StringTie	transcript	121011055	121011756	.	+	.	transcript_id "STRG.8871.7"; gene_id "STRG.8871"; gene_name "Ccndbp1"; xloc "XLOC_006626"; ref_gene_id "ENSMUSG00000023572"; contained_in "STRG.8871.5"; cmp_ref "ENSMUST00000135036"; class_code "="; tss_id "TSS15465";
+2	StringTie	exon	121011055	121011530	.	+	.	transcript_id "STRG.8871.7"; gene_id "STRG.8871"; exon_number "1";
+2	StringTie	exon	121011683	121011756	.	+	.	transcript_id "STRG.8871.7"; gene_id "STRG.8871"; exon_number "2";
+2	StringTie	transcript	120089175	120154606	.	-	.	transcript_id "STRG.8831.1"; gene_id "STRG.8831"; gene_name "Ehd4"; xloc "XLOC_007147"; ref_gene_id "ENSMUSG00000027293"; cmp_ref "ENSMUST00000028755"; class_code "="; tss_id "TSS16872"; p_id "P8912";
+2	StringTie	exon	120089175	120091684	.	-	.	transcript_id "STRG.8831.1"; gene_id "STRG.8831"; exon_number "1";
+2	StringTie	exon	120096963	120097127	.	-	.	transcript_id "STRG.8831.1"; gene_id "STRG.8831"; exon_number "2";
+2	StringTie	exon	120102020	120102432	.	-	.	transcript_id "STRG.8831.1"; gene_id "STRG.8831"; exon_number "3";
+2	StringTie	exon	120127592	120127689	.	-	.	transcript_id "STRG.8831.1"; gene_id "STRG.8831"; exon_number "4";
+2	StringTie	exon	120136899	120137075	.	-	.	transcript_id "STRG.8831.1"; gene_id "STRG.8831"; exon_number "5";
+2	StringTie	exon	120154240	120154606	.	-	.	transcript_id "STRG.8831.1"; gene_id "STRG.8831"; exon_number "6";
+2	StringTie	transcript	121194838	121221232	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; cmp_ref "ENSMUST00000110648"; class_code "j"; tss_id "TSS16904";
+2	StringTie	exon	121194838	121198607	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121198976	121199121	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121199607	121199806	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121200303	121200397	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	exon	121202543	121204548	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "5";
+2	StringTie	exon	121204920	121205111	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "6";
+2	StringTie	exon	121207699	121208129	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "7";
+2	StringTie	exon	121208355	121208504	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "8";
+2	StringTie	exon	121209081	121209352	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "9";
+2	StringTie	exon	121211270	121211422	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "10";
+2	StringTie	exon	121215667	121216171	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "11";
+2	StringTie	exon	121221158	121221232	.	-	.	transcript_id "STRG.8881.3"; gene_id "STRG.8881"; exon_number "12";
+2	StringTie	transcript	121199639	121204981	.	-	.	transcript_id "STRG.8881.7"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000147554"; class_code "="; tss_id "TSS16905";
+2	StringTie	exon	121199639	121199806	.	-	.	transcript_id "STRG.8881.7"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121200303	121200397	.	-	.	transcript_id "STRG.8881.7"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121202543	121202752	.	-	.	transcript_id "STRG.8881.7"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121204333	121204548	.	-	.	transcript_id "STRG.8881.7"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	exon	121204920	121204981	.	-	.	transcript_id "STRG.8881.7"; gene_id "STRG.8881"; exon_number "5";
+2	StringTie	transcript	121199639	121221232	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; cmp_ref "ENSMUST00000110648"; class_code "c"; tss_id "TSS16904";
+2	StringTie	exon	121199639	121199806	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121200303	121200397	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121202543	121202758	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121204333	121204548	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	exon	121204920	121205111	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "5";
+2	StringTie	exon	121207699	121208129	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "6";
+2	StringTie	exon	121208355	121208504	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "7";
+2	StringTie	exon	121209081	121209352	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "8";
+2	StringTie	exon	121211270	121211422	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "9";
+2	StringTie	exon	121215667	121216171	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "10";
+2	StringTie	exon	121221158	121221232	.	-	.	transcript_id "STRG.8881.4"; gene_id "STRG.8881"; exon_number "11";
+2	StringTie	transcript	121205081	121208574	.	-	.	transcript_id "STRG.8881.11"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000132812"; class_code "="; tss_id "TSS16906";
+2	StringTie	exon	121205081	121205111	.	-	.	transcript_id "STRG.8881.11"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121207699	121208129	.	-	.	transcript_id "STRG.8881.11"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121208355	121208574	.	-	.	transcript_id "STRG.8881.11"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	transcript	121208845	121221232	.	-	.	transcript_id "STRG.8881.9"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000124411"; class_code "="; tss_id "TSS16904";
+2	StringTie	exon	121208845	121209352	.	-	.	transcript_id "STRG.8881.9"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121211270	121211422	.	-	.	transcript_id "STRG.8881.9"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121215667	121216171	.	-	.	transcript_id "STRG.8881.9"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121221158	121221232	.	-	.	transcript_id "STRG.8881.9"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	transcript	121215889	121221379	.	-	.	transcript_id "STRG.8881.14"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000156493"; class_code "="; tss_id "TSS16907";
+2	StringTie	exon	121215889	121216171	.	-	.	transcript_id "STRG.8881.14"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121221158	121221379	.	-	.	transcript_id "STRG.8881.14"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	transcript	121216143	121247714	.	-	.	transcript_id "STRG.8881.5"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; cmp_ref "ENSMUST00000110648"; class_code "j"; tss_id "TSS16908";
+2	StringTie	exon	121216143	121216171	.	-	.	transcript_id "STRG.8881.5"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121221158	121221250	.	-	.	transcript_id "STRG.8881.5"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121223705	121223762	.	-	.	transcript_id "STRG.8881.5"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121227645	121228707	.	-	.	transcript_id "STRG.8881.5"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	exon	121235573	121236869	.	-	.	transcript_id "STRG.8881.5"; gene_id "STRG.8881"; exon_number "5";
+2	StringTie	exon	121243894	121244096	.	-	.	transcript_id "STRG.8881.5"; gene_id "STRG.8881"; exon_number "6";
+2	StringTie	exon	121247501	121247714	.	-	.	transcript_id "STRG.8881.5"; gene_id "STRG.8881"; exon_number "7";
+2	StringTie	transcript	121216143	121270286	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; cmp_ref "ENSMUST00000110648"; class_code "c"; tss_id "TSS16909";
+2	StringTie	exon	121216143	121216171	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121221158	121221250	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121223705	121223762	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121227645	121227848	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	exon	121228588	121228707	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "5";
+2	StringTie	exon	121235573	121236869	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "6";
+2	StringTie	exon	121243894	121244096	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "7";
+2	StringTie	exon	121247501	121247595	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "8";
+2	StringTie	exon	121248164	121248290	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "9";
+2	StringTie	exon	121251868	121252034	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "10";
+2	StringTie	exon	121253602	121253731	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "11";
+2	StringTie	exon	121256522	121256680	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "12";
+2	StringTie	exon	121259144	121259268	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "13";
+2	StringTie	exon	121269904	121269988	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "14";
+2	StringTie	exon	121270219	121270286	.	-	.	transcript_id "STRG.8881.2"; gene_id "STRG.8881"; exon_number "15";
+2	StringTie	transcript	121216143	121271321	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000131245"; class_code "="; tss_id "TSS16910"; p_id "P8932";
+2	StringTie	exon	121216143	121216171	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121221158	121221250	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121223705	121223762	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121227645	121227848	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	exon	121235573	121236869	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "5";
+2	StringTie	exon	121243894	121244096	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "6";
+2	StringTie	exon	121247501	121247595	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "7";
+2	StringTie	exon	121248164	121248290	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "8";
+2	StringTie	exon	121251868	121252034	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "9";
+2	StringTie	exon	121253602	121253731	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "10";
+2	StringTie	exon	121256522	121256680	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "11";
+2	StringTie	exon	121259144	121259268	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "12";
+2	StringTie	exon	121269904	121269988	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "13";
+2	StringTie	exon	121270219	121270309	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "14";
+2	StringTie	exon	121270524	121270708	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "15";
+2	StringTie	exon	121271272	121271321	.	-	.	transcript_id "STRG.8881.1"; gene_id "STRG.8881"; exon_number "16";
+2	StringTie	transcript	121228369	121235689	.	-	.	transcript_id "STRG.8881.13"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; contained_in "STRG.8881.5"; cmp_ref "ENSMUST00000142400"; class_code "="; tss_id "TSS16911"; p_id "P8931";
+2	StringTie	exon	121228369	121228707	.	-	.	transcript_id "STRG.8881.13"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121235573	121235689	.	-	.	transcript_id "STRG.8881.13"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	transcript	121256514	121271369	.	-	.	transcript_id "STRG.8881.6"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000136617"; class_code "="; tss_id "TSS16910";
+2	StringTie	exon	121256514	121256680	.	-	.	transcript_id "STRG.8881.6"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121259144	121259268	.	-	.	transcript_id "STRG.8881.6"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121269904	121269988	.	-	.	transcript_id "STRG.8881.6"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121270219	121270309	.	-	.	transcript_id "STRG.8881.6"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	exon	121270524	121270708	.	-	.	transcript_id "STRG.8881.6"; gene_id "STRG.8881"; exon_number "5";
+2	StringTie	exon	121271272	121271369	.	-	.	transcript_id "STRG.8881.6"; gene_id "STRG.8881"; exon_number "6";
+2	StringTie	transcript	121258886	121270286	.	-	.	transcript_id "STRG.8881.10"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000131426"; class_code "="; tss_id "TSS16909";
+2	StringTie	exon	121258886	121259268	.	-	.	transcript_id "STRG.8881.10"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121269904	121269988	.	-	.	transcript_id "STRG.8881.10"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121270219	121270286	.	-	.	transcript_id "STRG.8881.10"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	transcript	121267312	121271361	.	-	.	transcript_id "STRG.8881.8"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000140285"; class_code "="; tss_id "TSS16910";
+2	StringTie	exon	121267312	121269988	.	-	.	transcript_id "STRG.8881.8"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121270219	121270309	.	-	.	transcript_id "STRG.8881.8"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121270524	121270708	.	-	.	transcript_id "STRG.8881.8"; gene_id "STRG.8881"; exon_number "3";
+2	StringTie	exon	121271272	121271361	.	-	.	transcript_id "STRG.8881.8"; gene_id "STRG.8881"; exon_number "4";
+2	StringTie	transcript	121269630	121271370	.	-	.	transcript_id "STRG.8881.12"; gene_id "STRG.8881"; gene_name "Trp53bp1"; xloc "XLOC_007155"; ref_gene_id "ENSMUSG00000043909"; cmp_ref "ENSMUST00000124060"; class_code "="; tss_id "TSS16910";
+2	StringTie	exon	121269630	121269988	.	-	.	transcript_id "STRG.8881.12"; gene_id "STRG.8881"; exon_number "1";
+2	StringTie	exon	121270524	121270708	.	-	.	transcript_id "STRG.8881.12"; gene_id "STRG.8881"; exon_number "2";
+2	StringTie	exon	121271272	121271370	.	-	.	transcript_id "STRG.8881.12"; gene_id "STRG.8881"; exon_number "3";
+3	StringTie	transcript	57736062	57835231	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; gene_name "Rnf13"; xloc "XLOC_007425"; ref_gene_id "ENSMUSG00000036503"; cmp_ref "ENSMUST00000041826"; class_code "="; tss_id "TSS17634"; p_id "P9318";
+3	StringTie	exon	57736062	57736200	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "1";
+3	StringTie	exon	57764257	57764382	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "2";
+3	StringTie	exon	57769040	57769120	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "3";
+3	StringTie	exon	57779383	57779508	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "4";
+3	StringTie	exon	57796198	57796285	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "5";
+3	StringTie	exon	57802447	57802537	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "6";
+3	StringTie	exon	57807022	57807127	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "7";
+3	StringTie	exon	57820507	57820600	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "8";
+3	StringTie	exon	57832964	57833044	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "9";
+3	StringTie	exon	57833486	57835231	.	+	.	transcript_id "STRG.12098.3"; gene_id "STRG.12098"; exon_number "10";
+3	StringTie	transcript	57736082	57833888	.	+	.	transcript_id "STRG.12098.6"; gene_id "STRG.12098"; gene_name "Rnf13"; xloc "XLOC_007425"; ref_gene_id "ENSMUSG00000036503"; cmp_ref "ENSMUST00000197920"; class_code "="; tss_id "TSS17634";
+3	StringTie	exon	57736082	57736200	.	+	.	transcript_id "STRG.12098.6"; gene_id "STRG.12098"; exon_number "1";
+3	StringTie	exon	57833573	57833888	.	+	.	transcript_id "STRG.12098.6"; gene_id "STRG.12098"; exon_number "2";
+3	StringTie	transcript	57736082	57835233	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; gene_name "Rnf13"; xloc "XLOC_007425"; ref_gene_id "ENSMUSG00000036503"; cmp_ref "ENSMUST00000200497"; class_code "="; tss_id "TSS17634"; p_id "P9319";
+3	StringTie	exon	57736082	57736200	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "1";
+3	StringTie	exon	57764257	57764382	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "2";
+3	StringTie	exon	57769040	57769120	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "3";
+3	StringTie	exon	57779383	57779508	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "4";
+3	StringTie	exon	57796198	57796285	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "5";
+3	StringTie	exon	57802447	57802537	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "6";
+3	StringTie	exon	57807022	57807127	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "7";
+3	StringTie	exon	57820507	57820600	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "8";
+3	StringTie	exon	57832964	57833044	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "9";
+3	StringTie	exon	57833573	57835233	.	+	.	transcript_id "STRG.12098.2"; gene_id "STRG.12098"; exon_number "10";
+3	StringTie	transcript	57736113	57835119	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; gene_name "Rnf13"; xloc "XLOC_007425"; ref_gene_id "ENSMUSG00000036503"; cmp_ref "ENSMUST00000197205"; class_code "="; tss_id "TSS17634"; p_id "P9321";
+3	StringTie	exon	57736113	57736200	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "1";
+3	StringTie	exon	57764257	57764382	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "2";
+3	StringTie	exon	57769040	57769120	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "3";
+3	StringTie	exon	57779383	57779508	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "4";
+3	StringTie	exon	57796198	57796285	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "5";
+3	StringTie	exon	57801718	57802537	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "6";
+3	StringTie	exon	57807022	57807127	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "7";
+3	StringTie	exon	57820507	57820600	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "8";
+3	StringTie	exon	57832964	57833044	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "9";
+3	StringTie	exon	57833486	57835119	.	+	.	transcript_id "STRG.12098.1"; gene_id "STRG.12098"; exon_number "10";
+3	StringTie	transcript	57736120	57820993	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; gene_name "Rnf13"; xloc "XLOC_007425"; cmp_ref "ENSMUST00000197205"; class_code "j"; tss_id "TSS17634";
+3	StringTie	exon	57736120	57736200	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "1";
+3	StringTie	exon	57747891	57748034	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "2";
+3	StringTie	exon	57764257	57764382	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "3";
+3	StringTie	exon	57769040	57769120	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "4";
+3	StringTie	exon	57779383	57779508	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "5";
+3	StringTie	exon	57796198	57796285	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "6";
+3	StringTie	exon	57802447	57802537	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "7";
+3	StringTie	exon	57807022	57807127	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "8";
+3	StringTie	exon	57820507	57820993	.	+	.	transcript_id "STRG.12098.5"; gene_id "STRG.12098"; exon_number "9";
+3	StringTie	transcript	57736120	57833232	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; gene_name "Rnf13"; xloc "XLOC_007425"; ref_gene_id "ENSMUSG00000036503"; cmp_ref "ENSMUST00000199041"; class_code "="; tss_id "TSS17634"; p_id "P9320";
+3	StringTie	exon	57736120	57736200	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "1";
+3	StringTie	exon	57764257	57764382	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "2";
+3	StringTie	exon	57769040	57769120	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "3";
+3	StringTie	exon	57779383	57779508	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "4";
+3	StringTie	exon	57796198	57796285	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "5";
+3	StringTie	exon	57802447	57802537	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "6";
+3	StringTie	exon	57807022	57807127	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "7";
+3	StringTie	exon	57820507	57820600	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "8";
+3	StringTie	exon	57832964	57833232	.	+	.	transcript_id "STRG.12098.4"; gene_id "STRG.12098"; exon_number "9";
+3	StringTie	transcript	57644349	57651715	.	-	.	transcript_id "STRG.12092.1"; gene_id "STRG.12092"; gene_name "Commd2"; xloc "XLOC_007733"; ref_gene_id "ENSMUSG00000036513"; cmp_ref "ENSMUST00000160959"; class_code "="; tss_id "TSS18453"; p_id "P9796";
+3	StringTie	exon	57644349	57646876	.	-	.	transcript_id "STRG.12092.1"; gene_id "STRG.12092"; exon_number "1";
+3	StringTie	exon	57650042	57650215	.	-	.	transcript_id "STRG.12092.1"; gene_id "STRG.12092"; exon_number "2";
+3	StringTie	exon	57650691	57650773	.	-	.	transcript_id "STRG.12092.1"; gene_id "STRG.12092"; exon_number "3";
+3	StringTie	exon	57651422	57651499	.	-	.	transcript_id "STRG.12092.1"; gene_id "STRG.12092"; exon_number "4";
+3	StringTie	exon	57651587	57651715	.	-	.	transcript_id "STRG.12092.1"; gene_id "STRG.12092"; exon_number "5";
+3	StringTie	transcript	57651102	57651715	.	-	.	transcript_id "STRG.12092.2"; gene_id "STRG.12092"; gene_name "Commd2"; xloc "XLOC_007733"; ref_gene_id "ENSMUSG00000036513"; cmp_ref "ENSMUST00000163087"; class_code "="; tss_id "TSS18453";
+3	StringTie	exon	57651102	57651499	.	-	.	transcript_id "STRG.12092.2"; gene_id "STRG.12092"; exon_number "1";
+3	StringTie	exon	57651587	57651715	.	-	.	transcript_id "STRG.12092.2"; gene_id "STRG.12092"; exon_number "2";
+5	StringTie	transcript	110839983	110874133	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; gene_name "Chek2"; xloc "XLOC_009008"; ref_gene_id "ENSMUSG00000029521"; cmp_ref "ENSMUST00000199937"; class_code "="; tss_id "TSS21738"; p_id "P11495";
+5	StringTie	exon	110839983	110840048	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "1";
+5	StringTie	exon	110841206	110841543	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "2";
+5	StringTie	exon	110848389	110848513	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "3";
+5	StringTie	exon	110848630	110848777	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "4";
+5	StringTie	exon	110855725	110855833	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "5";
+5	StringTie	exon	110858374	110858427	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "6";
+5	StringTie	exon	110860863	110860924	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "7";
+5	StringTie	exon	110863258	110863357	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "8";
+5	StringTie	exon	110865522	110865608	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "9";
+5	StringTie	exon	110866263	110866426	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "10";
+5	StringTie	exon	110866938	110867053	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "11";
+5	StringTie	exon	110868008	110868093	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "12";
+5	StringTie	exon	110872027	110872107	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "13";
+5	StringTie	exon	110873480	110874133	.	+	.	transcript_id "STRG.22906.2"; gene_id "STRG.22906"; exon_number "14";
+5	StringTie	transcript	110840000	110874145	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; gene_name "Chek2"; xloc "XLOC_009008"; ref_gene_id "ENSMUSG00000029521"; cmp_ref "ENSMUST00000066160"; class_code "="; tss_id "TSS21738"; p_id "P11494";
+5	StringTie	exon	110840000	110840048	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "1";
+5	StringTie	exon	110841206	110841543	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "2";
+5	StringTie	exon	110848389	110848513	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "3";
+5	StringTie	exon	110848630	110848777	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "4";
+5	StringTie	exon	110849596	110849686	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "5";
+5	StringTie	exon	110855725	110855833	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "6";
+5	StringTie	exon	110858374	110858427	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "7";
+5	StringTie	exon	110860863	110860924	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "8";
+5	StringTie	exon	110863258	110863357	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "9";
+5	StringTie	exon	110865522	110865608	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "10";
+5	StringTie	exon	110866263	110866426	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "11";
+5	StringTie	exon	110866938	110867053	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "12";
+5	StringTie	exon	110868008	110868093	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "13";
+5	StringTie	exon	110872027	110872107	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "14";
+5	StringTie	exon	110873480	110874145	.	+	.	transcript_id "STRG.22906.1"; gene_id "STRG.22906"; exon_number "15";
+5	StringTie	transcript	110840254	110874013	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; gene_name "Chek2"; xloc "XLOC_009008"; cmp_ref "ENSMUST00000066160"; class_code "j"; tss_id "TSS21739";
+5	StringTie	exon	110840254	110841543	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "1";
+5	StringTie	exon	110848389	110848513	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "2";
+5	StringTie	exon	110848630	110848777	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "3";
+5	StringTie	exon	110849596	110849686	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "4";
+5	StringTie	exon	110855725	110855833	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "5";
+5	StringTie	exon	110858374	110858427	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "6";
+5	StringTie	exon	110860863	110860924	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "7";
+5	StringTie	exon	110863258	110863357	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "8";
+5	StringTie	exon	110865522	110865608	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "9";
+5	StringTie	exon	110866263	110866426	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "10";
+5	StringTie	exon	110866938	110867053	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "11";
+5	StringTie	exon	110868008	110868093	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "12";
+5	StringTie	exon	110872027	110874013	.	+	.	transcript_id "STRG.22906.3"; gene_id "STRG.22906"; exon_number "13";
+5	StringTie	transcript	110855690	110868215	.	+	.	transcript_id "STRG.22906.4"; gene_id "STRG.22906"; gene_name "Chek2"; xloc "XLOC_009008"; cmp_ref "ENSMUST00000066160"; class_code "j"; tss_id "TSS21740";
+5	StringTie	exon	110855690	110855833	.	+	.	transcript_id "STRG.22906.4"; gene_id "STRG.22906"; exon_number "1";
+5	StringTie	exon	110858374	110858427	.	+	.	transcript_id "STRG.22906.4"; gene_id "STRG.22906"; exon_number "2";
+5	StringTie	exon	110860863	110860924	.	+	.	transcript_id "STRG.22906.4"; gene_id "STRG.22906"; exon_number "3";
+5	StringTie	exon	110863258	110863357	.	+	.	transcript_id "STRG.22906.4"; gene_id "STRG.22906"; exon_number "4";
+5	StringTie	exon	110865522	110865608	.	+	.	transcript_id "STRG.22906.4"; gene_id "STRG.22906"; exon_number "5";
+5	StringTie	exon	110868008	110868215	.	+	.	transcript_id "STRG.22906.4"; gene_id "STRG.22906"; exon_number "6";
+5	StringTie	transcript	110866271	110866720	.	+	.	transcript_id "STRG.22906.5"; gene_id "STRG.22906"; gene_name "Chek2"; xloc "XLOC_009008"; ref_gene_id "ENSMUSG00000029521"; cmp_ref "ENSMUST00000196650"; class_code "="; tss_id "TSS21741";
+5	StringTie	exon	110866271	110866426	.	+	.	transcript_id "STRG.22906.5"; gene_id "STRG.22906"; exon_number "1";
+5	StringTie	exon	110866536	110866720	.	+	.	transcript_id "STRG.22906.5"; gene_id "STRG.22906"; exon_number "2";
+5	StringTie	transcript	110892839	111085034	.	+	.	transcript_id "STRG.22909.1"; gene_id "STRG.22909"; gene_name "Ttc28"; xloc "XLOC_009009"; cmp_ref "ENSMUST00000040111"; class_code "c"; tss_id "TSS21742";
+5	StringTie	exon	110892839	110893110	.	+	.	transcript_id "STRG.22909.1"; gene_id "STRG.22909"; exon_number "1";
+5	StringTie	exon	111085022	111085034	.	+	.	transcript_id "STRG.22909.1"; gene_id "STRG.22909"; exon_number "2";
+5	StringTie	transcript	111100698	111102068	.	+	.	transcript_id "STRG.22913.1"; gene_id "STRG.22913"; gene_name "Ttc28"; xloc "XLOC_009009"; cmp_ref "ENSMUST00000040111"; class_code "c"; tss_id "TSS21743";
+5	StringTie	exon	111100698	111100966	.	+	.	transcript_id "STRG.22913.1"; gene_id "STRG.22913"; exon_number "1";
+5	StringTie	exon	111101970	111102068	.	+	.	transcript_id "STRG.22913.1"; gene_id "STRG.22913"; exon_number "2";
+5	StringTie	transcript	111225458	111229415	.	+	.	transcript_id "STRG.22916.1"; gene_id "STRG.22916"; gene_name "Ttc28"; xloc "XLOC_009009"; ref_gene_id "ENSMUSG00000033209"; cmp_ref "ENSMUST00000125470"; class_code "="; tss_id "TSS21744";
+5	StringTie	exon	111225458	111226081	.	+	.	transcript_id "STRG.22916.1"; gene_id "STRG.22916"; exon_number "1";
+5	StringTie	exon	111229348	111229415	.	+	.	transcript_id "STRG.22916.1"; gene_id "STRG.22916"; exon_number "2";
+5	StringTie	transcript	111231101	111235600	.	+	.	transcript_id "STRG.22917.1"; gene_id "STRG.22917"; gene_name "Ttc28"; xloc "XLOC_009009"; cmp_ref "ENSMUST00000040111"; class_code "c"; tss_id "TSS21745";
+5	StringTie	exon	111231101	111231179	.	+	.	transcript_id "STRG.22917.1"; gene_id "STRG.22917"; exon_number "1";
+5	StringTie	exon	111233246	111233464	.	+	.	transcript_id "STRG.22917.1"; gene_id "STRG.22917"; exon_number "2";
+5	StringTie	exon	111235476	111235600	.	+	.	transcript_id "STRG.22917.1"; gene_id "STRG.22917"; exon_number "3";
+5	StringTie	transcript	111330763	111388359	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; gene_name "Pitpnb"; xloc "XLOC_009010"; ref_gene_id "ENSMUSG00000050017"; cmp_ref "ENSMUST00000086635"; class_code "="; tss_id "TSS21746"; p_id "P11496";
+5	StringTie	exon	111330763	111330833	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "1";
+5	StringTie	exon	111335495	111335525	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "2";
+5	StringTie	exon	111338283	111338428	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "3";
+5	StringTie	exon	111346483	111346574	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "4";
+5	StringTie	exon	111347120	111347127	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "5";
+5	StringTie	exon	111347781	111347855	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "6";
+5	StringTie	exon	111349491	111349574	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "7";
+5	StringTie	exon	111371312	111371389	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "8";
+5	StringTie	exon	111380192	111380302	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "9";
+5	StringTie	exon	111382988	111383110	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "10";
+5	StringTie	exon	111385520	111385604	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "11";
+5	StringTie	exon	111386503	111388359	.	+	.	transcript_id "STRG.22924.1"; gene_id "STRG.22924"; exon_number "12";
+5	StringTie	transcript	111330807	111388359	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; gene_name "Pitpnb"; xloc "XLOC_009010"; ref_gene_id "ENSMUSG00000050017"; cmp_ref "ENSMUST00000200298"; class_code "="; tss_id "TSS21746"; p_id "P11497";
+5	StringTie	exon	111330807	111330833	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "1";
+5	StringTie	exon	111335495	111335525	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "2";
+5	StringTie	exon	111338283	111338428	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "3";
+5	StringTie	exon	111346483	111346574	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "4";
+5	StringTie	exon	111347120	111347127	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "5";
+5	StringTie	exon	111347781	111347855	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "6";
+5	StringTie	exon	111349491	111349574	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "7";
+5	StringTie	exon	111371312	111371389	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "8";
+5	StringTie	exon	111380192	111380302	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "9";
+5	StringTie	exon	111382988	111383110	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "10";
+5	StringTie	exon	111386503	111388359	.	+	.	transcript_id "STRG.22924.2"; gene_id "STRG.22924"; exon_number "11";
+5	StringTie	transcript	111380169	111383703	.	+	.	transcript_id "STRG.22924.3"; gene_id "STRG.22924"; gene_name "Pitpnb"; xloc "XLOC_009010"; ref_gene_id "ENSMUSG00000050017"; cmp_ref "ENSMUST00000198137"; class_code "="; tss_id "TSS21747";
+5	StringTie	exon	111380169	111380302	.	+	.	transcript_id "STRG.22924.3"; gene_id "STRG.22924"; exon_number "1";
+5	StringTie	exon	111382988	111383703	.	+	.	transcript_id "STRG.22924.3"; gene_id "STRG.22924"; exon_number "2";
+5	StringTie	transcript	111417442	111454864	.	+	.	transcript_id "STRG.22929.1"; gene_id "STRG.22929"; gene_name "Mn1"; xloc "XLOC_009011"; cmp_ref "ENSMUST00000094463"; class_code "j"; tss_id "TSS21748";
+5	StringTie	exon	111417442	111417761	.	+	.	transcript_id "STRG.22929.1"; gene_id "STRG.22929"; exon_number "1";
+5	StringTie	exon	111419610	111421883	.	+	.	transcript_id "STRG.22929.1"; gene_id "STRG.22929"; exon_number "2";
+5	StringTie	exon	111454616	111454864	.	+	.	transcript_id "STRG.22929.1"; gene_id "STRG.22929"; exon_number "3";
+5	StringTie	transcript	111417442	111457033	.	+	.	transcript_id "STRG.22929.2"; gene_id "STRG.22929"; gene_name "Mn1"; xloc "XLOC_009011"; ref_gene_id "ENSMUSG00000070576"; cmp_ref "ENSMUST00000094463"; class_code "="; tss_id "TSS21748"; p_id "P11498";
+5	StringTie	exon	111417442	111421883	.	+	.	transcript_id "STRG.22929.2"; gene_id "STRG.22929"; exon_number "1";
+5	StringTie	exon	111454616	111457033	.	+	.	transcript_id "STRG.22929.2"; gene_id "STRG.22929"; exon_number "2";
+5	StringTie	transcript	111546621	111566751	.	+	.	transcript_id "STRG.22958.1"; gene_id "STRG.22958"; xloc "XLOC_009012"; class_code "u"; tss_id "TSS21749";
+5	StringTie	exon	111546621	111546787	.	+	.	transcript_id "STRG.22958.1"; gene_id "STRG.22958"; exon_number "1";
+5	StringTie	exon	111553852	111553928	.	+	.	transcript_id "STRG.22958.1"; gene_id "STRG.22958"; exon_number "2";
+5	StringTie	exon	111562387	111564386	.	+	.	transcript_id "STRG.22958.1"; gene_id "STRG.22958"; exon_number "3";
+5	StringTie	exon	111565966	111566751	.	+	.	transcript_id "STRG.22958.1"; gene_id "STRG.22958"; exon_number "4";
+5	StringTie	transcript	111553370	111564411	.	+	.	transcript_id "STRG.22958.2"; gene_id "STRG.22958"; xloc "XLOC_009012"; class_code "u"; tss_id "TSS21750";
+5	StringTie	exon	111553370	111553928	.	+	.	transcript_id "STRG.22958.2"; gene_id "STRG.22958"; exon_number "1";
+5	StringTie	exon	111562387	111563609	.	+	.	transcript_id "STRG.22958.2"; gene_id "STRG.22958"; exon_number "2";
+5	StringTie	exon	111564163	111564411	.	+	.	transcript_id "STRG.22958.2"; gene_id "STRG.22958"; exon_number "3";
+5	StringTie	transcript	111553370	111567041	.	+	.	transcript_id "STRG.22958.3"; gene_id "STRG.22958"; xloc "XLOC_009012"; class_code "u"; tss_id "TSS21750";
+5	StringTie	exon	111553370	111553928	.	+	.	transcript_id "STRG.22958.3"; gene_id "STRG.22958"; exon_number "1";
+5	StringTie	exon	111562387	111564386	.	+	.	transcript_id "STRG.22958.3"; gene_id "STRG.22958"; exon_number "2";
+5	StringTie	exon	111565037	111567041	.	+	.	transcript_id "STRG.22958.3"; gene_id "STRG.22958"; exon_number "3";
+5	StringTie	transcript	111581568	111582873	.	+	.	transcript_id "STRG.22963.1"; gene_id "STRG.22963"; gene_name "C130026L21Rik"; xloc "XLOC_009013"; ref_gene_id "ENSMUSG00000052848"; cmp_ref "ENSMUST00000196725"; class_code "="; tss_id "TSS21751";
+5	StringTie	exon	111581568	111581870	.	+	.	transcript_id "STRG.22963.1"; gene_id "STRG.22963"; exon_number "1";
+5	StringTie	exon	111582421	111582873	.	+	.	transcript_id "STRG.22963.1"; gene_id "STRG.22963"; exon_number "2";
+5	StringTie	transcript	112276691	112315361	.	+	.	transcript_id "STRG.22971.1"; gene_id "STRG.22971"; gene_name "Tpst2"; xloc "XLOC_009014"; ref_gene_id "ENSMUSG00000029344"; cmp_ref "ENSMUST00000031287"; class_code "="; tss_id "TSS21752"; p_id "P11499";
+5	StringTie	exon	112276691	112276771	.	+	.	transcript_id "STRG.22971.1"; gene_id "STRG.22971"; exon_number "1";
+5	StringTie	exon	112303900	112303971	.	+	.	transcript_id "STRG.22971.1"; gene_id "STRG.22971"; exon_number "2";
+5	StringTie	exon	112307566	112308477	.	+	.	transcript_id "STRG.22971.1"; gene_id "STRG.22971"; exon_number "3";
+5	StringTie	exon	112309689	112309887	.	+	.	transcript_id "STRG.22971.1"; gene_id "STRG.22971"; exon_number "4";
+5	StringTie	exon	112311684	112311734	.	+	.	transcript_id "STRG.22971.1"; gene_id "STRG.22971"; exon_number "5";
+5	StringTie	exon	112313242	112313290	.	+	.	transcript_id "STRG.22971.1"; gene_id "STRG.22971"; exon_number "6";
+5	StringTie	exon	112314891	112315361	.	+	.	transcript_id "STRG.22971.1"; gene_id "STRG.22971"; exon_number "7";
+5	StringTie	transcript	112276704	112309032	.	+	.	transcript_id "STRG.22971.3"; gene_id "STRG.22971"; gene_name "Tpst2"; xloc "XLOC_009014"; ref_gene_id "ENSMUSG00000029344"; cmp_ref "ENSMUST00000134071"; class_code "="; tss_id "TSS21752";
+5	StringTie	exon	112276704	112276771	.	+	.	transcript_id "STRG.22971.3"; gene_id "STRG.22971"; exon_number "1";
+5	StringTie	exon	112303900	112303971	.	+	.	transcript_id "STRG.22971.3"; gene_id "STRG.22971"; exon_number "2";
+5	StringTie	exon	112307566	112309032	.	+	.	transcript_id "STRG.22971.3"; gene_id "STRG.22971"; exon_number "3";
+5	StringTie	transcript	112276707	112315355	.	+	.	transcript_id "STRG.22971.2"; gene_id "STRG.22971"; gene_name "Tpst2"; xloc "XLOC_009014"; ref_gene_id "ENSMUSG00000029344"; cmp_ref "ENSMUST00000071455"; class_code "="; tss_id "TSS21752"; p_id "P11499";
+5	StringTie	exon	112276707	112276771	.	+	.	transcript_id "STRG.22971.2"; gene_id "STRG.22971"; exon_number "1";
+5	StringTie	exon	112307566	112308477	.	+	.	transcript_id "STRG.22971.2"; gene_id "STRG.22971"; exon_number "2";
+5	StringTie	exon	112309689	112309887	.	+	.	transcript_id "STRG.22971.2"; gene_id "STRG.22971"; exon_number "3";
+5	StringTie	exon	112311684	112311734	.	+	.	transcript_id "STRG.22971.2"; gene_id "STRG.22971"; exon_number "4";
+5	StringTie	exon	112313242	112313290	.	+	.	transcript_id "STRG.22971.2"; gene_id "STRG.22971"; exon_number "5";
+5	StringTie	exon	112314891	112315355	.	+	.	transcript_id "STRG.22971.2"; gene_id "STRG.22971"; exon_number "6";
+5	StringTie	transcript	112308291	112309812	.	+	.	transcript_id "STRG.22971.5"; gene_id "STRG.22971"; gene_name "Tpst2"; xloc "XLOC_009014"; ref_gene_id "ENSMUSG00000029344"; cmp_ref "ENSMUST00000140262"; class_code "="; tss_id "TSS21753"; p_id "P11500";
+5	StringTie	exon	112308291	112308554	.	+	.	transcript_id "STRG.22971.5"; gene_id "STRG.22971"; exon_number "1";
+5	StringTie	exon	112309689	112309812	.	+	.	transcript_id "STRG.22971.5"; gene_id "STRG.22971"; exon_number "2";
+5	StringTie	transcript	112312894	112314964	.	+	.	transcript_id "STRG.22971.4"; gene_id "STRG.22971"; gene_name "Tpst2"; xloc "XLOC_009014"; ref_gene_id "ENSMUSG00000029344"; cmp_ref "ENSMUST00000139482"; class_code "="; tss_id "TSS21754";
+5	StringTie	exon	112312894	112313290	.	+	.	transcript_id "STRG.22971.4"; gene_id "STRG.22971"; exon_number "1";
+5	StringTie	exon	112314891	112314964	.	+	.	transcript_id "STRG.22971.4"; gene_id "STRG.22971"; exon_number "2";
+5	StringTie	transcript	112326358	112338073	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; gene_name "Tfip11"; xloc "XLOC_009015"; ref_gene_id "ENSMUSG00000029345"; cmp_ref "ENSMUST00000031288"; class_code "="; tss_id "TSS21755"; p_id "P11501";
+5	StringTie	exon	112326358	112326473	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "1";
+5	StringTie	exon	112327485	112327670	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "2";
+5	StringTie	exon	112327962	112328182	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "3";
+5	StringTie	exon	112329366	112329519	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "4";
+5	StringTie	exon	112329747	112329903	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "5";
+5	StringTie	exon	112331091	112331218	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "6";
+5	StringTie	exon	112331868	112332020	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "7";
+5	StringTie	exon	112332964	112333491	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "8";
+5	StringTie	exon	112333575	112333681	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "9";
+5	StringTie	exon	112334317	112334485	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "10";
+5	StringTie	exon	112334860	112335103	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "11";
+5	StringTie	exon	112335573	112335715	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "12";
+5	StringTie	exon	112336015	112336180	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "13";
+5	StringTie	exon	112336986	112338073	.	+	.	transcript_id "STRG.22973.1"; gene_id "STRG.22973"; exon_number "14";
+5	StringTie	transcript	112335642	112337273	.	+	.	transcript_id "STRG.22973.2"; gene_id "STRG.22973"; gene_name "Tfip11"; xloc "XLOC_009015"; ref_gene_id "ENSMUSG00000029345"; cmp_ref "ENSMUST00000126736"; class_code "="; tss_id "TSS21756";
+5	StringTie	exon	112335642	112336180	.	+	.	transcript_id "STRG.22973.2"; gene_id "STRG.22973"; exon_number "1";
+5	StringTie	exon	112336986	112337273	.	+	.	transcript_id "STRG.22973.2"; gene_id "STRG.22973"; exon_number "2";
+5	StringTie	transcript	112343083	112378414	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; gene_name "Hps4"; xloc "XLOC_009016"; ref_gene_id "ENSMUSG00000042328"; cmp_ref "ENSMUST00000112359"; class_code "="; tss_id "TSS21757"; p_id "P11502";
+5	StringTie	exon	112343083	112343163	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "1";
+5	StringTie	exon	112344044	112345048	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "2";
+5	StringTie	exon	112346594	112346684	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "3";
+5	StringTie	exon	112349285	112349428	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "4";
+5	StringTie	exon	112363109	112363216	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "5";
+5	StringTie	exon	112363546	112363662	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "6";
+5	StringTie	exon	112364521	112364615	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "7";
+5	StringTie	exon	112366899	112366971	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "8";
+5	StringTie	exon	112368936	112368972	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "9";
+5	StringTie	exon	112369455	112369551	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "10";
+5	StringTie	exon	112369946	112370744	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "11";
+5	StringTie	exon	112374880	112375012	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "12";
+5	StringTie	exon	112375353	112375461	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "13";
+5	StringTie	exon	112377959	112378414	.	+	.	transcript_id "STRG.22978.2"; gene_id "STRG.22978"; exon_number "14";
+5	StringTie	transcript	112343093	112344747	.	+	.	transcript_id "STRG.22978.3"; gene_id "STRG.22978"; gene_name "Hps4"; xloc "XLOC_009016"; ref_gene_id "ENSMUSG00000042328"; cmp_ref "ENSMUST00000176737"; class_code "="; tss_id "TSS21757";
+5	StringTie	exon	112343093	112343122	.	+	.	transcript_id "STRG.22978.3"; gene_id "STRG.22978"; exon_number "1";
+5	StringTie	exon	112344044	112344747	.	+	.	transcript_id "STRG.22978.3"; gene_id "STRG.22978"; exon_number "2";
+5	StringTie	transcript	112343095	112378414	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; gene_name "Hps4"; xloc "XLOC_009016"; ref_gene_id "ENSMUSG00000042328"; cmp_ref "ENSMUST00000035279"; class_code "="; tss_id "TSS21757"; p_id "P11502";
+5	StringTie	exon	112343095	112343163	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "1";
+5	StringTie	exon	112344541	112345048	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "2";
+5	StringTie	exon	112346594	112346684	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "3";
+5	StringTie	exon	112349285	112349428	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "4";
+5	StringTie	exon	112363109	112363216	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "5";
+5	StringTie	exon	112363546	112363662	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "6";
+5	StringTie	exon	112364521	112364615	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "7";
+5	StringTie	exon	112366899	112366971	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "8";
+5	StringTie	exon	112368936	112368972	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "9";
+5	StringTie	exon	112369455	112369551	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "10";
+5	StringTie	exon	112369946	112370744	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "11";
+5	StringTie	exon	112374880	112375012	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "12";
+5	StringTie	exon	112375353	112375461	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "13";
+5	StringTie	exon	112377959	112378414	.	+	.	transcript_id "STRG.22978.1"; gene_id "STRG.22978"; exon_number "14";
+5	StringTie	transcript	112343099	112344747	.	+	.	transcript_id "STRG.22978.6"; gene_id "STRG.22978"; gene_name "Hps4"; xloc "XLOC_009016"; cmp_ref "ENSMUST00000133708"; class_code "c"; tss_id "TSS21757";
+5	StringTie	exon	112343099	112343122	.	+	.	transcript_id "STRG.22978.6"; gene_id "STRG.22978"; exon_number "1";
+5	StringTie	exon	112344541	112344747	.	+	.	transcript_id "STRG.22978.6"; gene_id "STRG.22978"; exon_number "2";
+5	StringTie	transcript	112368745	112369774	.	+	.	transcript_id "STRG.22978.5"; gene_id "STRG.22978"; gene_name "Hps4"; xloc "XLOC_009016"; ref_gene_id "ENSMUSG00000042328"; cmp_ref "ENSMUST00000129839"; class_code "="; tss_id "TSS21758";
+5	StringTie	exon	112368745	112368972	.	+	.	transcript_id "STRG.22978.5"; gene_id "STRG.22978"; exon_number "1";
+5	StringTie	exon	112369455	112369774	.	+	.	transcript_id "STRG.22978.5"; gene_id "STRG.22978"; exon_number "2";
+5	StringTie	transcript	112375335	112378401	.	+	.	transcript_id "STRG.22978.4"; gene_id "STRG.22978"; gene_name "Hps4"; xloc "XLOC_009016"; ref_gene_id "ENSMUSG00000042328"; cmp_ref "ENSMUST00000177121"; class_code "="; tss_id "TSS21759";
+5	StringTie	exon	112375335	112375461	.	+	.	transcript_id "STRG.22978.4"; gene_id "STRG.22978"; exon_number "1";
+5	StringTie	exon	112377959	112378401	.	+	.	transcript_id "STRG.22978.4"; gene_id "STRG.22978"; exon_number "2";
+5	StringTie	transcript	112793300	112795691	.	+	.	transcript_id "STRG.22983.1"; gene_id "STRG.22983"; gene_name "1700095B10Rik"; xloc "XLOC_009017"; ref_gene_id "ENSMUSG00000098230"; cmp_ref "ENSMUST00000189538"; class_code "="; tss_id "TSS21760";
+5	StringTie	exon	112793300	112793611	.	+	.	transcript_id "STRG.22983.1"; gene_id "STRG.22983"; exon_number "1";
+5	StringTie	exon	112795415	112795691	.	+	.	transcript_id "STRG.22983.1"; gene_id "STRG.22983"; exon_number "2";
+5	StringTie	transcript	110784488	110810097	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; gene_name "Ulk1"; xloc "XLOC_009424"; ref_gene_id "ENSMUSG00000029512"; cmp_ref "ENSMUST00000031490"; class_code "="; tss_id "TSS22921"; p_id "P12160";
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+5	StringTie	exon	110787084	110787241	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "3";
+5	StringTie	exon	110787574	110787692	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "4";
+5	StringTie	exon	110787773	110787945	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "5";
+5	StringTie	exon	110788110	110788300	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "6";
+5	StringTie	exon	110788729	110788872	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "7";
+5	StringTie	exon	110788948	110789057	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "8";
+5	StringTie	exon	110789342	110789535	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "9";
+5	StringTie	exon	110790212	110790480	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "10";
+5	StringTie	exon	110790850	110790936	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "11";
+5	StringTie	exon	110791052	110791197	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "12";
+5	StringTie	exon	110791601	110791726	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "13";
+5	StringTie	exon	110792102	110792191	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "14";
+5	StringTie	exon	110792397	110792457	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "15";
+5	StringTie	exon	110792966	110793113	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "16";
+5	StringTie	exon	110793815	110793903	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "17";
+5	StringTie	exon	110794193	110794243	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "18";
+5	StringTie	exon	110794585	110794667	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "19";
+5	StringTie	exon	110794747	110794805	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "20";
+5	StringTie	exon	110795732	110795833	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "21";
+5	StringTie	exon	110796156	110796229	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "22";
+5	StringTie	exon	110796327	110796500	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "23";
+5	StringTie	exon	110798882	110798918	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "24";
+5	StringTie	exon	110799124	110799156	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "25";
+5	StringTie	exon	110809005	110809046	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "26";
+5	StringTie	exon	110809127	110809219	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "27";
+5	StringTie	exon	110809614	110810097	.	-	.	transcript_id "STRG.22901.1"; gene_id "STRG.22901"; exon_number "28";
+5	StringTie	transcript	110786039	110787221	.	-	.	transcript_id "STRG.22901.9"; gene_id "STRG.22901"; gene_name "Ulk1"; xloc "XLOC_009424"; ref_gene_id "ENSMUSG00000029512"; cmp_ref "ENSMUST00000199717"; class_code "="; tss_id "TSS22922";
+5	StringTie	exon	110786039	110786435	.	-	.	transcript_id "STRG.22901.9"; gene_id "STRG.22901"; exon_number "1";
+5	StringTie	exon	110787084	110787221	.	-	.	transcript_id "STRG.22901.9"; gene_id "STRG.22901"; exon_number "2";
+5	StringTie	transcript	110786094	110796066	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; gene_name "Ulk1"; xloc "XLOC_009424"; cmp_ref "ENSMUST00000031490"; class_code "j"; tss_id "TSS22923";
+5	StringTie	exon	110786094	110786227	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "1";
+5	StringTie	exon	110786300	110786435	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "2";
+5	StringTie	exon	110787084	110787241	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "3";
+5	StringTie	exon	110787574	110787692	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "4";
+5	StringTie	exon	110787773	110787945	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "5";
+5	StringTie	exon	110788110	110788300	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "6";
+5	StringTie	exon	110788729	110788872	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "7";
+5	StringTie	exon	110788948	110789535	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "8";
+5	StringTie	exon	110790212	110790480	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "9";
+5	StringTie	exon	110790850	110790936	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "10";
+5	StringTie	exon	110791052	110791197	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "11";
+5	StringTie	exon	110791601	110791726	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "12";
+5	StringTie	exon	110792102	110792191	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "13";
+5	StringTie	exon	110792397	110792457	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "14";
+5	StringTie	exon	110792966	110793113	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "15";
+5	StringTie	exon	110793815	110793903	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "16";
+5	StringTie	exon	110794193	110794243	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "17";
+5	StringTie	exon	110794585	110794667	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "18";
+5	StringTie	exon	110794747	110794805	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "19";
+5	StringTie	exon	110795732	110796066	.	-	.	transcript_id "STRG.22901.3"; gene_id "STRG.22901"; exon_number "20";
+5	StringTie	transcript	110786094	110810053	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; gene_name "Ulk1"; xloc "XLOC_009424"; ref_gene_id "ENSMUSG00000029512"; cmp_ref "ENSMUST00000200299"; class_code "="; tss_id "TSS22921"; p_id "P12161";
+5	StringTie	exon	110786094	110786227	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "1";
+5	StringTie	exon	110786300	110786435	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "2";
+5	StringTie	exon	110787084	110787241	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "3";
+5	StringTie	exon	110787574	110787692	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "4";
+5	StringTie	exon	110787773	110787945	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "5";
+5	StringTie	exon	110788110	110788300	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "6";
+5	StringTie	exon	110788729	110788872	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "7";
+5	StringTie	exon	110788948	110789057	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "8";
+5	StringTie	exon	110789342	110789535	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "9";
+5	StringTie	exon	110790212	110790480	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "10";
+5	StringTie	exon	110790850	110790954	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "11";
+5	StringTie	exon	110791052	110791197	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "12";
+5	StringTie	exon	110791601	110791726	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "13";
+5	StringTie	exon	110792102	110792191	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "14";
+5	StringTie	exon	110792397	110792457	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "15";
+5	StringTie	exon	110792966	110793113	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "16";
+5	StringTie	exon	110793815	110793903	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "17";
+5	StringTie	exon	110794193	110794243	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "18";
+5	StringTie	exon	110794585	110794667	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "19";
+5	StringTie	exon	110794747	110794805	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "20";
+5	StringTie	exon	110795732	110795833	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "21";
+5	StringTie	exon	110796156	110796229	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "22";
+5	StringTie	exon	110796327	110796500	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "23";
+5	StringTie	exon	110798882	110798918	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "24";
+5	StringTie	exon	110799124	110799156	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "25";
+5	StringTie	exon	110809005	110809046	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "26";
+5	StringTie	exon	110809127	110809219	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "27";
+5	StringTie	exon	110809614	110810053	.	-	.	transcript_id "STRG.22901.2"; gene_id "STRG.22901"; exon_number "28";
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+5	StringTie	exon	110788110	110788667	.	-	.	transcript_id "STRG.22901.7"; gene_id "STRG.22901"; exon_number "2";
+5	StringTie	transcript	110791398	110792192	.	-	.	transcript_id "STRG.22901.8"; gene_id "STRG.22901"; gene_name "Ulk1"; xloc "XLOC_009424"; ref_gene_id "ENSMUSG00000029512"; cmp_ref "ENSMUST00000200099"; class_code "="; tss_id "TSS22925";
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+5	StringTie	exon	110792102	110792192	.	-	.	transcript_id "STRG.22901.8"; gene_id "STRG.22901"; exon_number "2";
+5	StringTie	transcript	110791673	110793405	.	-	.	transcript_id "STRG.22901.6"; gene_id "STRG.22901"; gene_name "Ulk1"; xloc "XLOC_009424"; ref_gene_id "ENSMUSG00000029512"; cmp_ref "ENSMUST00000196883"; class_code "="; tss_id "TSS22926";
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+5	StringTie	exon	110792102	110792191	.	-	.	transcript_id "STRG.22901.6"; gene_id "STRG.22901"; exon_number "2";
+5	StringTie	exon	110792397	110792457	.	-	.	transcript_id "STRG.22901.6"; gene_id "STRG.22901"; exon_number "3";
+5	StringTie	exon	110792966	110793405	.	-	.	transcript_id "STRG.22901.6"; gene_id "STRG.22901"; exon_number "4";
+5	StringTie	transcript	110792545	110796066	.	-	.	transcript_id "STRG.22901.5"; gene_id "STRG.22901"; gene_name "Ulk1"; xloc "XLOC_009424"; cmp_ref "ENSMUST00000031490"; class_code "j"; tss_id "TSS22923";
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+5	StringTie	exon	110793815	110793903	.	-	.	transcript_id "STRG.22901.5"; gene_id "STRG.22901"; exon_number "2";
+5	StringTie	exon	110794193	110794243	.	-	.	transcript_id "STRG.22901.5"; gene_id "STRG.22901"; exon_number "3";
+5	StringTie	exon	110794585	110794805	.	-	.	transcript_id "STRG.22901.5"; gene_id "STRG.22901"; exon_number "4";
+5	StringTie	exon	110795732	110796066	.	-	.	transcript_id "STRG.22901.5"; gene_id "STRG.22901"; exon_number "5";
+5	StringTie	transcript	110793601	110795834	.	-	.	transcript_id "STRG.22901.4"; gene_id "STRG.22901"; gene_name "Ulk1"; xloc "XLOC_009424"; ref_gene_id "ENSMUSG00000029512"; cmp_ref "ENSMUST00000198470"; class_code "="; tss_id "TSS22927";
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+5	StringTie	exon	110794193	110794243	.	-	.	transcript_id "STRG.22901.4"; gene_id "STRG.22901"; exon_number "2";
+5	StringTie	exon	110794585	110794667	.	-	.	transcript_id "STRG.22901.4"; gene_id "STRG.22901"; exon_number "3";
+5	StringTie	exon	110794747	110794805	.	-	.	transcript_id "STRG.22901.4"; gene_id "STRG.22901"; exon_number "4";
+5	StringTie	exon	110795732	110795834	.	-	.	transcript_id "STRG.22901.4"; gene_id "STRG.22901"; exon_number "5";
+5	StringTie	transcript	110829070	110839777	.	-	.	transcript_id "STRG.22905.1"; gene_id "STRG.22905"; gene_name "Hscb"; xloc "XLOC_009425"; ref_gene_id "ENSMUSG00000043510"; cmp_ref "ENSMUST00000056937"; class_code "="; tss_id "TSS22928"; p_id "P12162";
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+5	StringTie	exon	110830936	110830983	.	-	.	transcript_id "STRG.22905.1"; gene_id "STRG.22905"; exon_number "2";
+5	StringTie	exon	110834655	110834799	.	-	.	transcript_id "STRG.22905.1"; gene_id "STRG.22905"; exon_number "3";
+5	StringTie	exon	110835980	110836069	.	-	.	transcript_id "STRG.22905.1"; gene_id "STRG.22905"; exon_number "4";
+5	StringTie	exon	110836307	110836403	.	-	.	transcript_id "STRG.22905.1"; gene_id "STRG.22905"; exon_number "5";
+5	StringTie	exon	110839496	110839777	.	-	.	transcript_id "STRG.22905.1"; gene_id "STRG.22905"; exon_number "6";
+5	StringTie	transcript	110829080	110836320	.	-	.	transcript_id "STRG.22905.3"; gene_id "STRG.22905"; gene_name "Hscb"; xloc "XLOC_009425"; ref_gene_id "ENSMUSG00000043510"; cmp_ref "ENSMUST00000144850"; class_code "="; tss_id "TSS22929"; p_id "P12163";
+5	StringTie	exon	110829080	110829211	.	-	.	transcript_id "STRG.22905.3"; gene_id "STRG.22905"; exon_number "1";
+5	StringTie	exon	110830936	110830983	.	-	.	transcript_id "STRG.22905.3"; gene_id "STRG.22905"; exon_number "2";
+5	StringTie	exon	110834655	110834799	.	-	.	transcript_id "STRG.22905.3"; gene_id "STRG.22905"; exon_number "3";
+5	StringTie	exon	110835975	110836069	.	-	.	transcript_id "STRG.22905.3"; gene_id "STRG.22905"; exon_number "4";
+5	StringTie	exon	110836307	110836320	.	-	.	transcript_id "STRG.22905.3"; gene_id "STRG.22905"; exon_number "5";
+5	StringTie	transcript	110829080	110839575	.	-	.	transcript_id "STRG.22905.2"; gene_id "STRG.22905"; gene_name "Hscb"; xloc "XLOC_009425"; ref_gene_id "ENSMUSG00000043510"; cmp_ref "ENSMUST00000145318"; class_code "="; tss_id "TSS22930"; p_id "P12164";
+5	StringTie	exon	110829080	110829211	.	-	.	transcript_id "STRG.22905.2"; gene_id "STRG.22905"; exon_number "1";
+5	StringTie	exon	110830936	110830983	.	-	.	transcript_id "STRG.22905.2"; gene_id "STRG.22905"; exon_number "2";
+5	StringTie	exon	110835975	110836069	.	-	.	transcript_id "STRG.22905.2"; gene_id "STRG.22905"; exon_number "3";
+5	StringTie	exon	110836307	110836403	.	-	.	transcript_id "STRG.22905.2"; gene_id "STRG.22905"; exon_number "4";
+5	StringTie	exon	110839496	110839575	.	-	.	transcript_id "STRG.22905.2"; gene_id "STRG.22905"; exon_number "5";
+5	StringTie	transcript	110829081	110834895	.	-	.	transcript_id "STRG.22905.4"; gene_id "STRG.22905"; gene_name "Hscb"; xloc "XLOC_009425"; ref_gene_id "ENSMUSG00000043510"; cmp_ref "ENSMUST00000122921"; class_code "="; tss_id "TSS22931";
+5	StringTie	exon	110829081	110829211	.	-	.	transcript_id "STRG.22905.4"; gene_id "STRG.22905"; exon_number "1";
+5	StringTie	exon	110830936	110830983	.	-	.	transcript_id "STRG.22905.4"; gene_id "STRG.22905"; exon_number "2";
+5	StringTie	exon	110834655	110834895	.	-	.	transcript_id "STRG.22905.4"; gene_id "STRG.22905"; exon_number "3";
+5	StringTie	transcript	112337392	112340022	.	-	.	transcript_id "STRG.22974.4"; gene_id "STRG.22974"; gene_name "Srrd"; xloc "XLOC_009426"; ref_gene_id "ENSMUSG00000029346"; cmp_ref "ENSMUST00000155756"; class_code "="; tss_id "TSS22932";
+5	StringTie	exon	112337392	112337741	.	-	.	transcript_id "STRG.22974.4"; gene_id "STRG.22974"; exon_number "1";
+5	StringTie	exon	112338002	112338047	.	-	.	transcript_id "STRG.22974.4"; gene_id "STRG.22974"; exon_number "2";
+5	StringTie	exon	112338318	112338567	.	-	.	transcript_id "STRG.22974.4"; gene_id "STRG.22974"; exon_number "3";
+5	StringTie	exon	112339719	112339817	.	-	.	transcript_id "STRG.22974.4"; gene_id "STRG.22974"; exon_number "4";
+5	StringTie	exon	112339897	112340022	.	-	.	transcript_id "STRG.22974.4"; gene_id "STRG.22974"; exon_number "5";
+5	StringTie	transcript	112337392	112343020	.	-	.	transcript_id "STRG.22974.2"; gene_id "STRG.22974"; gene_name "Srrd"; xloc "XLOC_009426"; ref_gene_id "ENSMUSG00000029346"; cmp_ref "ENSMUST00000146510"; class_code "="; tss_id "TSS22933"; p_id "P12165";
+5	StringTie	exon	112337392	112337741	.	-	.	transcript_id "STRG.22974.2"; gene_id "STRG.22974"; exon_number "1";
+5	StringTie	exon	112338002	112338047	.	-	.	transcript_id "STRG.22974.2"; gene_id "STRG.22974"; exon_number "2";
+5	StringTie	exon	112338318	112338472	.	-	.	transcript_id "STRG.22974.2"; gene_id "STRG.22974"; exon_number "3";
+5	StringTie	exon	112339719	112339817	.	-	.	transcript_id "STRG.22974.2"; gene_id "STRG.22974"; exon_number "4";
+5	StringTie	exon	112339897	112340123	.	-	.	transcript_id "STRG.22974.2"; gene_id "STRG.22974"; exon_number "5";
+5	StringTie	exon	112341096	112341136	.	-	.	transcript_id "STRG.22974.2"; gene_id "STRG.22974"; exon_number "6";
+5	StringTie	exon	112342875	112343020	.	-	.	transcript_id "STRG.22974.2"; gene_id "STRG.22974"; exon_number "7";
+5	StringTie	transcript	112337392	112343040	.	-	.	transcript_id "STRG.22974.1"; gene_id "STRG.22974"; gene_name "Srrd"; xloc "XLOC_009426"; ref_gene_id "ENSMUSG00000029346"; cmp_ref "ENSMUST00000031289"; class_code "="; tss_id "TSS22933"; p_id "P12166";
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+5	StringTie	exon	112337976	112338047	.	-	.	transcript_id "STRG.22974.1"; gene_id "STRG.22974"; exon_number "2";
+5	StringTie	exon	112338318	112338472	.	-	.	transcript_id "STRG.22974.1"; gene_id "STRG.22974"; exon_number "3";
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+5	StringTie	exon	112339897	112340123	.	-	.	transcript_id "STRG.22974.1"; gene_id "STRG.22974"; exon_number "5";
+5	StringTie	exon	112341096	112341136	.	-	.	transcript_id "STRG.22974.1"; gene_id "STRG.22974"; exon_number "6";
+5	StringTie	exon	112342875	112343040	.	-	.	transcript_id "STRG.22974.1"; gene_id "STRG.22974"; exon_number "7";
+5	StringTie	transcript	112337909	112339932	.	-	.	transcript_id "STRG.22974.5"; gene_id "STRG.22974"; gene_name "Srrd"; xloc "XLOC_009426"; ref_gene_id "ENSMUSG00000029346"; cmp_ref "ENSMUST00000125628"; class_code "="; tss_id "TSS22932";
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+5	StringTie	exon	112339719	112339817	.	-	.	transcript_id "STRG.22974.5"; gene_id "STRG.22974"; exon_number "2";
+5	StringTie	exon	112339897	112339932	.	-	.	transcript_id "STRG.22974.5"; gene_id "STRG.22974"; exon_number "3";
+5	StringTie	transcript	112337972	112343018	.	-	.	transcript_id "STRG.22974.3"; gene_id "STRG.22974"; gene_name "Srrd"; xloc "XLOC_009426"; ref_gene_id "ENSMUSG00000029346"; cmp_ref "ENSMUST00000156083"; class_code "="; tss_id "TSS22933";
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+5	StringTie	exon	112339719	112339817	.	-	.	transcript_id "STRG.22974.3"; gene_id "STRG.22974"; exon_number "3";
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+5	StringTie	transcript	112339719	112340219	.	-	.	transcript_id "STRG.22974.6"; gene_id "STRG.22974"; gene_name "Srrd"; xloc "XLOC_009426"; ref_gene_id "ENSMUSG00000029346"; cmp_ref "ENSMUST00000147940"; class_code "="; tss_id "TSS22934";
+5	StringTie	exon	112339719	112339817	.	-	.	transcript_id "STRG.22974.6"; gene_id "STRG.22974"; exon_number "1";
+5	StringTie	exon	112339897	112340219	.	-	.	transcript_id "STRG.22974.6"; gene_id "STRG.22974"; exon_number "2";
+5	StringTie	transcript	112419352	112425650	.	-	.	transcript_id "STRG.22982.1"; gene_id "STRG.22982"; gene_name "Sez6l"; xloc "XLOC_009427"; cmp_ref "ENSMUST00000075387"; class_code "c"; tss_id "TSS22935";
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+5	StringTie	exon	112424623	112424725	.	-	.	transcript_id "STRG.22982.1"; gene_id "STRG.22982"; exon_number "2";
+5	StringTie	exon	112425614	112425650	.	-	.	transcript_id "STRG.22982.1"; gene_id "STRG.22982"; exon_number "3";
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+5	StringTie	exon	112715381	112715518	.	-	.	transcript_id "STRG.22984.3"; gene_id "STRG.22984"; exon_number "3";
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+5	StringTie	exon	112757455	112757640	.	-	.	transcript_id "STRG.22984.3"; gene_id "STRG.22984"; exon_number "6";
+5	StringTie	exon	112760316	112760453	.	-	.	transcript_id "STRG.22984.3"; gene_id "STRG.22984"; exon_number "7";
+5	StringTie	exon	112761324	112761407	.	-	.	transcript_id "STRG.22984.3"; gene_id "STRG.22984"; exon_number "8";
+5	StringTie	exon	112762657	112762773	.	-	.	transcript_id "STRG.22984.3"; gene_id "STRG.22984"; exon_number "9";
+5	StringTie	exon	112764448	112764561	.	-	.	transcript_id "STRG.22984.3"; gene_id "STRG.22984"; exon_number "10";
+5	StringTie	exon	112765835	112765931	.	-	.	transcript_id "STRG.22984.3"; gene_id "STRG.22984"; exon_number "11";
+5	StringTie	transcript	112688918	112871586	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; gene_name "Myo18b"; xloc "XLOC_009428"; cmp_ref "ENSMUST00000086617"; class_code "c"; tss_id "TSS22937";
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+5	StringTie	exon	112715381	112715518	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "3";
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+5	StringTie	exon	112757455	112757640	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "6";
+5	StringTie	exon	112760316	112760453	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "7";
+5	StringTie	exon	112761324	112761407	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "8";
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+5	StringTie	exon	112775253	112775405	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "11";
+5	StringTie	exon	112782585	112782689	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "12";
+5	StringTie	exon	112785557	112785667	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "13";
+5	StringTie	exon	112789990	112790190	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "14";
+5	StringTie	exon	112791077	112791200	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "15";
+5	StringTie	exon	112795395	112795549	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "16";
+5	StringTie	exon	112798817	112798941	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "17";
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+5	StringTie	exon	112803189	112803308	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "19";
+5	StringTie	exon	112809662	112809751	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "20";
+5	StringTie	exon	112811586	112811729	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "21";
+5	StringTie	exon	112811986	112812114	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "22";
+5	StringTie	exon	112817630	112817695	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "23";
+5	StringTie	exon	112827977	112828086	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "24";
+5	StringTie	exon	112830160	112830379	.	-	.	transcript_id "STRG.22984.1"; gene_id "STRG.22984"; exon_number "25";
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+5	StringTie	exon	112925245	112925798	.	-	.	transcript_id "STRG.22985.5"; gene_id "STRG.22985"; exon_number "3";
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+12	StringTie	exon	69209312	69209994	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "8";
+12	StringTie	exon	69211373	69211445	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "9";
+12	StringTie	exon	69212223	69212271	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "10";
+12	StringTie	exon	69212987	69213043	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "11";
+12	StringTie	exon	69213829	69213912	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "12";
+12	StringTie	exon	69215311	69215385	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "13";
+12	StringTie	exon	69221977	69222070	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "14";
+12	StringTie	exon	69222399	69222476	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "15";
+12	StringTie	exon	69223104	69223179	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "16";
+12	StringTie	exon	69226338	69226438	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "17";
+12	StringTie	exon	69228097	69228169	.	-	.	transcript_id "STRG.52021.2"; gene_id "STRG.52021"; exon_number "18";
+12	StringTie	transcript	69201779	69228190	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; gene_name "Pole2"; xloc "XLOC_002837"; ref_gene_id "ENSMUSG00000020974"; cmp_ref "ENSMUST00000021359"; class_code "="; tss_id "TSS6896"; p_id "P3723";
+12	StringTie	exon	69201779	69201882	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "1";
+12	StringTie	exon	69202907	69202974	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "2";
+12	StringTie	exon	69204091	69204267	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "3";
+12	StringTie	exon	69206410	69206518	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "4";
+12	StringTie	exon	69207859	69207936	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "5";
+12	StringTie	exon	69208021	69208080	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "6";
+12	StringTie	exon	69208917	69208971	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "7";
+12	StringTie	exon	69209312	69209401	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "8";
+12	StringTie	exon	69209822	69209994	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "9";
+12	StringTie	exon	69211373	69211445	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "10";
+12	StringTie	exon	69212223	69212271	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "11";
+12	StringTie	exon	69212987	69213043	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "12";
+12	StringTie	exon	69213829	69213912	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "13";
+12	StringTie	exon	69215311	69215385	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "14";
+12	StringTie	exon	69221977	69222070	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "15";
+12	StringTie	exon	69222399	69222476	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "16";
+12	StringTie	exon	69223104	69223179	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "17";
+12	StringTie	exon	69226338	69226438	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "18";
+12	StringTie	exon	69228097	69228190	.	-	.	transcript_id "STRG.52021.1"; gene_id "STRG.52021"; exon_number "19";
diff -r 000000000000 -r 7e572e148175 test-data/gffcompare_output.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gffcompare_output.bed	Thu Jan 11 11:16:51 2018 -0500
@@ -0,0 +1,124 @@
+1	43776566	43778980	STRG.1163.2_i	0	-	43776566	43778980	100,100,100	3	1094,244,100	0,1948,2314
+1	43776566	43778980	STRG.1163.1_i	0	-	43776566	43778980	100,100,100	3	1155,122,100	0,1887,2314
+1	45331686	45332998	STRG.1209.1_c	0	+	45331686	45332998	100,100,100	4	90,54,108,34	0,286,448,1278
+1	6453836	6460700	STRG.88.1_u	0	+	6453836	6460700	100,100,100	2	50,156	0,6708
+1	86703818	87050095	STRG.2299.1	0	+	86703818	87050095	100,100,100	22	53,148,158,54,102,42,229,101,248,174,80,113,108,234,80,184,87,148,131,105,102,473	0,40862,41522,50408,56469,87597,117403,150541,153308,174584,226935,255924,269581,286273,317219,340198,341011,343218,343629,343869,345014,345804
+1	86703827	86882439	STRG.2299.5	0	+	86703827	86882439	100,100,100	11	44,148,158,54,102,42,78,229,101,248,4037	0,40853,41513,50399,56460,87588,108684,117394,150532,153299,174575
+1	86703827	87049195	STRG.2299.3	0	+	86703827	87049195	100,100,100	21	44,148,158,54,102,78,229,101,248,174,80,113,108,234,80,184,87,148,131,105,363	0,40853,41513,50399,56460,108684,117394,150532,153299,174575,226926,255915,269572,286264,317210,340189,341002,343209,343620,343860,345005
+1	86703842	87050092	STRG.2299.4_j	0	+	86703842	87050092	100,100,100	21	29,148,158,54,102,78,229,101,248,174,80,113,234,80,184,87,148,131,105,102,470	0,40838,41498,50384,56445,108669,117379,150517,153284,174560,226911,255900,286249,317195,340174,340987,343194,343605,343845,344990,345780
+1	86703842	87050092	STRG.2299.2	0	+	86703842	87050092	100,100,100	21	29,148,158,54,102,229,101,248,174,80,113,108,234,80,184,87,148,131,105,102,470	0,40838,41498,50384,56445,117379,150517,153284,174560,226911,255900,269557,286249,317195,340174,340987,343194,343605,343845,344990,345780
+1	86754158	86767638	STRG.2299.6_j	0	+	86754158	86767638	100,100,100	3	122,102,509	0,6129,12971
+1	9941958	9944118	STRG.229.1	0	-	9941958	9944118	100,100,100	4	197,69,108,99	0,364,651,2061
+1	9942022	9943223	STRG.229.5	0	-	9942022	9943223	100,100,100	3	133,69,614	0,300,587
+1	9942024	9942897	STRG.229.7	0	-	9942024	9942897	100,100,100	2	367,288	0,585
+1	9942024	9944103	STRG.229.6_j	0	-	9942024	9944103	100,100,100	3	131,395,84	0,298,1995
+1	9942024	9944103	STRG.229.4	0	-	9942024	9944103	100,100,100	3	367,108,84	0,585,1995
+1	9942024	9944103	STRG.229.3_j	0	-	9942024	9944103	100,100,100	4	131,62,108,84	0,298,585,1995
+1	9942024	9944117	STRG.229.2	0	-	9942024	9944117	100,100,100	4	125,69,108,98	0,298,585,1995
+1	86908792	86909683	STRG.2297.1_i	0	-	86908792	86909683	100,100,100	2	319,285	0,606
+1	193145390	193173087	STRG.5202.1_j	0	+	193145390	193173087	100,100,100	8	42,177,205,129,159,393,119,3806	0,11825,16222,17211,20375,22048,23126,23891
+1	193156668	193164181	STRG.5202.2	0	+	193156668	193164181	100,100,100	3	724,205,1580	0,4944,5933
+1	193167974	193173087	STRG.5202.3_j	0	+	193167974	193173087	100,100,100	3	157,119,3806	0,542,1307
+1	193168502	193169489	STRG.5202.4	0	+	193168502	193169489	100,100,100	2	133,208	0,779
+2	119749138	119749844	STRG.8811.1_j	0	+	119749138	119749844	100,100,100	3	148,217,172	0,223,534
+2	119972463	120018974	STRG.8821.1_j	0	+	119972463	120018974	100,100,100	19	17,223,92,63,58,171,138,183,161,190,147,176,92,126,71,122,76,112,53	0,482,26018,38279,38538,39469,40129,40448,41155,42159,42879,43229,44316,44676,45117,45292,45835,46024,46458
+2	120011686	120013094	STRG.8821.3	0	+	120011686	120013094	100,100,100	3	417,138,183	0,906,1225
+2	120013042	120015605	STRG.8821.2	0	+	120013042	120015605	100,100,100	4	52,161,190,263	0,576,1580,2300
+2	121008402	121016904	STRG.8871.1	0	+	121008402	121016904	100,100,100	11	207,60,80,82,97,74,77,278,61,47,506	0,315,640,1424,3031,3280,3950,4296,5555,7728,7996
+2	121008431	121015120	STRG.8871.3	0	+	121008431	121015120	100,100,100	10	178,60,80,82,97,74,77,278,61,608	0,286,611,1395,3002,3251,3921,4267,5526,6081
+2	121008447	121016904	STRG.8871.2	0	+	121008447	121016904	100,100,100	10	330,80,82,97,74,77,278,61,47,506	0,595,1379,2986,3235,3905,4251,5510,7683,7951
+2	121008466	121011756	STRG.8871.5_j	0	+	121008466	121011756	100,100,100	4	311,80,1704,74	0,576,1360,3216
+2	121008466	121012948	STRG.8871.4	0	+	121008466	121012948	100,100,100	8	143,60,80,82,125,74,77,250	0,251,576,1360,2967,3216,3886,4232
+2	121008703	121010577	STRG.8871.6	0	+	121008703	121010577	100,100,100	3	74,80,751	0,339,1123
+2	121011054	121011756	STRG.8871.7	0	+	121011054	121011756	100,100,100	2	476,74	0,628
+2	120089174	120154606	STRG.8831.1	0	-	120089174	120154606	100,100,100	6	2510,165,413,98,177,367	0,7788,12845,38417,47724,65065
+2	121194837	121221232	STRG.8881.3_j	0	-	121194837	121221232	100,100,100	12	3770,146,200,95,2006,192,431,150,272,153,505,75	0,4138,4769,5465,7705,10082,12861,13517,14243,16432,20829,26320
+2	121199638	121204981	STRG.8881.7	0	-	121199638	121204981	100,100,100	5	168,95,210,216,62	0,664,2904,4694,5281
+2	121199638	121221232	STRG.8881.4_c	0	-	121199638	121221232	100,100,100	11	168,95,216,216,192,431,150,272,153,505,75	0,664,2904,4694,5281,8060,8716,9442,11631,16028,21519
+2	121205080	121208574	STRG.8881.11	0	-	121205080	121208574	100,100,100	3	31,431,220	0,2618,3274
+2	121208844	121221232	STRG.8881.9	0	-	121208844	121221232	100,100,100	4	508,153,505,75	0,2425,6822,12313
+2	121215888	121221379	STRG.8881.14	0	-	121215888	121221379	100,100,100	2	283,222	0,5269
+2	121216142	121247714	STRG.8881.5_j	0	-	121216142	121247714	100,100,100	7	29,93,58,1063,1297,203,214	0,5015,7562,11502,19430,27751,31358
+2	121216142	121270286	STRG.8881.2_c	0	-	121216142	121270286	100,100,100	15	29,93,58,204,120,1297,203,95,127,167,130,159,125,85,68	0,5015,7562,11502,12445,19430,27751,31358,32021,35725,37459,40379,43001,53761,54076
+2	121216142	121271321	STRG.8881.1	0	-	121216142	121271321	100,100,100	16	29,93,58,204,1297,203,95,127,167,130,159,125,85,91,185,50	0,5015,7562,11502,19430,27751,31358,32021,35725,37459,40379,43001,53761,54076,54381,55129
+2	121228368	121235689	STRG.8881.13	0	-	121228368	121235689	100,100,100	2	339,117	0,7204
+2	121256513	121271369	STRG.8881.6	0	-	121256513	121271369	100,100,100	6	167,125,85,91,185,98	0,2630,13390,13705,14010,14758
+2	121258885	121270286	STRG.8881.10	0	-	121258885	121270286	100,100,100	3	383,85,68	0,11018,11333
+2	121267311	121271361	STRG.8881.8	0	-	121267311	121271361	100,100,100	4	2677,91,185,90	0,2907,3212,3960
+2	121269629	121271370	STRG.8881.12	0	-	121269629	121271370	100,100,100	3	359,185,99	0,894,1642
+3	57736061	57835231	STRG.12098.3	0	+	57736061	57835231	100,100,100	10	139,126,81,126,88,91,106,94,81,1746	0,28195,32978,43321,60136,66385,70960,84445,96902,97424
+3	57736081	57833888	STRG.12098.6	0	+	57736081	57833888	100,100,100	2	119,316	0,97491
+3	57736081	57835233	STRG.12098.2	0	+	57736081	57835233	100,100,100	10	119,126,81,126,88,91,106,94,81,1661	0,28175,32958,43301,60116,66365,70940,84425,96882,97491
+3	57736112	57835119	STRG.12098.1	0	+	57736112	57835119	100,100,100	10	88,126,81,126,88,820,106,94,81,1634	0,28144,32927,43270,60085,65605,70909,84394,96851,97373
+3	57736119	57820993	STRG.12098.5_j	0	+	57736119	57820993	100,100,100	9	81,144,126,81,126,88,91,106,487	0,11771,28137,32920,43263,60078,66327,70902,84387
+3	57736119	57833232	STRG.12098.4	0	+	57736119	57833232	100,100,100	9	81,126,81,126,88,91,106,94,269	0,28137,32920,43263,60078,66327,70902,84387,96844
+3	57644348	57651715	STRG.12092.1	0	-	57644348	57651715	100,100,100	5	2528,174,83,78,129	0,5693,6342,7073,7238
+3	57651101	57651715	STRG.12092.2	0	-	57651101	57651715	100,100,100	2	398,129	0,485
+5	110839982	110874133	STRG.22906.2	0	+	110839982	110874133	100,100,100	14	66,338,125,148,109,54,62,100,87,164,116,86,81,654	0,1223,8406,8647,15742,18391,20880,23275,25539,26280,26955,28025,32044,33497
+5	110839999	110874145	STRG.22906.1	0	+	110839999	110874145	100,100,100	15	49,338,125,148,91,109,54,62,100,87,164,116,86,81,666	0,1206,8389,8630,9596,15725,18374,20863,23258,25522,26263,26938,28008,32027,33480
+5	110840253	110874013	STRG.22906.3_j	0	+	110840253	110874013	100,100,100	13	1290,125,148,91,109,54,62,100,87,164,116,86,1987	0,8135,8376,9342,15471,18120,20609,23004,25268,26009,26684,27754,31773
+5	110855689	110868215	STRG.22906.4_j	0	+	110855689	110868215	100,100,100	6	144,54,62,100,87,208	0,2684,5173,7568,9832,12318
+5	110866270	110866720	STRG.22906.5	0	+	110866270	110866720	100,100,100	2	156,185	0,265
+5	110892838	111085034	STRG.22909.1_c	0	+	110892838	111085034	100,100,100	2	272,13	0,192183
+5	111100697	111102068	STRG.22913.1_c	0	+	111100697	111102068	100,100,100	2	269,99	0,1272
+5	111225457	111229415	STRG.22916.1	0	+	111225457	111229415	100,100,100	2	624,68	0,3890
+5	111231100	111235600	STRG.22917.1_c	0	+	111231100	111235600	100,100,100	3	79,219,125	0,2145,4375
+5	111330762	111388359	STRG.22924.1	0	+	111330762	111388359	100,100,100	12	71,31,146,92,8,75,84,78,111,123,85,1857	0,4732,7520,15720,16357,17018,18728,40549,49429,52225,54757,55740
+5	111330806	111388359	STRG.22924.2	0	+	111330806	111388359	100,100,100	11	27,31,146,92,8,75,84,78,111,123,1857	0,4688,7476,15676,16313,16974,18684,40505,49385,52181,55696
+5	111380168	111383703	STRG.22924.3	0	+	111380168	111383703	100,100,100	2	134,716	0,2819
+5	111417441	111454864	STRG.22929.1_j	0	+	111417441	111454864	100,100,100	3	320,2274,249	0,2168,37174
+5	111417441	111457033	STRG.22929.2	0	+	111417441	111457033	100,100,100	2	4442,2418	0,37174
+5	111546620	111566751	STRG.22958.1_u	0	+	111546620	111566751	100,100,100	4	167,77,2000,786	0,7231,15766,19345
+5	111553369	111564411	STRG.22958.2_u	0	+	111553369	111564411	100,100,100	3	559,1223,249	0,9017,10793
+5	111553369	111567041	STRG.22958.3_u	0	+	111553369	111567041	100,100,100	3	559,2000,2005	0,9017,11667
+5	111581567	111582873	STRG.22963.1	0	+	111581567	111582873	100,100,100	2	303,453	0,853
+5	112276690	112315361	STRG.22971.1	0	+	112276690	112315361	100,100,100	7	81,72,912,199,51,49,471	0,27209,30875,32998,34993,36551,38200
+5	112276703	112309032	STRG.22971.3	0	+	112276703	112309032	100,100,100	3	68,72,1467	0,27196,30862
+5	112276706	112315355	STRG.22971.2	0	+	112276706	112315355	100,100,100	6	65,912,199,51,49,465	0,30859,32982,34977,36535,38184
+5	112308290	112309812	STRG.22971.5	0	+	112308290	112309812	100,100,100	2	264,124	0,1398
+5	112312893	112314964	STRG.22971.4	0	+	112312893	112314964	100,100,100	2	397,74	0,1997
+5	112326357	112338073	STRG.22973.1	0	+	112326357	112338073	100,100,100	14	116,186,221,154,157,128,153,528,107,169,244,143,166,1088	0,1127,1604,3008,3389,4733,5510,6606,7217,7959,8502,9215,9657,10628
+5	112335641	112337273	STRG.22973.2	0	+	112335641	112337273	100,100,100	2	539,288	0,1344
+5	112343082	112378414	STRG.22978.2	0	+	112343082	112378414	100,100,100	14	81,1005,91,144,108,117,95,73,37,97,799,133,109,456	0,961,3511,6202,20026,20463,21438,23816,25853,26372,26863,31797,32270,34876
+5	112343092	112344747	STRG.22978.3	0	+	112343092	112344747	100,100,100	2	30,704	0,951
+5	112343094	112378414	STRG.22978.1	0	+	112343094	112378414	100,100,100	14	69,508,91,144,108,117,95,73,37,97,799,133,109,456	0,1446,3499,6190,20014,20451,21426,23804,25841,26360,26851,31785,32258,34864
+5	112343098	112344747	STRG.22978.6_c	0	+	112343098	112344747	100,100,100	2	24,207	0,1442
+5	112368744	112369774	STRG.22978.5	0	+	112368744	112369774	100,100,100	2	228,320	0,710
+5	112375334	112378401	STRG.22978.4	0	+	112375334	112378401	100,100,100	2	127,443	0,2624
+5	112793299	112795691	STRG.22983.1	0	+	112793299	112795691	100,100,100	2	312,277	0,2115
+5	110784487	110810097	STRG.22901.1	0	-	110784487	110810097	100,100,100	28	1740,136,158,119,173,191,144,110,194,269,87,146,126,90,61,148,89,51,83,59,102,74,174,37,33,42,93,484	0,1812,2596,3086,3285,3622,4241,4460,4854,5724,6362,6564,7113,7614,7909,8478,9327,9705,10097,10259,11244,11668,11839,14394,14636,24517,24639,25126
+5	110786038	110787221	STRG.22901.9	0	-	110786038	110787221	100,100,100	2	397,138	0,1045
+5	110786093	110796066	STRG.22901.3_j	0	-	110786093	110796066	100,100,100	20	134,136,158,119,173,191,144,588,269,87,146,126,90,61,148,89,51,83,59,335	0,206,990,1480,1679,2016,2635,2854,4118,4756,4958,5507,6008,6303,6872,7721,8099,8491,8653,9638
+5	110786093	110810053	STRG.22901.2	0	-	110786093	110810053	100,100,100	28	134,136,158,119,173,191,144,110,194,269,105,146,126,90,61,148,89,51,83,59,102,74,174,37,33,42,93,440	0,206,990,1480,1679,2016,2635,2854,3248,4118,4756,4958,5507,6008,6303,6872,7721,8099,8491,8653,9638,10062,10233,12788,13030,22911,23033,23520
+5	110787890	110788667	STRG.22901.7	0	-	110787890	110788667	100,100,100	2	55,558	0,219
+5	110791397	110792192	STRG.22901.8	0	-	110791397	110792192	100,100,100	2	329,91	0,704
+5	110791672	110793405	STRG.22901.6	0	-	110791672	110793405	100,100,100	4	54,90,61,440	0,429,724,1293
+5	110792544	110796066	STRG.22901.5_j	0	-	110792544	110796066	100,100,100	5	569,89,51,221,335	0,1270,1648,2040,3187
+5	110793600	110795834	STRG.22901.4	0	-	110793600	110795834	100,100,100	5	303,51,83,59,103	0,592,984,1146,2131
+5	110829069	110839777	STRG.22905.1	0	-	110829069	110839777	100,100,100	6	142,48,145,90,97,282	0,1866,5585,6910,7237,10426
+5	110829079	110836320	STRG.22905.3	0	-	110829079	110836320	100,100,100	5	132,48,145,95,14	0,1856,5575,6895,7227
+5	110829079	110839575	STRG.22905.2	0	-	110829079	110839575	100,100,100	5	132,48,95,97,80	0,1856,6895,7227,10416
+5	110829080	110834895	STRG.22905.4	0	-	110829080	110834895	100,100,100	3	131,48,241	0,1855,5574
+5	112337391	112340022	STRG.22974.4	0	-	112337391	112340022	100,100,100	5	350,46,250,99,126	0,610,926,2327,2505
+5	112337391	112343020	STRG.22974.2	0	-	112337391	112343020	100,100,100	7	350,46,155,99,227,41,146	0,610,926,2327,2505,3704,5483
+5	112337391	112343040	STRG.22974.1	0	-	112337391	112343040	100,100,100	7	350,72,155,99,227,41,166	0,584,926,2327,2505,3704,5483
+5	112337908	112339932	STRG.22974.5	0	-	112337908	112339932	100,100,100	3	564,99,36	0,1810,1988
+5	112337971	112343018	STRG.22974.3	0	-	112337971	112343018	100,100,100	6	76,250,99,227,41,144	0,346,1747,1925,3124,4903
+5	112339718	112340219	STRG.22974.6	0	-	112339718	112340219	100,100,100	2	99,323	0,178
+5	112419351	112425650	STRG.22982.1_c	0	-	112419351	112425650	100,100,100	3	2687,103,37	0,5271,6262
+5	112688877	112765931	STRG.22984.3	0	-	112688877	112765931	100,100,100	11	220,1240,138,45,131,186,138,84,117,114,97	0,3218,26503,28109,34929,68577,71438,72446,73779,75570,76957
+5	112688917	112871586	STRG.22984.1_c	0	-	112688917	112871586	100,100,100	38	180,1240,138,45,131,186,138,84,117,114,153,105,111,201,124,155,125,109,120,90,144,129,66,110,220,184,160,151,81,193,91,174,145,64,101,143,199,166	0,3178,26463,28069,34889,68537,71398,72406,73739,75530,86335,93667,96639,101072,102159,106477,109899,113448,114271,120744,122668,123068,128712,139059,141242,142153,145457,148833,150699,151702,154286,157353,169484,176322,176739,177426,179276,182503
+5	112772885	112871586	STRG.22984.2	0	-	112772885	112871586	100,100,100	29	1641,388,105,111,201,124,155,125,109,120,90,144,129,66,110,220,184,160,151,81,193,91,174,145,64,101,143,199,166	0,2132,9699,12671,17104,18191,22509,25931,29480,30303,36776,38700,39100,44744,55091,57274,58185,61489,64865,66731,67734,70318,73385,85516,92354,92771,93458,95308,98535
+5	112871741	112874253	STRG.22984.5_j	0	-	112871741	112874253	100,100,100	3	755,67,361	0,1753,2151
+5	112875222	112896379	STRG.22984.4_j	0	-	112875222	112896379	100,100,100	3	104,159,124	0,2762,21033
+5	112879419	112896379	STRG.22984.6_c	0	-	112879419	112896379	100,100,100	2	159,124	0,16836
+5	112910481	113015514	STRG.22985.1	0	-	112910481	113015514	100,100,100	21	4593,114,137,163,96,67,101,67,108,95,131,79,100,92,52,62,75,102,74,77,148	0,5568,8344,9526,13467,14914,18174,19191,27227,31151,34436,36105,43344,44682,46833,51105,56430,58686,63025,75283,104885
+5	112912598	113015514	STRG.22985.2	0	-	112912598	113015514	100,100,100	21	2476,114,137,163,96,67,101,67,108,95,131,79,100,92,52,62,75,141,74,77,148	0,3451,6227,7409,11350,12797,16057,17074,25110,29034,32319,33988,41227,42565,44716,48988,54313,56569,60908,73166,102768
+5	112916109	112924375	STRG.22985.4	0	-	112916109	112924375	100,100,100	4	54,137,163,427	0,2716,3898,7839
+5	112920061	112925798	STRG.22985.5	0	-	112920061	112925798	100,100,100	3	109,96,554	0,3887,5183
+5	112960543	113015503	STRG.22985.3	0	-	112960543	113015503	100,100,100	6	1105,75,102,74,77,137	0,6368,8624,12963,25221,54823
+5	113086322	113163351	STRG.22991.1	0	-	113086322	113163351	100,100,100	8	4702,83,143,119,175,241,119,294	0,6092,6779,7643,9267,11275,15136,76735
+5	113184127	113192079	STRG.22997.1_u	0	-	113184127	113192079	100,100,100	3	590,88,1476	0,4158,6476
+12	69229664	69231901	STRG.52020.2_u	0	+	69229664	69231901	100,100,100	2	62,203	0,2034
+12	69199878	69228169	STRG.52021.2_j	0	-	69199878	69228169	100,100,100	18	2004,68,177,109,78,60,55,683,73,49,57,84,75,94,78,76,101,73	0,3028,4212,6531,7980,8142,9038,9433,11494,12344,13108,13950,15432,22098,22520,23225,26459,28218
+12	69201778	69228190	STRG.52021.1	0	-	69201778	69228190	100,100,100	19	104,68,177,109,78,60,55,90,173,73,49,57,84,75,94,78,76,101,94	0,1128,2312,4631,6080,6242,7138,7533,8043,9594,10444,11208,12050,13532,20198,20620,21325,24559,26318
diff -r 000000000000 -r 7e572e148175 test-data/gffcompare_output_j.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gffcompare_output_j.bed	Thu Jan 11 11:16:51 2018 -0500
@@ -0,0 +1,20 @@
+1	86703842	87050092	STRG.2299.4_j	0	+	86703842	87050092	100,100,100	21	29,148,158,54,102,78,229,101,248,174,80,113,234,80,184,87,148,131,105,102,470	0,40838,41498,50384,56445,108669,117379,150517,153284,174560,226911,255900,286249,317195,340174,340987,343194,343605,343845,344990,345780
+1	86754158	86767638	STRG.2299.6_j	0	+	86754158	86767638	100,100,100	3	122,102,509	0,6129,12971
+1	9942024	9944103	STRG.229.6_j	0	-	9942024	9944103	100,100,100	3	131,395,84	0,298,1995
+1	9942024	9944103	STRG.229.3_j	0	-	9942024	9944103	100,100,100	4	131,62,108,84	0,298,585,1995
+1	193145390	193173087	STRG.5202.1_j	0	+	193145390	193173087	100,100,100	8	42,177,205,129,159,393,119,3806	0,11825,16222,17211,20375,22048,23126,23891
+1	193167974	193173087	STRG.5202.3_j	0	+	193167974	193173087	100,100,100	3	157,119,3806	0,542,1307
+2	119749138	119749844	STRG.8811.1_j	0	+	119749138	119749844	100,100,100	3	148,217,172	0,223,534
+2	119972463	120018974	STRG.8821.1_j	0	+	119972463	120018974	100,100,100	19	17,223,92,63,58,171,138,183,161,190,147,176,92,126,71,122,76,112,53	0,482,26018,38279,38538,39469,40129,40448,41155,42159,42879,43229,44316,44676,45117,45292,45835,46024,46458
+2	121008466	121011756	STRG.8871.5_j	0	+	121008466	121011756	100,100,100	4	311,80,1704,74	0,576,1360,3216
+2	121194837	121221232	STRG.8881.3_j	0	-	121194837	121221232	100,100,100	12	3770,146,200,95,2006,192,431,150,272,153,505,75	0,4138,4769,5465,7705,10082,12861,13517,14243,16432,20829,26320
+2	121216142	121247714	STRG.8881.5_j	0	-	121216142	121247714	100,100,100	7	29,93,58,1063,1297,203,214	0,5015,7562,11502,19430,27751,31358
+3	57736119	57820993	STRG.12098.5_j	0	+	57736119	57820993	100,100,100	9	81,144,126,81,126,88,91,106,487	0,11771,28137,32920,43263,60078,66327,70902,84387
+5	110840253	110874013	STRG.22906.3_j	0	+	110840253	110874013	100,100,100	13	1290,125,148,91,109,54,62,100,87,164,116,86,1987	0,8135,8376,9342,15471,18120,20609,23004,25268,26009,26684,27754,31773
+5	110855689	110868215	STRG.22906.4_j	0	+	110855689	110868215	100,100,100	6	144,54,62,100,87,208	0,2684,5173,7568,9832,12318
+5	111417441	111454864	STRG.22929.1_j	0	+	111417441	111454864	100,100,100	3	320,2274,249	0,2168,37174
+5	110786093	110796066	STRG.22901.3_j	0	-	110786093	110796066	100,100,100	20	134,136,158,119,173,191,144,588,269,87,146,126,90,61,148,89,51,83,59,335	0,206,990,1480,1679,2016,2635,2854,4118,4756,4958,5507,6008,6303,6872,7721,8099,8491,8653,9638
+5	110792544	110796066	STRG.22901.5_j	0	-	110792544	110796066	100,100,100	5	569,89,51,221,335	0,1270,1648,2040,3187
+5	112871741	112874253	STRG.22984.5_j	0	-	112871741	112874253	100,100,100	3	755,67,361	0,1753,2151
+5	112875222	112896379	STRG.22984.4_j	0	-	112875222	112896379	100,100,100	3	104,159,124	0,2762,21033
+12	69199878	69228169	STRG.52021.2_j	0	-	69199878	69228169	100,100,100	18	2004,68,177,109,78,60,55,683,73,49,57,84,75,94,78,76,101,73	0,3028,4212,6531,7980,8142,9038,9433,11494,12344,13108,13950,15432,22098,22520,23225,26459,28218
diff -r 000000000000 -r 7e572e148175 test-data/gffcompare_output_jeipux.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gffcompare_output_jeipux.bed	Thu Jan 11 11:16:51 2018 -0500
@@ -0,0 +1,29 @@
+1	43776566	43778980	STRG.1163.2_i	0	-	43776566	43778980	100,100,100	3	1094,244,100	0,1948,2314
+1	43776566	43778980	STRG.1163.1_i	0	-	43776566	43778980	100,100,100	3	1155,122,100	0,1887,2314
+1	6453836	6460700	STRG.88.1_u	0	+	6453836	6460700	100,100,100	2	50,156	0,6708
+1	86703842	87050092	STRG.2299.4_j	0	+	86703842	87050092	100,100,100	21	29,148,158,54,102,78,229,101,248,174,80,113,234,80,184,87,148,131,105,102,470	0,40838,41498,50384,56445,108669,117379,150517,153284,174560,226911,255900,286249,317195,340174,340987,343194,343605,343845,344990,345780
+1	86754158	86767638	STRG.2299.6_j	0	+	86754158	86767638	100,100,100	3	122,102,509	0,6129,12971
+1	9942024	9944103	STRG.229.6_j	0	-	9942024	9944103	100,100,100	3	131,395,84	0,298,1995
+1	9942024	9944103	STRG.229.3_j	0	-	9942024	9944103	100,100,100	4	131,62,108,84	0,298,585,1995
+1	86908792	86909683	STRG.2297.1_i	0	-	86908792	86909683	100,100,100	2	319,285	0,606
+1	193145390	193173087	STRG.5202.1_j	0	+	193145390	193173087	100,100,100	8	42,177,205,129,159,393,119,3806	0,11825,16222,17211,20375,22048,23126,23891
+1	193167974	193173087	STRG.5202.3_j	0	+	193167974	193173087	100,100,100	3	157,119,3806	0,542,1307
+2	119749138	119749844	STRG.8811.1_j	0	+	119749138	119749844	100,100,100	3	148,217,172	0,223,534
+2	119972463	120018974	STRG.8821.1_j	0	+	119972463	120018974	100,100,100	19	17,223,92,63,58,171,138,183,161,190,147,176,92,126,71,122,76,112,53	0,482,26018,38279,38538,39469,40129,40448,41155,42159,42879,43229,44316,44676,45117,45292,45835,46024,46458
+2	121008466	121011756	STRG.8871.5_j	0	+	121008466	121011756	100,100,100	4	311,80,1704,74	0,576,1360,3216
+2	121194837	121221232	STRG.8881.3_j	0	-	121194837	121221232	100,100,100	12	3770,146,200,95,2006,192,431,150,272,153,505,75	0,4138,4769,5465,7705,10082,12861,13517,14243,16432,20829,26320
+2	121216142	121247714	STRG.8881.5_j	0	-	121216142	121247714	100,100,100	7	29,93,58,1063,1297,203,214	0,5015,7562,11502,19430,27751,31358
+3	57736119	57820993	STRG.12098.5_j	0	+	57736119	57820993	100,100,100	9	81,144,126,81,126,88,91,106,487	0,11771,28137,32920,43263,60078,66327,70902,84387
+5	110840253	110874013	STRG.22906.3_j	0	+	110840253	110874013	100,100,100	13	1290,125,148,91,109,54,62,100,87,164,116,86,1987	0,8135,8376,9342,15471,18120,20609,23004,25268,26009,26684,27754,31773
+5	110855689	110868215	STRG.22906.4_j	0	+	110855689	110868215	100,100,100	6	144,54,62,100,87,208	0,2684,5173,7568,9832,12318
+5	111417441	111454864	STRG.22929.1_j	0	+	111417441	111454864	100,100,100	3	320,2274,249	0,2168,37174
+5	111546620	111566751	STRG.22958.1_u	0	+	111546620	111566751	100,100,100	4	167,77,2000,786	0,7231,15766,19345
+5	111553369	111564411	STRG.22958.2_u	0	+	111553369	111564411	100,100,100	3	559,1223,249	0,9017,10793
+5	111553369	111567041	STRG.22958.3_u	0	+	111553369	111567041	100,100,100	3	559,2000,2005	0,9017,11667
+5	110786093	110796066	STRG.22901.3_j	0	-	110786093	110796066	100,100,100	20	134,136,158,119,173,191,144,588,269,87,146,126,90,61,148,89,51,83,59,335	0,206,990,1480,1679,2016,2635,2854,4118,4756,4958,5507,6008,6303,6872,7721,8099,8491,8653,9638
+5	110792544	110796066	STRG.22901.5_j	0	-	110792544	110796066	100,100,100	5	569,89,51,221,335	0,1270,1648,2040,3187
+5	112871741	112874253	STRG.22984.5_j	0	-	112871741	112874253	100,100,100	3	755,67,361	0,1753,2151
+5	112875222	112896379	STRG.22984.4_j	0	-	112875222	112896379	100,100,100	3	104,159,124	0,2762,21033
+5	113184127	113192079	STRG.22997.1_u	0	-	113184127	113192079	100,100,100	3	590,88,1476	0,4158,6476
+12	69229664	69231901	STRG.52020.2_u	0	+	69229664	69231901	100,100,100	2	62,203	0,2034
+12	69199878	69228169	STRG.52021.2_j	0	-	69199878	69228169	100,100,100	18	2004,68,177,109,78,60,55,683,73,49,57,84,75,94,78,76,101,73	0,3028,4212,6531,7980,8142,9038,9433,11494,12344,13108,13950,15432,22098,22520,23225,26459,28218