书不如思贵，意不可言传

#####Introduction

This post describes the usage of program parseGTF.py as well as sortGTF.py.

The GTF(General Transfer Format) file save a subset of biological sequence also known as a feature in one line to faciliate adding and computing.

Here GTF file mainly refers to gene annotation file got from UCSC. Please check UCSC usage to see how to get RefSeq gene or UCSC gene annotation file in GTF format or other format. Besides, you can also get gene annotation file as well as sub-gene regions like 5’ UTR, 3’UTR and coding exons in bed format simultaneously.

But what would you do if you want to extract the above mentioned sub-gene regions when you already have a GTF file. It may be very hard to extract the sub-gene regions from UCSC since the version of GTF file in UCSC is updated since you last access. If you remember the version number of your GTF annotation, there may be a way to get the sub-gene regions corresponding to that version. But I did not try it. Besides, what would you do if the GTF file is got from other place, or you want to get other sub-regions which can not be got from UCSC directly like the mRNA regions flanking start codon and stop codon?

The script parseGTF.py is designed to solve this problem. It takes a sorted GTF and a chromosome-size file as input and outputs all regions mentioned above as showed below.

#####Evaluation I have tested this script for various gene structures in mouse RefSeq gene annotation and all works well. Besides, the output result of this script matches very well with sub-regions directly got from UCSC. However, there may still contain other bugs that I have not noticed. If you found one, please let me know.

#####Usage

Require two files, one is GTF file, the other is chromsome-size file. Please also check UCSC usage to see how to get this file.
Sort GTF file using sortGTF.py.

sortGTF.py mm9.gene.refgene.gtf > mm9.gene.refgene.sorted.gtf

Parse GTF file using parseGTF.py

parseGTF.py mm9.gene.refgene.sorted.gtf mm9.chrom.sizes >mm9.gene.refgene.gtf.bed

#####File formats

Output file format
- TSS represents transcription start site while TTS represents translation terminal site. TSS500 represents 500 nt regions centered by TSS. TSS-UP0-500 represents the upstream 500 nt regions of TSS. TSS-DW0-500 represents the downstream 500 nt regions of TSS.

chr17 25377309 25377388 NM_026676_11.Intron.1 0 +

chr17 25377197 25377309 NM_026676_11.Coding_exon.1 0 +

chr17 25377608 25378008 NM_026676_11.Intron.2 0 +

chr17 25378202 25378632 NM_026676_11.Intron.3 0 +

chr17 25378806 25379103 NM_026676_11.Intron.4 0 +

chr17 25379167 25379398 NM_026676_11.Intron.5 0 +

chr17 25377388 25377608 NM_026676_11.Coding_exon.2 0 +

chr17 25378008 25378202 NM_026676_11.Coding_exon.3 0 +

chr17 25378632 25378806 NM_026676_11.Coding_exon.4 0 +

chr17 25379103 25379167 NM_026676_11.Coding_exon.5 0 +

chr17 25379398 25379606 NM_026676_11.Coding_exon.6 0 +

chr17 25377114 25379744 NM_026676_11 0610007P22Rik +

chr17 25376864 25377364 NM_026676_11.TSS500 0 +

chr17 25379493 25379993 NM_026676_11.TTS500 0 +

chr17 25376614 25377614 NM_026676_11.TSS1000 0 +

chr17 25379243 25380243 NM_026676_11.TTS1000 0 +

chr17 25376114 25378114 NM_026676_11.TSS2000 0 +

chr17 25378743 25380743 NM_026676_11.TTS2000 0 +

chr17 25374614 25379614 NM_026676_11.TSS5000 0 +

chr17 25377243 25382243 NM_026676_11.TTS5000 0 +

chr17 25376614 25377114 NM_026676_11.TSS-UP0-500 0 +

chr17 25379743 25380243 NM_026676_11.TTS-DW0-500 0 +

chr17 25376114 25376614 NM_026676_11.TSS-UP500-1000 0 +

chr17 25380243 25380743 NM_026676_11.TTS-DW500-1000 0 +

chr17 25375114 25376114 NM_026676_11.TSS-UP1000-2000 0 +

chr17 25380743 25381743 NM_026676_11.TTS-DW1000-2000 0 +

chr17 25372114 25375114 NM_026676_11.TSS-UP2000-5000 0 +

chr17 25381743 25384743 NM_026676_11.TTS-DW2000-5000 0 +

chr17 25377114 25377197 NM_026676_11.UTR5 0 +

chr17 25379606 25379744 NM_026676_11.UTR3 0 +

Input file format
- All types of special GTF structures processed during writing scripts

chr2 refGene stop_codon 176083705 176083707 . - 0 gene_id “100043387”; transcript_id “NM_001099327”; exon_number “1”; exon_id “NM_001099327.1”; gene_name “100043387”;

chr2 refGene exon 176083705 176085010 . - . gene_id “100043387”; transcript_id “NM_001099327”; exon_number “1”; exon_id “NM_001099327.1”; gene_name “100043387”;

chr2 refGene exon 176086169 176086229 . - . gene_id “100043387”; transcript_id “NM_001099327”; exon_number “2”; exon_id “NM_001099327.2”; gene_name “100043387”;

chr2 refGene exon 176086435 176086561 . - . gene_id “100043387”; transcript_id “NM_001099327”; exon_number “3”; exon_id “NM_001099327.3”; gene_name “100043387”;

chr2 refGene start_codon 176093582 176093584 . - 0 gene_id “100043387”; transcript_id “NM_001099327”; exon_number “1”; exon_id “NM_001099327.1”; gene_name “100043387”;

chr2 refGene exon 176093582 176093636 . - . gene_id “100043387”; transcript_id “NM_001099327”; exon_number “4”; exon_id “NM_001099327.4”; gene_name “100043387”;

chr2 refGene exon 176097100 176097171 . - . gene_id “100043387”; transcript_id “NM_001099327”; exon_number “5”; exon_id “NM_001099327.5”; gene_name “100043387”;

chr4 refGene exon 41452042 41452201 . - . gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “1”; exon_id “NM_001048005.1”; gene_name “1110017D15Rik”;

chr4 refGene stop_codon 41452601 41452603 . - 0 gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “1”; exon_id “NM_001048005.1”; gene_name “1110017D15Rik”;

chr4 refGene exon 41452601 41452687 . - . gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “2”; exon_id “NM_001048005.2”; gene_name “1110017D15Rik”;

chr4 refGene exon 41454132 41454361 . - . gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “3”; exon_id “NM_001048005.3”; gene_name “1110017D15Rik”;

chr4 refGene exon 41454554 41454626 . - . gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “4”; exon_id “NM_001048005.4”; gene_name “1110017D15Rik”;

chr4 refGene exon 41455550 41455662 . - . gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “5”; exon_id “NM_001048005.5”; gene_name “1110017D15Rik”;

chr4 refGene exon 41458465 41458609 . - . gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “6”; exon_id “NM_001048005.6”; gene_name “1110017D15Rik”;

chr4 refGene exon 41464061 41464366 . - . gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “7”; exon_id “NM_001048005.7”; gene_name “1110017D15Rik”;

chr4 refGene start_codon 41464193 41464195 . - 0 gene_id “1110017D15Rik”; transcript_id “NM_001048005”; exon_number “1”; exon_id “NM_001048005.1”; gene_name “1110017D15Rik”;

chr10 refGene exon 79635689 79635919 . + . gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “1”; exon_id “NM_027207.1”; gene_name “1600002K03Rik”;

chr10 refGene start_codon 79635711 79635713 . + 0 gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “1”; exon_id “NM_027207.1”; gene_name “1600002K03Rik”;

chr10 refGene exon 79636954 79637070 . + . gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “2”; exon_id “NM_027207.2”; gene_name “1600002K03Rik”;

chr10 refGene stop_codon 79637069 79637070 . + 0 gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “1”; exon_id “NM_027207.1”; gene_name “1600002K03Rik”;

chr10 refGene stop_codon 79637562 79637562 . + 1 gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “1”; exon_id “NM_027207.1”; gene_name “1600002K03Rik”;

chr10 refGene exon 79637562 79637864 . + . gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “3”; exon_id “NM_027207.3”; gene_name “1600002K03Rik”;

chr7 refGene exon 97273346 97273542 . - . gene_id “2310010J17Rik”; transcript_id “NR_046007”; exon_number “1”; exon_id “NR_046007.1”; gene_name “2310010J17Rik”;

chr7 refGene exon 97275438 97275554 . - . gene_id “2310010J17Rik”; transcript_id “NR_046007”; exon_number “2”; exon_id “NR_046007.2”; gene_name “2310010J17Rik”;

chr7 refGene exon 97278382 97278446 . - . gene_id “2310010J17Rik”; transcript_id “NR_046007”; exon_number “3”; exon_id “NR_046007.3”; gene_name “2310010J17Rik”;

chr16 refGene start_codon 32271695 32271697 . + 0 gene_id “2310010M20Rik”; transcript_id “NM_183283”; exon_number “1”; exon_id “NM_183283.1”; gene_name “2310010M20Rik”;

chr16 refGene exon 32271695 32271744 . + . gene_id “2310010M20Rik”; transcript_id “NM_183283”; exon_number “1”; exon_id “NM_183283.1”; gene_name “2310010M20Rik”;

chr16 refGene exon 32273242 32273391 . + . gene_id “2310010M20Rik”; transcript_id “NM_183283”; exon_number “2”; exon_id “NM_183283.2”; gene_name “2310010M20Rik”;

chr16 refGene exon 32273799 32274865 . + . gene_id “2310010M20Rik”; transcript_id “NM_183283”; exon_number “3”; exon_id “NM_183283.3”; gene_name “2310010M20Rik”;

chr16 refGene stop_codon 32274241 32274243 . + 0 gene_id “2310010M20Rik”; transcript_id “NM_183283”; exon_number “1”; exon_id “NM_183283.1”; gene_name “2310010M20Rik”;

chr7 mm9_refGene exon 147995576 147999213 0.000000 - . gene_id “NM_001001180”; transcript_id “NM_001001180”;

chr7 mm9_refGene stop_codon 147997328 147997330 0.000000 - . gene_id “NM_001001180”; transcript_id “NM_001001180”;

chr7 mm9_refGene exon 148004487 148004613 0.000000 - . gene_id “NM_001001180”; transcript_id “NM_001001180”;

chr7 mm9_refGene start_codon 148007934 148007936 0.000000 - . gene_id “NM_001001180”; transcript_id “NM_001001180”;

chr7 mm9_refGene exon 148007934 148008077 0.000000 - . gene_id “NM_001001180”; transcript_id “NM_001001180”;

chr1 mm9_refGene exon 58519615 58521134 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene stop_codon 58521048 58521050 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58522839 58522957 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58524495 58524556 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58526512 58526683 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58527784 58527930 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58529149 58529245 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58531653 58531785 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58533278 58533387 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58537095 58537193 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58537804 58537997 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58540487 58540547 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58549701 58549732 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58550505 58550594 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58554220 58554309 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene exon 58558167 58558270 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr1 mm9_refGene start_codon 58558258 58558260 0.000000 - . gene_id “NM_001025378”; transcript_id “NM_001025378”;

chr18 mm9_refGene exon 48204989 48205099 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr18 mm9_refGene exon 48206387 48208037 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr18 mm9_refGene start_codon 48206411 48206413 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr18 mm9_refGene stop_codon 48207713 48207715 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149611433 149611449 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149613582 149613675 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene start_codon 149613591 149613593 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149615154 149615249 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149616231 149616289 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149618114 149618183 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149618350 149618483 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149619224 149619446 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149620679 149620876 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149621560 149621761 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149621940 149622048 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149622170 149622228 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene exon 149622595 149622982 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr4 mm9_refGene stop_codon 149622662 149622664 0.000000 + . gene_id “NM_001025388”; transcript_id “NM_001025388”;

chr16 mm9_refGene exon 26581791 26581972 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26624241 26624305 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene start_codon 26624242 26624244 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26676795 26677080 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26680189 26680375 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26692831 26692996 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26695308 26695379 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26698913 26699039 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26701174 26701322 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26710567 26710716 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26712203 26712346 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26722442 26723017 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene stop_codon 26723017 26723017 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene stop_codon 26723307 26723308 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr16 mm9_refGene exon 26723307 26725233 0.000000 + . gene_id “NM_001159317”; transcript_id “NM_001159317”;

chr1 mm9_refGene exon 100317701 100318074 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene start_codon 100317783 100317785 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100319666 100319926 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100324843 100325028 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100328810 100328906 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100340205 100340323 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100343290 100343399 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100363235 100363379 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100377168 100377363 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100387074 100387227 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100392762 100392949 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100394054 100394118 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100396336 100396473 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene stop_codon 100396473 100396473 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene stop_codon 100405796 100405797 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chr1 mm9_refGene exon 100405796 100405957 0.000000 + . gene_id “NM_001164233”; transcript_id “NM_001164233”;

chrUn_random mm9_refGene exon 527839 528262 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chrUn_random mm9_refGene stop_codon 528232 528234 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chrUn_random mm9_refGene exon 528345 528527 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chrUn_random mm9_refGene exon 528622 528742 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chrUn_random mm9_refGene exon 528831 528969 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chrUn_random mm9_refGene start_codon 528895 528897 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chr4 mm9_refGene exon 41774207 41774345 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chr4 mm9_refGene start_codon 41774279 41774281 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chr4 mm9_refGene exon 41774434 41774554 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chr4 mm9_refGene exon 41774649 41774831 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chr4 mm9_refGene exon 41774914 41775337 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chr4 mm9_refGene stop_codon 41774942 41774944 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666”;

chrUn_random mm9_refGene exon 739163 739586 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chrUn_random mm9_refGene stop_codon 739556 739558 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chrUn_random mm9_refGene exon 739669 739851 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chrUn_random mm9_refGene exon 739946 740066 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chrUn_random mm9_refGene exon 740155 740293 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chrUn_random mm9_refGene start_codon 740219 740221 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chr4 mm9_refGene exon 41985510 41985648 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chr4 mm9_refGene start_codon 41985582 41985584 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chr4 mm9_refGene exon 41985737 41985857 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chr4 mm9_refGene exon 41985952 41986134 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chr4 mm9_refGene exon 41986217 41986640 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chr4 mm9_refGene stop_codon 41986245 41986247 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup1”;

chr4 mm9_refGene exon 42391950 42392373 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup2”;

chr4 mm9_refGene stop_codon 42392343 42392345 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup2”;

chr4 mm9_refGene exon 42392456 42392638 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup2”;

chr4 mm9_refGene exon 42392733 42392853 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup2”;

chr4 mm9_refGene exon 42392942 42393080 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup2”;

chr4 mm9_refGene start_codon 42393006 42393008 0.000000 - . gene_id “NM_001193666”; transcript_id “NM_001193666_dup2”;

chr4 mm9_refGene exon 42625655 42625793 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup3”;

chr4 mm9_refGene start_codon 42625727 42625729 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup3”;

chr4 mm9_refGene exon 42625882 42626002 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup3”;

chr4 mm9_refGene exon 42626097 42626279 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup3”;

chr4 mm9_refGene exon 42626362 42626785 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup3”;

chr4 mm9_refGene stop_codon 42626390 42626392 0.000000 + . gene_id “NM_001193666”; transcript_id “NM_001193666_dup3”;

chrUn_random mm9_refGene exon 1737773 1737846 0.000000 + . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chrUn_random mm9_refGene exon 1738982 1739295 0.000000 + . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chrUn_random mm9_refGene start_codon 1739009 1739011 0.000000 + . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chrUn_random mm9_refGene exon 1739750 1740340 0.000000 + . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chrUn_random mm9_refGene exon 1741238 1741852 0.000000 + . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chrUn_random mm9_refGene stop_codon 1741803 1741805 0.000000 + . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chr5 mm9_refGene exon 94495480 94496094 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chr5 mm9_refGene stop_codon 94495527 94495529 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chr5 mm9_refGene exon 94496992 94497582 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chr5 mm9_refGene exon 94498037 94498350 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chr5 mm9_refGene start_codon 94498321 94498323 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chr5 mm9_refGene exon 94499498 94499571 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457”;

chr5 mm9_refGene exon 96161111 96161725 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457_dup1”;

chr5 mm9_refGene stop_codon 96161158 96161160 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457_dup1”;

chr5 mm9_refGene exon 96162623 96163213 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457_dup1”;

chr5 mm9_refGene exon 96163668 96163981 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457_dup1”;

chr5 mm9_refGene start_codon 96163952 96163954 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457_dup1”;

chr5 mm9_refGene exon 96165119 96165192 0.000000 - . gene_id “NM_001270457”; transcript_id “NM_001270457_dup1”;

chr17 mm9_refGene exon 31298341 31298538 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr17 mm9_refGene stop_codon 31298522 31298524 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr17 mm9_refGene exon 31299600 31299752 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr17 mm9_refGene exon 31301872 31301998 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr17 mm9_refGene start_codon 31301963 31301965 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr5 mm9_refGene exon 143285577 143285774 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr5 mm9_refGene stop_codon 143285758 143285760 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr5 mm9_refGene exon 143286836 143286988 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr5 mm9_refGene exon 143289108 143289234 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr5 mm9_refGene start_codon 143289199 143289201 0.000000 - . gene_id “NM_009362”; transcript_id “NM_009362”;

chr11 mm9_refGene exon 68902030 68902129 0.000000 + . gene_id “NM_009497”; transcript_id “NM_009497”;

chr11 mm9_refGene start_codon 68902128 68902129 0.000000 + . gene_id “NM_009497”; transcript_id “NM_009497”;

chr11 mm9_refGene start_codon 68902608 68902608 0.000000 + . gene_id “NM_009497”; transcript_id “NM_009497”;

chr11 mm9_refGene exon 68902608 68902728 0.000000 + . gene_id “NM_009497”; transcript_id “NM_009497”;

chr11 mm9_refGene exon 68903233 68903391 0.000000 + . gene_id “NM_009497”; transcript_id “NM_009497”;

chr11 mm9_refGene exon 68903478 68903529 0.000000 + . gene_id “NM_009497”; transcript_id “NM_009497”;

chr11 mm9_refGene exon 68904152 68905883 0.000000 + . gene_id “NM_009497”; transcript_id “NM_009497”;

chr11 mm9_refGene stop_codon 68904166 68904168 0.000000 + . gene_id “NM_009497”; transcript_id “NM_009497”;

chrY mm9_refGene exon 155156 155257 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene start_codon 157264 157266 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 157264 157380 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 157495 157550 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 157635 157803 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 157893 158027 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 158589 158695 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 158902 158992 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 159587 159719 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 161891 161988 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 162085 162231 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 162342 162518 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 162621 162725 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 162814 162894 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 163205 163360 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 165209 165374 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 165584 165780 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 167702 167766 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 168018 168213 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 168767 168841 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 168947 169139 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 170618 170706 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 178411 178503 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 178623 178814 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 179367 179468 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 179577 179677 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene exon 179830 180667 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY mm9_refGene stop_codon 179963 179965 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43172478 43172579 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene start_codon 43174586 43174588 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43174586 43174702 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43174817 43174872 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43174957 43175125 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43175215 43175349 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43175911 43176017 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43176224 43176314 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43176909 43177041 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43179213 43179310 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43179407 43179553 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43179664 43179840 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43179943 43180047 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43180136 43180216 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43180527 43180682 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43182531 43182696 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43182906 43183102 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43185024 43185088 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43185340 43185535 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43186089 43186163 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43186269 43186461 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43187940 43188028 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43195733 43195825 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43195945 43196136 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43196689 43196790 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43196899 43196999 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene exon 43197152 43197989 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chrY_random mm9_refGene stop_codon 43197285 43197287 0.000000 + . gene_id “NM_011667”; transcript_id “NM_011667”;

chr12 mm9_refGene exon 31596534 31597092 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene start_codon 31597092 31597092 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene start_codon 31607100 31607101 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31607100 31607210 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31609629 31609742 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31611675 31611739 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31624439 31624551 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31625156 31625284 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31626832 31626994 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31627655 31627733 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31643713 31643769 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene exon 31644669 31645014 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr12 mm9_refGene stop_codon 31644857 31644859 0.000000 + . gene_id “NM_013709”; transcript_id “NM_013709”;

chr17_random mm9_refGene exon 581195 581311 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene exon 600251 600446 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene start_codon 600275 600277 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene exon 602234 602362 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene exon 604618 604715 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene exon 609590 609716 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene exon 610273 610367 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene exon 611771 611951 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene exon 612164 612733 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17_random mm9_refGene stop_codon 612274 612276 0.000000 + . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene exon 54100940 54101509 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene stop_codon 54101397 54101399 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene exon 54101722 54101902 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene exon 54103306 54103400 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene exon 54103957 54104083 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene exon 54108958 54109055 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene exon 54111311 54111439 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene exon 54113227 54113422 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene start_codon 54113396 54113398 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr17 mm9_refGene exon 54129840 54129956 0.000000 - . gene_id “NM_018751”; transcript_id “NM_018751”;

chr11 mm9_refGene exon 79314484 79316529 0.000000 - . gene_id “NM_019409”; transcript_id “NM_019409”;

chr11 mm9_refGene stop_codon 79315201 79315203 0.000000 - . gene_id “NM_019409”; transcript_id “NM_019409”;

chr11 mm9_refGene start_codon 79317405 79317407 0.000000 - . gene_id “NM_019409”; transcript_id “NM_019409”;

chr11 mm9_refGene exon 79317405 79317584 0.000000 - . gene_id “NM_019409”; transcript_id “NM_019409”;

chr10 mm9_refGene exon 127496038 127496342 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene start_codon 127496341 127496342 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene start_codon 127505728 127505728 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene exon 127505728 127505841 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene exon 127506272 127506341 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene exon 127507190 127507288 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene exon 127509124 127509213 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene exon 127511278 127511340 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene exon 127512394 127512418 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene exon 127513123 127514310 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr10 mm9_refGene stop_codon 127513140 127513142 0.000000 + . gene_id “NM_019766”; transcript_id “NM_019766”;

chr17_random mm9_refGene exon 39677 41691 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene stop_codon 40445 40447 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 42329 42443 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 43007 43202 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 44596 44705 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 45129 45290 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 45800 45966 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 47141 47207 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 47495 47548 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 47638 47718 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene start_codon 47662 47664 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17_random mm9_refGene exon 48466 48574 0.000000 - . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8118865 8118973 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8119721 8119801 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene start_codon 8119775 8119777 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8119891 8119944 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8120232 8120298 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8121473 8121639 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8122149 8122310 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8122734 8122843 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8124237 8124432 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8124996 8125110 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene exon 8125748 8127762 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr17 mm9_refGene stop_codon 8126992 8126994 0.000000 + . gene_id “NM_145968”; transcript_id “NM_145968”;

chr3 mm9_refGene exon 138868857 138868971 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene start_codon 138868863 138868865 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138875216 138875328 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138878222 138878350 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138881153 138881317 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138895162 138895274 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138906038 138906149 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138961369 138961476 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138969108 138969264 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138972046 138972206 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 138980356 138980445 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 139082669 139082828 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 139185822 139185940 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 139364589 139364737 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene stop_codon 139364736 139364737 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene stop_codon 139372137 139372137 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr3 mm9_refGene exon 139372137 139373263 0.000000 + . gene_id “NM_198659”; transcript_id “NM_198659”;

chr10 refGene exon 79635689 79635919 . + . gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “1”; exon_id “NM_027207.1”; gene_name “1600002K03Rik”;

chr10 refGene start_codon 79635711 79635713 . + 0 gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “1”; exon_id “NM_027207.1”; gene_name “1600002K03Rik”;

chr10 refGene exon 79636954 79637070 . + . gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “2”; exon_id “NM_027207.2”; gene_name “1600002K03Rik”;

chr10 refGene stop_codon 79637069 79637070 . + 0 gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “1”; exon_id “NM_027207.1”; gene_name “1600002K03Rik”;

chr10 refGene stop_codon 79637562 79637562 . + 1 gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “1”; exon_id “NM_027207.1”; gene_name “1600002K03Rik”;

chr10 refGene exon 79637562 79637864 . + . gene_id “1600002K03Rik”; transcript_id “NM_027207”; exon_number “3”; exon_id “NM_027207.3”; gene_name “1600002K03Rik”;

chr11 refGene exon 110829347 110829409 . + . gene_id “Kcnj16”; transcript_id “NM_001252207”; exon_number “1”; exon_id “NM_001252207.1”; gene_name “Kcnj16”;

chr11 refGene exon 110847744 110847824 . + . gene_id “Kcnj16”; transcript_id “NM_001252207”; exon_number “2”; exon_id “NM_001252207.2”; gene_name “Kcnj16”;

chr11 refGene exon 110885723 110889281 . + . gene_id “Kcnj16”; transcript_id “NM_001252207”; exon_number “3”; exon_id “NM_001252207.3”; gene_name “Kcnj16”;

chr11 refGene start_codon 110885828 110885830 . + 0 gene_id “Kcnj16”; transcript_id “NM_001252207”; exon_number “1”; exon_id “NM_001252207.1”; gene_name “Kcnj16”;

chr11 refGene stop_codon 110887085 110887087 . + 0 gene_id “Kcnj16”; transcript_id “NM_001252207”; exon_number “1”; exon_id “NM_001252207.1”; gene_name “Kcnj16”;

chrY_random refGene exon 4246223 4247319 . - . gene_id “LOC434960”; transcript_id “NM_001025241”; exon_number “1”; exon_id “NM_001025241.1”; gene_name “LOC434960”;

chrY_random refGene stop_codon 4246355 4246357 . - 0 gene_id “LOC434960”; transcript_id “NM_001025241”; exon_number “1”; exon_id “NM_001025241.1”; gene_name “LOC434960”;

chrY_random refGene start_codon 4247036 4247038 . - 0 gene_id “LOC434960”; transcript_id “NM_001025241”; exon_number “1”; exon_id “NM_001025241.1”; gene_name “LOC434960”;

chrY_random refGene exon 4248546 4248568 . - . gene_id “LOC434960”; transcript_id “NM_001025241”; exon_number “2”; exon_id “NM_001025241.2”; gene_name “LOC434960”;

chrY_random refGene exon 52515006 52515028 . + . gene_id “LOC434960”; transcript_id “NM_001025241_3”; exon_number “1”; exon_id “NM_001025241_3.1”; gene_name “LOC434960”;

chrY_random refGene exon 52516257 52517353 . + . gene_id “LOC434960”; transcript_id “NM_001025241_3”; exon_number “2”; exon_id “NM_001025241_3.2”; gene_name “LOC434960”;

chrY_random refGene start_codon 52516538 52516540 . + 0 gene_id “LOC434960”; transcript_id “NM_001025241_3”; exon_number “1”; exon_id “NM_001025241_3.1”; gene_name “LOC434960”;

chrY_random refGene stop_codon 52517219 52517221 . + 0 gene_id “LOC434960”; transcript_id “NM_001025241_3”; exon_number “1”; exon_id “NM_001025241_3.1”; gene_name “LOC434960”;

chr10 refGene exon 57857121 57857348 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “1”; exon_id “NM_001193303.1”; gene_name “Lims1”;

chr10 refGene start_codon 57857167 57857169 . + 0 gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “1”; exon_id “NM_001193303.1”; gene_name “Lims1”;

chr10 refGene exon 57861769 57861928 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “2”; exon_id “NM_001193303.2”; gene_name “Lims1”;

chr10 refGene exon 57870818 57870884 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “3”; exon_id “NM_001193303.3”; gene_name “Lims1”;

chr10 refGene exon 57872308 57872428 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “4”; exon_id “NM_001193303.4”; gene_name “Lims1”;

chr10 refGene exon 57872801 57872950 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “5”; exon_id “NM_001193303.5”; gene_name “Lims1”;

chr10 refGene exon 57875151 57875301 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “6”; exon_id “NM_001193303.6”; gene_name “Lims1”;

chr10 refGene exon 57876721 57876813 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “7”; exon_id “NM_001193303.7”; gene_name “Lims1”;

chr10 refGene exon 57879382 57879430 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “8”; exon_id “NM_001193303.8”; gene_name “Lims1”;

chr10 refGene exon 57881147 57881222 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “9”; exon_id “NM_001193303.9”; gene_name “Lims1”;

chr10 refGene exon 57881395 57881534 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “10”; exon_id “NM_001193303.10”; gene_name “Lims1”;

chr10 refGene stop_codon 57881534 57881534 . + 0 gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “1”; exon_id “NM_001193303.1”; gene_name “Lims1”;

chr10 refGene stop_codon 57884202 57884203 . + 2 gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “1”; exon_id “NM_001193303.1”; gene_name “Lims1”;

chr10 refGene exon 57884202 57887439 . + . gene_id “Lims1”; transcript_id “NM_001193303”; exon_number “11”; exon_id “NM_001193303.11”; gene_name “Lims1”;

chr1 refGene exon 20880703 20880767 . + . gene_id “Paqr8”; transcript_id “NM_028829”; exon_number “1”; exon_id “NM_028829.1”; gene_name “Paqr8”;

chr1 refGene exon 20922141 20922320 . + . gene_id “Paqr8”; transcript_id “NM_028829”; exon_number “2”; exon_id “NM_028829.2”; gene_name “Paqr8”;

chr1 refGene exon 20924663 20928837 . + . gene_id “Paqr8”; transcript_id “NM_028829”; exon_number “3”; exon_id “NM_028829.3”; gene_name “Paqr8”;

chr1 refGene start_codon 20924705 20924707 . + 0 gene_id “Paqr8”; transcript_id “NM_028829”; exon_number “1”; exon_id “NM_028829.1”; gene_name “Paqr8”;

chr1 refGene stop_codon 20925767 20925769 . + 0 gene_id “Paqr8”; transcript_id “NM_028829”; exon_number “1”; exon_id “NM_028829.1”; gene_name “Paqr8”;

chr1 refGene exon 9535489 9537536 . + . gene_id “Rrs1”; transcript_id “NM_021511”; exon_number “1”; exon_id “NM_021511.1”; gene_name “Rrs1”;

chr1 refGene start_codon 9535605 9535607 . + 0 gene_id “Rrs1”; transcript_id “NM_021511”; exon_number “1”; exon_id “NM_021511.1”; gene_name “Rrs1”;

chr1 refGene stop_codon 9536700 9536702 . + 0 gene_id “Rrs1”; transcript_id “NM_021511”; exon_number “1”; exon_id “NM_021511.1”; gene_name “Rrs1”;

chr1 refGene exon 157882857 157883050 . + . gene_id “Tor1aip2”; transcript_id “NM_001160180”; exon_number “1”; exon_id “NM_001160180.1”; gene_name “Tor1aip2”;

chr1 refGene exon 157888205 157888264 . + . gene_id “Tor1aip2”; transcript_id “NM_001160180”; exon_number “2”; exon_id “NM_001160180.2”; gene_name “Tor1aip2”;

chr1 refGene exon 157898424 157900866 . + . gene_id “Tor1aip2”; transcript_id “NM_001160180”; exon_number “3”; exon_id “NM_001160180.3”; gene_name “Tor1aip2”;

chr1 refGene start_codon 157899008 157899010 . + 0 gene_id “Tor1aip2”; transcript_id “NM_001160180”; exon_number “1”; exon_id “NM_001160180.1”; gene_name “Tor1aip2”;

chr1 refGene stop_codon 157899401 157899403 . + 0 gene_id “Tor1aip2”; transcript_id “NM_001160180”; exon_number “1”; exon_id “NM_001160180.1”; gene_name “Tor1aip2”;

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