Mercurial > repos > iuc > tetoolkit_tetranscripts
changeset 0:2dfbcb88d16a draft
"planemo upload for repository https://github.com/mhammell-laboratory/TEtranscripts commit 0afd89b76ba658b8bc9faa1463a1aa160ddb2339"
| author | iuc |
|---|---|
| date | Wed, 13 May 2020 12:57:29 -0400 |
| parents | |
| children | bf4ee2810759 |
| files | test-data/control1.bam test-data/control2.bam test-data/gtf.gtf test-data/te.gtf test-data/treatment1.bam test-data/treatment2.bam tetranscript.xml |
| diffstat | 7 files changed, 1944 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtf.gtf Wed May 13 12:57:29 2020 -0400 @@ -0,0 +1,779 @@ +chrX refGene exon 14118058 14118761 . + . gene_id "l(1)G0007"; transcript_id "NM_167396"; exon_number "3"; exon_id "NM_167396.3"; gene_name "l(1)G0007"; +chrX refGene 3UTR 14118656 14118761 . + . gene_id "l(1)G0007"; transcript_id "NM_167396"; exon_number "3"; exon_id "NM_167396.3"; gene_name "l(1)G0007"; +chr2L refGene exon 18711071 18711733 . - . gene_id "Irk3"; transcript_id "NM_136059"; exon_number "1"; exon_id "NM_136059.1"; gene_name "Irk3"; +chr2L refGene 3UTR 18711071 18711336 . - . gene_id "Irk3"; transcript_id "NM_136059"; exon_number "1"; exon_id "NM_136059.1"; gene_name "Irk3"; +chr2L refGene exon 11128807 11129335 . + . gene_id "Nup160"; transcript_id "NM_135649"; exon_number "14"; exon_id "NM_135649.14"; gene_name "Nup160"; +chr2L refGene 3UTR 11128927 11129335 . + . gene_id "Nup160"; transcript_id "NM_135649"; exon_number "14"; exon_id "NM_135649.14"; gene_name "Nup160"; +chr2L refGene exon 10324379 10324990 . + . gene_id "CG4995"; transcript_id "NM_135536"; exon_number "5"; exon_id "NM_135536.5"; gene_name "CG4995"; +chr2L refGene CDS 10324379 10324962 . + 2 gene_id "CG4995"; transcript_id "NM_135536"; exon_number "5"; exon_id "NM_135536.5"; gene_name "CG4995"; +chr2L refGene 3UTR 10324966 10324990 . + . gene_id "CG4995"; transcript_id "NM_135536"; exon_number "5"; exon_id "NM_135536.5"; gene_name "CG4995"; +chr2L refGene stop_codon 10324963 10324965 . + 0 gene_id "CG4995"; transcript_id "NM_135536"; exon_number "1"; exon_id "NM_135536.1"; gene_name "CG4995"; +chr2L refGene exon 6487562 6488372 . - . gene_id "KFase"; transcript_id "NM_135192"; exon_number "1"; exon_id "NM_135192.1"; gene_name "KFase"; +chr2L refGene 3UTR 6487562 6487596 . - . gene_id "KFase"; transcript_id "NM_135192"; exon_number "1"; exon_id "NM_135192.1"; gene_name "KFase"; +chr2L refGene exon 6063562 6063771 . - . gene_id "Fbw5"; transcript_id "NM_135145"; exon_number "1"; exon_id "NM_135145.1"; gene_name "Fbw5"; +chr2L refGene 3UTR 6063562 6063687 . - . gene_id "Fbw5"; transcript_id "NM_135145"; exon_number "1"; exon_id "NM_135145.1"; gene_name "Fbw5"; +chr2L refGene exon 4461657 4462563 . - . gene_id "CG15443"; transcript_id "NM_134995"; exon_number "1"; exon_id "NM_134995.1"; gene_name "CG15443"; +chr2L refGene 3UTR 4461657 4461823 . - . gene_id "CG15443"; transcript_id "NM_134995"; exon_number "1"; exon_id "NM_134995.1"; gene_name "CG15443"; +chr2L refGene exon 5521281 5522007 . - . gene_id "CG7371"; transcript_id "NM_135087"; exon_number "1"; exon_id "NM_135087.1"; gene_name "CG7371"; +chr2L refGene 3UTR 5521281 5521377 . - . gene_id "CG7371"; transcript_id "NM_135087"; exon_number "1"; exon_id "NM_135087.1"; gene_name "CG7371"; +chr2L refGene stop_codon 5521378 5521380 . - 0 gene_id "CG7371"; transcript_id "NM_135087"; exon_number "1"; exon_id "NM_135087.1"; gene_name "CG7371"; +chr2L refGene exon 4969285 4970216 . + . gene_id "CG3756"; transcript_id "NM_135041"; exon_number "2"; exon_id "NM_135041.2"; gene_name "CG3756"; +chr2L refGene 3UTR 4970147 4970216 . + . gene_id "CG3756"; transcript_id "NM_135041"; exon_number "2"; exon_id "NM_135041.2"; gene_name "CG3756"; +chr2L refGene exon 4815680 4815891 . + . gene_id "CG15629"; transcript_id "NM_135015"; exon_number "4"; exon_id "NM_135015.4"; gene_name "CG15629"; +chr2L refGene CDS 4815680 4815779 . + 1 gene_id "CG15629"; transcript_id "NM_135015"; exon_number "4"; exon_id "NM_135015.4"; gene_name "CG15629"; +chr2R refGene exon 3709615 3709990 . - . gene_id "cathD"; transcript_id "NM_143756"; exon_number "1"; exon_id "NM_143756.1"; gene_name "cathD"; +chr2R refGene 3UTR 3709615 3709729 . - . gene_id "cathD"; transcript_id "NM_143756"; exon_number "1"; exon_id "NM_143756.1"; gene_name "cathD"; +chr2R refGene exon 11428922 11430003 . + . gene_id "Vha36-1"; transcript_id "NM_143730"; exon_number "1"; exon_id "NM_143730.1"; gene_name "Vha36-1"; +chr2R refGene CDS 11429042 11429779 . + 0 gene_id "Vha36-1"; transcript_id "NM_143730"; exon_number "1"; exon_id "NM_143730.1"; gene_name "Vha36-1"; +chr3R refGene exon 27625356 27626336 . - . gene_id "CG42233"; transcript_id "NM_143642"; exon_number "1"; exon_id "NM_143642.1"; gene_name "CG42233"; +chr3R refGene 3UTR 27625356 27625893 . - . gene_id "CG42233"; transcript_id "NM_143642"; exon_number "1"; exon_id "NM_143642.1"; gene_name "CG42233"; +chr3R refGene exon 25629467 25630105 . + . gene_id "CG7789"; transcript_id "NM_143471"; exon_number "2"; exon_id "NM_143471.2"; gene_name "CG7789"; +chr3R refGene 3UTR 25630009 25630105 . + . gene_id "CG7789"; transcript_id "NM_143471"; exon_number "2"; exon_id "NM_143471.2"; gene_name "CG7789"; +chr3R refGene exon 25499702 25499945 . + . gene_id "ppk19"; transcript_id "NM_143451"; exon_number "5"; exon_id "NM_143451.5"; gene_name "ppk19"; +chr3R refGene CDS 25499702 25499942 . + 1 gene_id "ppk19"; transcript_id "NM_143451"; exon_number "5"; exon_id "NM_143451.5"; gene_name "ppk19"; +chr2R refGene exon 16152361 16152650 . - . gene_id "CR43812"; transcript_id "NR_073891"; exon_number "1"; exon_id "NR_073891.1"; gene_name "CR43812"; +chr3L refGene exon 22726252 22726688 . - . gene_id "CG11241"; transcript_id "NM_168960"; exon_number "1"; exon_id "NM_168960.1"; gene_name "CG11241"; +chr3L refGene 3UTR 22726252 22726553 . - . gene_id "CG11241"; transcript_id "NM_168960"; exon_number "1"; exon_id "NM_168960.1"; gene_name "CG11241"; +chr3L refGene exon 19538783 19539064 . + . gene_id "Rcd7"; transcript_id "NM_168803"; exon_number "2"; exon_id "NM_168803.2"; gene_name "Rcd7"; +chr3L refGene CDS 19538784 19539064 . + 0 gene_id "Rcd7"; transcript_id "NM_168803"; exon_number "2"; exon_id "NM_168803.2"; gene_name "Rcd7"; +chr2R refGene exon 12953476 12954959 . - . gene_id "CG30460"; transcript_id "NM_001169701"; exon_number "1"; exon_id "NM_001169701.1"; gene_name "CG30460"; +chr2R refGene 3UTR 12953476 12954286 . - . gene_id "CG30460"; transcript_id "NM_001169701"; exon_number "1"; exon_id "NM_001169701.1"; gene_name "CG30460"; +chr2R refGene exon 10755738 10756067 . - . gene_id "Inr-a"; transcript_id "NM_001169682"; exon_number "2"; exon_id "NM_001169682.2"; gene_name "Inr-a"; +chr2R refGene CDS 10755738 10756067 . - 0 gene_id "Inr-a"; transcript_id "NM_001169682"; exon_number "2"; exon_id "NM_001169682.2"; gene_name "Inr-a"; +chr2L refGene exon 21157444 21157647 . - . gene_id "CG9249"; transcript_id "NM_001169558"; exon_number "1"; exon_id "NM_001169558.1"; gene_name "CG9249"; +chr2L refGene CDS 21157520 21157647 . - 2 gene_id "CG9249"; transcript_id "NM_001169558"; exon_number "1"; exon_id "NM_001169558.1"; gene_name "CG9249"; +chr3R refGene exon 11102162 11103277 . - . gene_id "MRG15"; transcript_id "NM_142185"; exon_number "1"; exon_id "NM_142185.1"; gene_name "MRG15"; +chr3R refGene 3UTR 11102162 11102306 . - . gene_id "MRG15"; transcript_id "NM_142185"; exon_number "1"; exon_id "NM_142185.1"; gene_name "MRG15"; +chr2L refGene exon 115365 116488 . - . gene_id "CG13694"; transcript_id "NM_134648"; exon_number "1"; exon_id "NM_134648.1"; gene_name "CG13694"; +chr2L refGene 3UTR 115365 115712 . - . gene_id "CG13694"; transcript_id "NM_134648"; exon_number "1"; exon_id "NM_134648.1"; gene_name "CG13694"; +chr2LHet refGene exon 20723 21383 . - . gene_id "CG12567"; transcript_id "NM_001170362"; exon_number "2"; exon_id "NM_001170362.2"; gene_name "CG12567"; +chr2LHet refGene CDS 20723 21383 . - 0 gene_id "CG12567"; transcript_id "NM_001170362"; exon_number "2"; exon_id "NM_001170362.2"; gene_name "CG12567"; +chr2L refGene exon 12035194 12036137 . + . gene_id "CG18788"; transcript_id "NM_144408"; exon_number "3"; exon_id "NM_144408.3"; gene_name "CG18788"; +chr2L refGene 3UTR 12035986 12036137 . + . gene_id "CG18788"; transcript_id "NM_144408"; exon_number "3"; exon_id "NM_144408.3"; gene_name "CG18788"; +chr3L refGene exon 357981 358486 . + . gene_id "Roc1b"; transcript_id "NM_144356"; exon_number "1"; exon_id "NM_144356.1"; gene_name "Roc1b"; +chr3L refGene CDS 358031 358396 . + 0 gene_id "Roc1b"; transcript_id "NM_144356"; exon_number "1"; exon_id "NM_144356.1"; gene_name "Roc1b"; +chr2R refGene exon 10044555 10044651 . - . gene_id "CG13018"; transcript_id "NM_144123"; exon_number "1"; exon_id "NM_144123.1"; gene_name "CG13018"; +chr2R refGene 3UTR 10044555 10044609 . - . gene_id "CG13018"; transcript_id "NM_144123"; exon_number "1"; exon_id "NM_144123.1"; gene_name "CG13018"; +chr2R refGene CDS 10044613 10044651 . - 0 gene_id "CG13018"; transcript_id "NM_144123"; exon_number "1"; exon_id "NM_144123.1"; gene_name "CG13018"; +chr2R refGene stop_codon 10044610 10044612 . - 0 gene_id "CG13018"; transcript_id "NM_144123"; exon_number "1"; exon_id "NM_144123.1"; gene_name "CG13018"; +chrX refGene exon 8486279 8486423 . - . gene_id "CG12659"; transcript_id "NM_167163"; exon_number "3"; exon_id "NM_167163.3"; gene_name "CG12659"; +chrX refGene 5UTR 8486279 8486423 . - . gene_id "CG12659"; transcript_id "NM_167163"; exon_number "3"; exon_id "NM_167163.3"; gene_name "CG12659"; +chr2L refGene exon 5055982 5058248 . - . gene_id "CG31918"; transcript_id "NM_135060"; exon_number "1"; exon_id "NM_135060.1"; gene_name "CG31918"; +chr2L refGene 3UTR 5055982 5056246 . - . gene_id "CG31918"; transcript_id "NM_135060"; exon_number "1"; exon_id "NM_135060.1"; gene_name "CG31918"; +chr2L refGene exon 5062636 5063442 . - . gene_id "CR43820"; transcript_id "NR_073722"; exon_number "1"; exon_id "NR_073722.1"; gene_name "CR43820"; +chr3R refGene exon 4830231 4831053 . + . gene_id "CG11980"; transcript_id "NM_169251"; exon_number "2"; exon_id "NM_169251.2"; gene_name "CG11980"; +chr3R refGene 3UTR 4830973 4831053 . + . gene_id "CG11980"; transcript_id "NM_169251"; exon_number "2"; exon_id "NM_169251.2"; gene_name "CG11980"; +chr2R refGene exon 17573705 17574110 . - . gene_id "Tbp"; transcript_id "NM_079081"; exon_number "1"; exon_id "NM_079081.1"; gene_name "Tbp"; +chr2R refGene 3UTR 17573705 17573831 . - . gene_id "Tbp"; transcript_id "NM_079081"; exon_number "1"; exon_id "NM_079081.1"; gene_name "Tbp"; +chr3L refGene exon 15965259 15968196 . - . gene_id "brm"; transcript_id "NM_168641"; exon_number "3"; exon_id "NM_168641.3"; gene_name "brm"; +chr3L refGene CDS 15965259 15968196 . - 0 gene_id "brm"; transcript_id "NM_168641"; exon_number "3"; exon_id "NM_168641.3"; gene_name "brm"; +chr3L refGene exon 9069958 9070556 . + . gene_id "Tequila"; transcript_id "NM_168315"; exon_number "6"; exon_id "NM_168315.6"; gene_name "Tequila"; +chr3L refGene 3UTR 9070122 9070556 . + . gene_id "Tequila"; transcript_id "NM_168315"; exon_number "6"; exon_id "NM_168315.6"; gene_name "Tequila"; +chr3L refGene exon 2267870 2268530 . + . gene_id "obst-I"; transcript_id "NM_167943"; exon_number "1"; exon_id "NM_167943.1"; gene_name "obst-I"; +chr3L refGene CDS 2267870 2268526 . + 0 gene_id "obst-I"; transcript_id "NM_167943"; exon_number "1"; exon_id "NM_167943.1"; gene_name "obst-I"; +chr2L refGene exon 115365 116182 . - . gene_id "CG13694"; transcript_id "NM_001272868"; exon_number "1"; exon_id "NM_001272868.1"; gene_name "CG13694"; +chr2L refGene 3UTR 115365 115712 . - . gene_id "CG13694"; transcript_id "NM_001272868"; exon_number "1"; exon_id "NM_001272868.1"; gene_name "CG13694"; +chr3L refGene exon 9420487 9421771 . + . gene_id "Shc"; transcript_id "NM_079944"; exon_number "2"; exon_id "NM_079944.2"; gene_name "Shc"; +chr3L refGene CDS 9420487 9421531 . + 1 gene_id "Shc"; transcript_id "NM_079944"; exon_number "2"; exon_id "NM_079944.2"; gene_name "Shc"; +chr3L refGene exon 9479548 9480455 . - . gene_id "pall"; transcript_id "NM_140068"; exon_number "1"; exon_id "NM_140068.1"; gene_name "pall"; +chr3L refGene 3UTR 9479548 9479722 . - . gene_id "pall"; transcript_id "NM_140068"; exon_number "1"; exon_id "NM_140068.1"; gene_name "pall"; +chr2R refGene exon 12115905 12117379 . + . gene_id "Tsf3"; transcript_id "NM_079035"; exon_number "4"; exon_id "NM_079035.4"; gene_name "Tsf3"; +chr2R refGene CDS 12115905 12117281 . + 0 gene_id "Tsf3"; transcript_id "NM_079035"; exon_number "4"; exon_id "NM_079035.4"; gene_name "Tsf3"; +chr2R refGene exon 10766861 10767682 . - . gene_id "Cyp6a9"; transcript_id "NM_079024"; exon_number "1"; exon_id "NM_079024.1"; gene_name "Cyp6a9"; +chr2R refGene 3UTR 10766861 10767263 . - . gene_id "Cyp6a9"; transcript_id "NM_079024"; exon_number "1"; exon_id "NM_079024.1"; gene_name "Cyp6a9"; +chr3L refGene exon 6952240 6952686 . + . gene_id "Surf1"; transcript_id "NM_080019"; exon_number "4"; exon_id "NM_080019.4"; gene_name "Surf1"; +chr3L refGene 3UTR 6952622 6952686 . + . gene_id "Surf1"; transcript_id "NM_080019"; exon_number "4"; exon_id "NM_080019.4"; gene_name "Surf1"; +chr3L refGene exon 9363295 9363802 . - . gene_id "Fdxh"; transcript_id "NM_079269"; exon_number "1"; exon_id "NM_079269.1"; gene_name "Fdxh"; +chr3L refGene 3UTR 9363295 9363450 . - . gene_id "Fdxh"; transcript_id "NM_079269"; exon_number "1"; exon_id "NM_079269.1"; gene_name "Fdxh"; +chr2R refGene exon 20916469 20917609 . + . gene_id "uzip"; transcript_id "NM_079137"; exon_number "5"; exon_id "NM_079137.5"; gene_name "uzip"; +chr2R refGene CDS 20916469 20916873 . + 0 gene_id "uzip"; transcript_id "NM_079137"; exon_number "5"; exon_id "NM_079137.5"; gene_name "uzip"; +chr2R refGene exon 19415328 19415963 . - . gene_id "bw"; transcript_id "NM_079100"; exon_number "1"; exon_id "NM_079100.1"; gene_name "bw"; +chr2R refGene 3UTR 19415328 19415775 . - . gene_id "bw"; transcript_id "NM_079100"; exon_number "1"; exon_id "NM_079100.1"; gene_name "bw"; +chrX refGene exon 12989478 12989770 . + . gene_id "CG2200"; transcript_id "NM_132624"; exon_number "3"; exon_id "NM_132624.3"; gene_name "CG2200"; +chrX refGene 3UTR 12989539 12989770 . + . gene_id "CG2200"; transcript_id "NM_132624"; exon_number "3"; exon_id "NM_132624.3"; gene_name "CG2200"; +chrX refGene exon 9977415 9978875 . + . gene_id "CG2972"; transcript_id "NM_132375"; exon_number "2"; exon_id "NM_132375.2"; gene_name "CG2972"; +chrX refGene CDS 9977415 9978755 . + 0 gene_id "CG2972"; transcript_id "NM_132375"; exon_number "2"; exon_id "NM_132375.2"; gene_name "CG2972"; +chrX refGene exon 8329051 8330244 . - . gene_id "CG12125"; transcript_id "NM_132248"; exon_number "2"; exon_id "NM_132248.2"; gene_name "CG12125"; +chrX refGene CDS 8329051 8330244 . - 0 gene_id "CG12125"; transcript_id "NM_132248"; exon_number "2"; exon_id "NM_132248.2"; gene_name "CG12125"; +chrX refGene exon 8292973 8294036 . + . gene_id "CG10555"; transcript_id "NM_132246"; exon_number "1"; exon_id "NM_132246.1"; gene_name "CG10555"; +chrX refGene 5UTR 8292973 8293427 . + . gene_id "CG10555"; transcript_id "NM_132246"; exon_number "1"; exon_id "NM_132246.1"; gene_name "CG10555"; +chrX refGene exon 7810988 7811478 . + . gene_id "snz"; transcript_id "NM_132193"; exon_number "11"; exon_id "NM_132193.11"; gene_name "snz"; +chrX refGene CDS 7810988 7811353 . + 0 gene_id "snz"; transcript_id "NM_132193"; exon_number "11"; exon_id "NM_132193.11"; gene_name "snz"; +chrX refGene exon 5211462 5213104 . + . gene_id "Sas10"; transcript_id "NM_131987"; exon_number "1"; exon_id "NM_131987.1"; gene_name "Sas10"; +chrX refGene 3UTR 5212824 5213104 . + . gene_id "Sas10"; transcript_id "NM_131987"; exon_number "1"; exon_id "NM_131987.1"; gene_name "Sas10"; +chrX refGene exon 4891572 4892219 . + . gene_id "CG12680"; transcript_id "NM_131973"; exon_number "1"; exon_id "NM_131973.1"; gene_name "CG12680"; +chrX refGene CDS 4891572 4892216 . + 0 gene_id "CG12680"; transcript_id "NM_131973"; exon_number "1"; exon_id "NM_131973.1"; gene_name "CG12680"; +chrX refGene exon 822831 824131 . - . gene_id "CG3708"; transcript_id "NM_130515"; exon_number "1"; exon_id "NM_130515.1"; gene_name "CG3708"; +chrX refGene 3UTR 822831 822928 . - . gene_id "CG3708"; transcript_id "NM_130515"; exon_number "1"; exon_id "NM_130515.1"; gene_name "CG3708"; +chr2L refGene exon 10324379 10324990 . + . gene_id "CG4995"; transcript_id "NM_001273396"; exon_number "4"; exon_id "NM_001273396.4"; gene_name "CG4995"; +chr2L refGene CDS 10324379 10324962 . + 2 gene_id "CG4995"; transcript_id "NM_001273396"; exon_number "4"; exon_id "NM_001273396.4"; gene_name "CG4995"; +chr2L refGene 3UTR 10324966 10324990 . + . gene_id "CG4995"; transcript_id "NM_001273396"; exon_number "4"; exon_id "NM_001273396.4"; gene_name "CG4995"; +chr2L refGene stop_codon 10324963 10324965 . + 0 gene_id "CG4995"; transcript_id "NM_001273396"; exon_number "1"; exon_id "NM_001273396.1"; gene_name "CG4995"; +chr2R refGene exon 12953476 12954959 . - . gene_id "CG30460"; transcript_id "NM_001144214"; exon_number "1"; exon_id "NM_001144214.1"; gene_name "CG30460"; +chr2R refGene 3UTR 12953476 12954286 . - . gene_id "CG30460"; transcript_id "NM_001144214"; exon_number "1"; exon_id "NM_001144214.1"; gene_name "CG30460"; +chr2R refGene exon 12953476 12954959 . - . gene_id "CG30460"; transcript_id "NM_001144213"; exon_number "1"; exon_id "NM_001144213.1"; gene_name "CG30460"; +chr2R refGene 3UTR 12953476 12954286 . - . gene_id "CG30460"; transcript_id "NM_001144213"; exon_number "1"; exon_id "NM_001144213.1"; gene_name "CG30460"; +chr3R refGene exon 7790396 7791208 . - . gene_id "CG12213"; transcript_id "NM_001104284"; exon_number "1"; exon_id "NM_001104284.1"; gene_name "CG12213"; +chr3R refGene 3UTR 7790396 7791146 . - . gene_id "CG12213"; transcript_id "NM_001104284"; exon_number "1"; exon_id "NM_001104284.1"; gene_name "CG12213"; +chr3R refGene exon 7790396 7791208 . - . gene_id "CG12213"; transcript_id "NM_169442"; exon_number "1"; exon_id "NM_169442.1"; gene_name "CG12213"; +chr3R refGene 3UTR 7790396 7791146 . - . gene_id "CG12213"; transcript_id "NM_169442"; exon_number "1"; exon_id "NM_169442.1"; gene_name "CG12213"; +chr3R refGene exon 7790396 7791208 . - . gene_id "CG12213"; transcript_id "NM_001275560"; exon_number "1"; exon_id "NM_001275560.1"; gene_name "CG12213"; +chr3R refGene 3UTR 7790396 7791146 . - . gene_id "CG12213"; transcript_id "NM_001275560"; exon_number "1"; exon_id "NM_001275560.1"; gene_name "CG12213"; +chr2L refGene exon 6674682 6675062 . - . gene_id "cort"; transcript_id "NM_001273215"; exon_number "1"; exon_id "NM_001273215.1"; gene_name "cort"; +chr2L refGene 3UTR 6674682 6674799 . - . gene_id "cort"; transcript_id "NM_001273215"; exon_number "1"; exon_id "NM_001273215.1"; gene_name "cort"; +chr2L refGene exon 6674682 6675062 . - . gene_id "cort"; transcript_id "NM_078770"; exon_number "1"; exon_id "NM_078770.1"; gene_name "cort"; +chr2L refGene 3UTR 6674682 6674799 . - . gene_id "cort"; transcript_id "NM_078770"; exon_number "1"; exon_id "NM_078770.1"; gene_name "cort"; +chr3R refGene exon 9860740 9861000 . - . gene_id "CG9922"; transcript_id "NM_001275627"; exon_number "1"; exon_id "NM_001275627.1"; gene_name "CG9922"; +chr3R refGene 3UTR 9860740 9860901 . - . gene_id "CG9922"; transcript_id "NM_001275627"; exon_number "1"; exon_id "NM_001275627.1"; gene_name "CG9922"; +chr3L refGene exon 18605667 18605863 . + . gene_id "CG32199"; transcript_id "NM_168770"; exon_number "3"; exon_id "NM_168770.3"; gene_name "CG32199"; +chr3L refGene CDS 18605667 18605863 . + 1 gene_id "CG32199"; transcript_id "NM_168770"; exon_number "3"; exon_id "NM_168770.3"; gene_name "CG32199"; +chr3R refGene exon 9860740 9861000 . - . gene_id "CG9922"; transcript_id "NM_142072"; exon_number "1"; exon_id "NM_142072.1"; gene_name "CG9922"; +chr3R refGene 3UTR 9860740 9860901 . - . gene_id "CG9922"; transcript_id "NM_142072"; exon_number "1"; exon_id "NM_142072.1"; gene_name "CG9922"; +chr3R refGene exon 1295185 1296181 . - . gene_id "mRpL44"; transcript_id "NM_141284"; exon_number "1"; exon_id "NM_141284.1"; gene_name "mRpL44"; +chr3R refGene 3UTR 1295185 1295282 . - . gene_id "mRpL44"; transcript_id "NM_141284"; exon_number "1"; exon_id "NM_141284.1"; gene_name "mRpL44"; +chr3L refGene exon 8233400 8233701 . - . gene_id "CG7213"; transcript_id "NM_139938"; exon_number "4"; exon_id "NM_139938.4"; gene_name "CG7213"; +chr3L refGene CDS 8233400 8233577 . - 0 gene_id "CG7213"; transcript_id "NM_139938"; exon_number "4"; exon_id "NM_139938.4"; gene_name "CG7213"; +chr3L refGene exon 19538704 19539064 . + . gene_id "Rcd7"; transcript_id "NM_140868"; exon_number "1"; exon_id "NM_140868.1"; gene_name "Rcd7"; +chr3L refGene CDS 19538784 19539064 . + 0 gene_id "Rcd7"; transcript_id "NM_140868"; exon_number "1"; exon_id "NM_140868.1"; gene_name "Rcd7"; +chr3L refGene exon 6964679 6965329 . - . gene_id "CG10063"; transcript_id "NM_139811"; exon_number "1"; exon_id "NM_139811.1"; gene_name "CG10063"; +chr3L refGene 3UTR 6964679 6964757 . - . gene_id "CG10063"; transcript_id "NM_139811"; exon_number "1"; exon_id "NM_139811.1"; gene_name "CG10063"; +chr3L refGene exon 17901685 17902783 . + . gene_id "CG14353"; transcript_id "NM_140768"; exon_number "2"; exon_id "NM_140768.2"; gene_name "CG14353"; +chr3L refGene 3UTR 17902538 17902783 . + . gene_id "CG14353"; transcript_id "NM_140768"; exon_number "2"; exon_id "NM_140768.2"; gene_name "CG14353"; +chr3L refGene exon 5805165 5805328 . + . gene_id "CG5537"; transcript_id "NM_139733"; exon_number "3"; exon_id "NM_139733.3"; gene_name "CG5537"; +chr3L refGene 3UTR 5805165 5805328 . + . gene_id "CG5537"; transcript_id "NM_139733"; exon_number "3"; exon_id "NM_139733.3"; gene_name "CG5537"; +chr3L refGene exon 5760117 5761233 . - . gene_id "Ppat-Dpck"; transcript_id "NM_139728"; exon_number "1"; exon_id "NM_139728.1"; gene_name "Ppat-Dpck"; +chr3L refGene 3UTR 5760117 5760235 . - . gene_id "Ppat-Dpck"; transcript_id "NM_139728"; exon_number "1"; exon_id "NM_139728.1"; gene_name "Ppat-Dpck"; +chr3R refGene exon 1418969 1420421 . + . gene_id "Vha26"; transcript_id "NM_079513"; exon_number "5"; exon_id "NM_079513.5"; gene_name "Vha26"; +chr3R refGene 3UTR 1419077 1420421 . + . gene_id "Vha26"; transcript_id "NM_079513"; exon_number "5"; exon_id "NM_079513.5"; gene_name "Vha26"; +chr3R refGene exon 1418969 1420421 . + . gene_id "Vha26"; transcript_id "NM_169073"; exon_number "4"; exon_id "NM_169073.4"; gene_name "Vha26"; +chr3R refGene 3UTR 1419077 1420421 . + . gene_id "Vha26"; transcript_id "NM_169073"; exon_number "4"; exon_id "NM_169073.4"; gene_name "Vha26"; +chr2R refGene exon 11427059 11427908 . - . gene_id "CG8187"; transcript_id "NM_137201"; exon_number "1"; exon_id "NM_137201.1"; gene_name "CG8187"; +chr2R refGene 3UTR 11427059 11427534 . - . gene_id "CG8187"; transcript_id "NM_137201"; exon_number "1"; exon_id "NM_137201.1"; gene_name "CG8187"; +chr2L refGene exon 8305586 8306741 . + . gene_id "CG7840"; transcript_id "NM_135359"; exon_number "1"; exon_id "NM_135359.1"; gene_name "CG7840"; +chr2L refGene 3UTR 8306666 8306741 . + . gene_id "CG7840"; transcript_id "NM_135359"; exon_number "1"; exon_id "NM_135359.1"; gene_name "CG7840"; +chr2L refGene exon 9787352 9788499 . + . gene_id "IP3K1"; transcript_id "NM_135469"; exon_number "4"; exon_id "NM_135469.4"; gene_name "IP3K1"; +chr2L refGene CDS 9787352 9788168 . + 1 gene_id "IP3K1"; transcript_id "NM_135469"; exon_number "4"; exon_id "NM_135469.4"; gene_name "IP3K1"; +chr2L refGene exon 9961018 9962104 . + . gene_id "CR43683"; transcript_id "NR_073752"; exon_number "1"; exon_id "NR_073752.1"; gene_name "CR43683"; +chr2L refGene exon 4446670 4447851 . - . gene_id "MFS18"; transcript_id "NM_134991"; exon_number "1"; exon_id "NM_134991.1"; gene_name "MFS18"; +chr2L refGene 3UTR 4446670 4446987 . - . gene_id "MFS18"; transcript_id "NM_134991"; exon_number "1"; exon_id "NM_134991.1"; gene_name "MFS18"; +chr2L refGene exon 4461657 4462563 . - . gene_id "CG15443"; transcript_id "NM_001273100"; exon_number "1"; exon_id "NM_001273100.1"; gene_name "CG15443"; +chr2L refGene 3UTR 4461657 4461823 . - . gene_id "CG15443"; transcript_id "NM_001273100"; exon_number "1"; exon_id "NM_001273100.1"; gene_name "CG15443"; +chr2L refGene exon 21159272 21160783 . + . gene_id "CG9248"; transcript_id "NM_165356"; exon_number "2"; exon_id "NM_165356.2"; gene_name "CG9248"; +chr2L refGene 3UTR 21160568 21160783 . + . gene_id "CG9248"; transcript_id "NM_165356"; exon_number "2"; exon_id "NM_165356.2"; gene_name "CG9248"; +chr2L refGene exon 20829608 20830073 . + . gene_id "CG31673"; transcript_id "NM_165346"; exon_number "1"; exon_id "NM_165346.1"; gene_name "CG31673"; +chr2L refGene CDS 20829670 20830073 . + 0 gene_id "CG31673"; transcript_id "NM_165346"; exon_number "1"; exon_id "NM_165346.1"; gene_name "CG31673"; +chr2L refGene exon 18133588 18134826 . - . gene_id "kel"; transcript_id "NM_165242"; exon_number "4"; exon_id "NM_165242.4"; gene_name "kel"; +chr2L refGene CDS 18133617 18134826 . - 1 gene_id "kel"; transcript_id "NM_165242"; exon_number "4"; exon_id "NM_165242.4"; gene_name "kel"; +chr2R refGene exon 19918493 19918725 . - . gene_id "CG30172"; transcript_id "NM_166649"; exon_number "2"; exon_id "NM_166649.2"; gene_name "CG30172"; +chr2R refGene CDS 19918493 19918688 . - 0 gene_id "CG30172"; transcript_id "NM_166649"; exon_number "2"; exon_id "NM_166649.2"; gene_name "CG30172"; +chrX refGene exon 8916051 8916272 . + . gene_id "rdgA"; transcript_id "NM_001201636"; exon_number "12"; exon_id "NM_001201636.12"; gene_name "rdgA"; +chrX refGene CDS 8916051 8916272 . + 2 gene_id "rdgA"; transcript_id "NM_001201636"; exon_number "12"; exon_id "NM_001201636.12"; gene_name "rdgA"; +chrX refGene exon 8916051 8916272 . + . gene_id "rdgA"; transcript_id "NM_001201635"; exon_number "12"; exon_id "NM_001201635.12"; gene_name "rdgA"; +chrX refGene CDS 8916051 8916272 . + 2 gene_id "rdgA"; transcript_id "NM_001201635"; exon_number "12"; exon_id "NM_001201635.12"; gene_name "rdgA"; +chr3L refGene exon 11683326 11683412 . - . gene_id "pallidin"; transcript_id "NM_001169948"; exon_number "2"; exon_id "NM_001169948.2"; gene_name "pallidin"; +chr3L refGene 3UTR 11683326 11683412 . - . gene_id "pallidin"; transcript_id "NM_001169948"; exon_number "2"; exon_id "NM_001169948.2"; gene_name "pallidin"; +chr3R refGene exon 9950148 9950584 . - . gene_id "140up"; transcript_id "NM_057603"; exon_number "1"; exon_id "NM_057603.1"; gene_name "140up"; +chr3R refGene 3UTR 9950148 9950226 . - . gene_id "140up"; transcript_id "NM_057603"; exon_number "1"; exon_id "NM_057603.1"; gene_name "140up"; +chr3L refGene exon 7233144 7233345 . + . gene_id "BHD"; transcript_id "NM_139833"; exon_number "3"; exon_id "NM_139833.3"; gene_name "BHD"; +chr3L refGene 3UTR 7233265 7233345 . + . gene_id "BHD"; transcript_id "NM_139833"; exon_number "3"; exon_id "NM_139833.3"; gene_name "BHD"; +chr3R refGene exon 18217911 18219247 . - . gene_id "CG13857"; transcript_id "NM_142778"; exon_number "1"; exon_id "NM_142778.1"; gene_name "CG13857"; +chr3R refGene 3UTR 18217911 18218211 . - . gene_id "CG13857"; transcript_id "NM_142778"; exon_number "1"; exon_id "NM_142778.1"; gene_name "CG13857"; +chr3R refGene exon 16416746 16417333 . - . gene_id "CG4159"; transcript_id "NM_142642"; exon_number "1"; exon_id "NM_142642.1"; gene_name "CG4159"; +chr3R refGene 3UTR 16416746 16416807 . - . gene_id "CG4159"; transcript_id "NM_142642"; exon_number "1"; exon_id "NM_142642.1"; gene_name "CG4159"; +chr3R refGene exon 14985332 14985600 . - . gene_id "CG11779"; transcript_id "NM_142529"; exon_number "4"; exon_id "NM_142529.4"; gene_name "CG11779"; +chr3R refGene 5UTR 14985428 14985600 . - . gene_id "CG11779"; transcript_id "NM_142529"; exon_number "4"; exon_id "NM_142529.4"; gene_name "CG11779"; +chr3R refGene exon 13621717 13622039 . + . gene_id "CG7713"; transcript_id "NM_142398"; exon_number "5"; exon_id "NM_142398.5"; gene_name "CG7713"; +chr3R refGene 3UTR 13621801 13622039 . + . gene_id "CG7713"; transcript_id "NM_142398"; exon_number "5"; exon_id "NM_142398.5"; gene_name "CG7713"; +chr3R refGene exon 12149648 12150850 . + . gene_id "CG6901"; transcript_id "NM_142274"; exon_number "3"; exon_id "NM_142274.3"; gene_name "CG6901"; +chr3R refGene CDS 12149648 12150772 . + 0 gene_id "CG6901"; transcript_id "NM_142274"; exon_number "3"; exon_id "NM_142274.3"; gene_name "CG6901"; +chr3L refGene exon 259043 259913 . - . gene_id "Tudor-SN"; transcript_id "NM_001274266"; exon_number "1"; exon_id "NM_001274266.1"; gene_name "Tudor-SN"; +chr3L refGene 3UTR 259043 259502 . - . gene_id "Tudor-SN"; transcript_id "NM_001274266"; exon_number "1"; exon_id "NM_001274266.1"; gene_name "Tudor-SN"; +chr3L refGene exon 260311 261746 . - . gene_id "Tudor-SN"; transcript_id "NM_001274266"; exon_number "2"; exon_id "NM_001274266.2"; gene_name "Tudor-SN"; +chr3L refGene CDS 260311 261746 . - 2 gene_id "Tudor-SN"; transcript_id "NM_001274266"; exon_number "2"; exon_id "NM_001274266.2"; gene_name "Tudor-SN"; +chr3L refGene exon 260311 261746 . - . gene_id "Tudor-SN"; transcript_id "NM_138177"; exon_number "2"; exon_id "NM_138177.2"; gene_name "Tudor-SN"; +chr3L refGene CDS 260311 261746 . - 2 gene_id "Tudor-SN"; transcript_id "NM_138177"; exon_number "2"; exon_id "NM_138177.2"; gene_name "Tudor-SN"; +chr3L refGene exon 16837307 16837685 . + . gene_id "TSG101"; transcript_id "NM_079396"; exon_number "7"; exon_id "NM_079396.7"; gene_name "TSG101"; +chr3L refGene 3UTR 16837494 16837685 . + . gene_id "TSG101"; transcript_id "NM_079396"; exon_number "7"; exon_id "NM_079396.7"; gene_name "TSG101"; +chr3L refGene exon 21722775 21723554 . - . gene_id "CG14570"; transcript_id "NM_141096"; exon_number "1"; exon_id "NM_141096.1"; gene_name "CG14570"; +chr3L refGene 3UTR 21722775 21722841 . - . gene_id "CG14570"; transcript_id "NM_141096"; exon_number "1"; exon_id "NM_141096.1"; gene_name "CG14570"; +chr3L refGene exon 8124529 8125034 . - . gene_id "CG7504"; transcript_id "NM_001144435"; exon_number "1"; exon_id "NM_001144435.1"; gene_name "CG7504"; +chr3L refGene 3UTR 8124529 8124896 . - . gene_id "CG7504"; transcript_id "NM_001144435"; exon_number "1"; exon_id "NM_001144435.1"; gene_name "CG7504"; +chr3L refGene exon 8124529 8125034 . - . gene_id "CG7504"; transcript_id "NM_139920"; exon_number "1"; exon_id "NM_139920.1"; gene_name "CG7504"; +chr3L refGene 3UTR 8124529 8124896 . - . gene_id "CG7504"; transcript_id "NM_139920"; exon_number "1"; exon_id "NM_139920.1"; gene_name "CG7504"; +chr3L refGene exon 8188951 8189673 . + . gene_id "MED24"; transcript_id "NM_139928"; exon_number "7"; exon_id "NM_139928.7"; gene_name "MED24"; +chr3L refGene 3UTR 8189576 8189673 . + . gene_id "MED24"; transcript_id "NM_139928"; exon_number "7"; exon_id "NM_139928.7"; gene_name "MED24"; +chr3L refGene exon 16837668 16837962 . - . gene_id "CG9669"; transcript_id "NM_140668"; exon_number "1"; exon_id "NM_140668.1"; gene_name "CG9669"; +chr3L refGene 3UTR 16837668 16837724 . - . gene_id "CG9669"; transcript_id "NM_140668"; exon_number "1"; exon_id "NM_140668.1"; gene_name "CG9669"; +chr3L refGene exon 3897444 3897940 . - . gene_id "CG14980"; transcript_id "NM_139578"; exon_number "1"; exon_id "NM_139578.1"; gene_name "CG14980"; +chr3L refGene 3UTR 3897444 3897458 . - . gene_id "CG14980"; transcript_id "NM_139578"; exon_number "1"; exon_id "NM_139578.1"; gene_name "CG14980"; +chr3L refGene exon 2642184 2642887 . - . gene_id "CG14949"; transcript_id "NM_139477"; exon_number "1"; exon_id "NM_139477.1"; gene_name "CG14949"; +chr3L refGene CDS 2642416 2642887 . - 1 gene_id "CG14949"; transcript_id "NM_139477"; exon_number "1"; exon_id "NM_139477.1"; gene_name "CG14949"; +chr3L refGene exon 11683326 11683412 . - . gene_id "pallidin"; transcript_id "NM_140237"; exon_number "2"; exon_id "NM_140237.2"; gene_name "pallidin"; +chr3L refGene CDS 11683326 11683412 . - 0 gene_id "pallidin"; transcript_id "NM_140237"; exon_number "2"; exon_id "NM_140237.2"; gene_name "pallidin"; +chr2L refGene exon 10485538 10485790 . - . gene_id "CG7456"; transcript_id "NM_135569"; exon_number "1"; exon_id "NM_135569.1"; gene_name "CG7456"; +chr2L refGene CDS 10485751 10485790 . - 1 gene_id "CG7456"; transcript_id "NM_135569"; exon_number "1"; exon_id "NM_135569.1"; gene_name "CG7456"; +chr2L refGene exon 10981487 10982395 . + . gene_id "SCAR"; transcript_id "NM_001259037"; exon_number "6"; exon_id "NM_001259037.6"; gene_name "SCAR"; +chr2L refGene 3UTR 10981666 10982395 . + . gene_id "SCAR"; transcript_id "NM_001259037"; exon_number "6"; exon_id "NM_001259037.6"; gene_name "SCAR"; +chr2L refGene exon 10981487 10982395 . + . gene_id "SCAR"; transcript_id "NM_001259038"; exon_number "6"; exon_id "NM_001259038.6"; gene_name "SCAR"; +chr2L refGene 3UTR 10981666 10982395 . + . gene_id "SCAR"; transcript_id "NM_001259038"; exon_number "6"; exon_id "NM_001259038.6"; gene_name "SCAR"; +chr2L refGene exon 10981487 10982395 . + . gene_id "SCAR"; transcript_id "NM_001273439"; exon_number "7"; exon_id "NM_001273439.7"; gene_name "SCAR"; +chr2L refGene 3UTR 10981666 10982395 . + . gene_id "SCAR"; transcript_id "NM_001273439"; exon_number "7"; exon_id "NM_001273439.7"; gene_name "SCAR"; +chr2L refGene exon 10981487 10982395 . + . gene_id "SCAR"; transcript_id "NM_001273440"; exon_number "5"; exon_id "NM_001273440.5"; gene_name "SCAR"; +chr2L refGene 3UTR 10981723 10982395 . + . gene_id "SCAR"; transcript_id "NM_001273440"; exon_number "5"; exon_id "NM_001273440.5"; gene_name "SCAR"; +chr2L refGene exon 10981487 10982395 . + . gene_id "SCAR"; transcript_id "NM_135633"; exon_number "5"; exon_id "NM_135633.5"; gene_name "SCAR"; +chr2L refGene 3UTR 10981666 10982395 . + . gene_id "SCAR"; transcript_id "NM_135633"; exon_number "5"; exon_id "NM_135633.5"; gene_name "SCAR"; +chr2L refGene exon 1132332 1134098 . - . gene_id "Iris"; transcript_id "NM_134726"; exon_number "1"; exon_id "NM_134726.1"; gene_name "Iris"; +chr2L refGene 3UTR 1132332 1132477 . - . gene_id "Iris"; transcript_id "NM_134726"; exon_number "1"; exon_id "NM_134726.1"; gene_name "Iris"; +chr2L refGene exon 10324379 10324990 . + . gene_id "CG4995"; transcript_id "NM_164915"; exon_number "4"; exon_id "NM_164915.4"; gene_name "CG4995"; +chr2L refGene CDS 10324379 10324962 . + 2 gene_id "CG4995"; transcript_id "NM_164915"; exon_number "4"; exon_id "NM_164915.4"; gene_name "CG4995"; +chr2L refGene 3UTR 10324966 10324990 . + . gene_id "CG4995"; transcript_id "NM_164915"; exon_number "4"; exon_id "NM_164915.4"; gene_name "CG4995"; +chr2L refGene stop_codon 10324963 10324965 . + 0 gene_id "CG4995"; transcript_id "NM_164915"; exon_number "1"; exon_id "NM_164915.1"; gene_name "CG4995"; +chr2L refGene exon 10324379 10324990 . + . gene_id "CG4995"; transcript_id "NM_164914"; exon_number "5"; exon_id "NM_164914.5"; gene_name "CG4995"; +chr2L refGene CDS 10324379 10324962 . + 2 gene_id "CG4995"; transcript_id "NM_164914"; exon_number "5"; exon_id "NM_164914.5"; gene_name "CG4995"; +chr2L refGene 3UTR 10324966 10324990 . + . gene_id "CG4995"; transcript_id "NM_164914"; exon_number "5"; exon_id "NM_164914.5"; gene_name "CG4995"; +chr2L refGene stop_codon 10324963 10324965 . + 0 gene_id "CG4995"; transcript_id "NM_164914"; exon_number "1"; exon_id "NM_164914.1"; gene_name "CG4995"; +chr3R refGene exon 4576502 4578463 . - . gene_id "CG34135"; transcript_id "NM_001275456"; exon_number "2"; exon_id "NM_001275456.2"; gene_name "CG34135"; +chr3R refGene 5UTR 4576638 4578463 . - . gene_id "CG34135"; transcript_id "NM_001275456"; exon_number "2"; exon_id "NM_001275456.2"; gene_name "CG34135"; +chr3R refGene exon 4576502 4580132 . - . gene_id "CG11768"; transcript_id "NM_001260065"; exon_number "2"; exon_id "NM_001260065.2"; gene_name "CG11768"; +chr3R refGene 3UTR 4576502 4579830 . - . gene_id "CG11768"; transcript_id "NM_001260065"; exon_number "2"; exon_id "NM_001260065.2"; gene_name "CG11768"; +chr3R refGene exon 4538628 4541390 . - . gene_id "Cks85A"; transcript_id "NM_001275454"; exon_number "1"; exon_id "NM_001275454.1"; gene_name "Cks85A"; +chr3R refGene 3UTR 4538628 4541158 . - . gene_id "Cks85A"; transcript_id "NM_001275454"; exon_number "1"; exon_id "NM_001275454.1"; gene_name "Cks85A"; +chr3R refGene exon 603219 604061 . - . gene_id "CG14655"; transcript_id "NM_141237"; exon_number "1"; exon_id "NM_141237.1"; gene_name "CG14655"; +chr3R refGene 3UTR 603219 603549 . - . gene_id "CG14655"; transcript_id "NM_141237"; exon_number "1"; exon_id "NM_141237.1"; gene_name "CG14655"; +chr3L refGene exon 16404102 16404939 . - . gene_id "fax"; transcript_id "NM_079382"; exon_number "5"; exon_id "NM_079382.5"; gene_name "fax"; +chr3L refGene CDS 16404102 16404518 . - 0 gene_id "fax"; transcript_id "NM_079382"; exon_number "5"; exon_id "NM_079382.5"; gene_name "fax"; +chr3L refGene exon 16404102 16404939 . - . gene_id "fax"; transcript_id "NM_001014587"; exon_number "5"; exon_id "NM_001014587.5"; gene_name "fax"; +chr3L refGene CDS 16404102 16404518 . - 0 gene_id "fax"; transcript_id "NM_001014587"; exon_number "5"; exon_id "NM_001014587.5"; gene_name "fax"; +chrX refGene exon 8916051 8916272 . + . gene_id "rdgA"; transcript_id "NM_001103446"; exon_number "11"; exon_id "NM_001103446.11"; gene_name "rdgA"; +chrX refGene CDS 8916051 8916272 . + 2 gene_id "rdgA"; transcript_id "NM_001103446"; exon_number "11"; exon_id "NM_001103446.11"; gene_name "rdgA"; +chr2L refGene exon 16305355 16305940 . + . gene_id "c(2)M"; transcript_id "NM_135944"; exon_number "8"; exon_id "NM_135944.8"; gene_name "c(2)M"; +chr2L refGene 3UTR 16305480 16305940 . + . gene_id "c(2)M"; transcript_id "NM_135944"; exon_number "8"; exon_id "NM_135944.8"; gene_name "c(2)M"; +chr3L refGene exon 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_001144486"; exon_number "2"; exon_id "NM_001144486.2"; gene_name "Taf4"; +chr3L refGene 5UTR 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_001144486"; exon_number "2"; exon_id "NM_001144486.2"; gene_name "Taf4"; +chr3L refGene exon 16106996 16107241 . + . gene_id "Taf4"; transcript_id "NM_001169982"; exon_number "2"; exon_id "NM_001169982.2"; gene_name "Taf4"; +chr3L refGene 5UTR 16106996 16107241 . + . gene_id "Taf4"; transcript_id "NM_001169982"; exon_number "2"; exon_id "NM_001169982.2"; gene_name "Taf4"; +chr3L refGene exon 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_001274998"; exon_number "2"; exon_id "NM_001274998.2"; gene_name "Taf4"; +chr3L refGene 5UTR 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_001274998"; exon_number "2"; exon_id "NM_001274998.2"; gene_name "Taf4"; +chr3L refGene exon 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_001274999"; exon_number "2"; exon_id "NM_001274999.2"; gene_name "Taf4"; +chr3L refGene 5UTR 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_001274999"; exon_number "2"; exon_id "NM_001274999.2"; gene_name "Taf4"; +chr3L refGene exon 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_176333"; exon_number "2"; exon_id "NM_176333.2"; gene_name "Taf4"; +chr3L refGene 5UTR 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_176333"; exon_number "2"; exon_id "NM_176333.2"; gene_name "Taf4"; +chr3L refGene exon 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_079378"; exon_number "2"; exon_id "NM_079378.2"; gene_name "Taf4"; +chr3L refGene 5UTR 16106985 16107241 . + . gene_id "Taf4"; transcript_id "NM_079378"; exon_number "2"; exon_id "NM_079378.2"; gene_name "Taf4"; +chr3L refGene exon 16106890 16107241 . + . gene_id "Taf4"; transcript_id "NM_168651"; exon_number "1"; exon_id "NM_168651.1"; gene_name "Taf4"; +chr3L refGene 5UTR 16106890 16107241 . + . gene_id "Taf4"; transcript_id "NM_168651"; exon_number "1"; exon_id "NM_168651.1"; gene_name "Taf4"; +chr3L refGene exon 19792378 19792432 . + . gene_id "Ir76a"; transcript_id "NM_001104177"; exon_number "1"; exon_id "NM_001104177.1"; gene_name "Ir76a"; +chr3L refGene CDS 19792378 19792432 . + 0 gene_id "Ir76a"; transcript_id "NM_001104177"; exon_number "1"; exon_id "NM_001104177.1"; gene_name "Ir76a"; +chr3R refGene exon 464266 464561 . - . gene_id "CG9775"; transcript_id "NM_169012"; exon_number "2"; exon_id "NM_169012.2"; gene_name "CG9775"; +chr3R refGene CDS 464266 464561 . - 1 gene_id "CG9775"; transcript_id "NM_169012"; exon_number "2"; exon_id "NM_169012.2"; gene_name "CG9775"; +chr3R refGene exon 463732 464561 . - . gene_id "CG9775"; transcript_id "NM_001170036"; exon_number "1"; exon_id "NM_001170036.1"; gene_name "CG9775"; +chr3R refGene CDS 464156 464561 . - 1 gene_id "CG9775"; transcript_id "NM_001170036"; exon_number "1"; exon_id "NM_001170036.1"; gene_name "CG9775"; +chr3R refGene exon 464266 464561 . - . gene_id "CG9775"; transcript_id "NM_141225"; exon_number "2"; exon_id "NM_141225.2"; gene_name "CG9775"; +chr3R refGene CDS 464266 464561 . - 1 gene_id "CG9775"; transcript_id "NM_141225"; exon_number "2"; exon_id "NM_141225.2"; gene_name "CG9775"; +chr3R refGene exon 464266 464561 . - . gene_id "CG9775"; transcript_id "NM_001275328"; exon_number "2"; exon_id "NM_001275328.2"; gene_name "CG9775"; +chr3R refGene CDS 464266 464561 . - 1 gene_id "CG9775"; transcript_id "NM_001275328"; exon_number "2"; exon_id "NM_001275328.2"; gene_name "CG9775"; +chr3L refGene exon 16096532 16097378 . - . gene_id "IntS9"; transcript_id "NM_140581"; exon_number "1"; exon_id "NM_140581.1"; gene_name "IntS9"; +chr3L refGene 3UTR 16096532 16096580 . - . gene_id "IntS9"; transcript_id "NM_140581"; exon_number "1"; exon_id "NM_140581.1"; gene_name "IntS9"; +chr3L refGene exon 15965259 15968196 . - . gene_id "brm"; transcript_id "NM_080498"; exon_number "3"; exon_id "NM_080498.3"; gene_name "brm"; +chr3L refGene CDS 15965259 15968196 . - 0 gene_id "brm"; transcript_id "NM_080498"; exon_number "3"; exon_id "NM_080498.3"; gene_name "brm"; +chr3L refGene exon 15965259 15968196 . - . gene_id "brm"; transcript_id "NM_168640"; exon_number "3"; exon_id "NM_168640.3"; gene_name "brm"; +chr3L refGene CDS 15965259 15968196 . - 0 gene_id "brm"; transcript_id "NM_168640"; exon_number "3"; exon_id "NM_168640.3"; gene_name "brm"; +chr3L refGene exon 15965259 15968196 . - . gene_id "brm"; transcript_id "NM_001274977"; exon_number "3"; exon_id "NM_001274977.3"; gene_name "brm"; +chr3L refGene CDS 15965259 15968196 . - 0 gene_id "brm"; transcript_id "NM_001274977"; exon_number "3"; exon_id "NM_001274977.3"; gene_name "brm"; +chr3L refGene exon 15965259 15968196 . - . gene_id "brm"; transcript_id "NM_001274978"; exon_number "3"; exon_id "NM_001274978.3"; gene_name "brm"; +chr3L refGene CDS 15965259 15968196 . - 0 gene_id "brm"; transcript_id "NM_001274978"; exon_number "3"; exon_id "NM_001274978.3"; gene_name "brm"; +chr3L refGene exon 15965259 15968196 . - . gene_id "brm"; transcript_id "NM_080497"; exon_number "3"; exon_id "NM_080497.3"; gene_name "brm"; +chr3L refGene CDS 15965259 15968196 . - 0 gene_id "brm"; transcript_id "NM_080497"; exon_number "3"; exon_id "NM_080497.3"; gene_name "brm"; +chr3L refGene exon 21190649 21190737 . - . gene_id "CG33054"; transcript_id "NM_176375"; exon_number "2"; exon_id "NM_176375.2"; gene_name "CG33054"; +chr3L refGene CDS 21190649 21190737 . - 0 gene_id "CG33054"; transcript_id "NM_176375"; exon_number "2"; exon_id "NM_176375.2"; gene_name "CG33054"; +chr3L refGene exon 21190511 21190737 . - . gene_id "CG33054"; transcript_id "NM_176376"; exon_number "1"; exon_id "NM_176376.1"; gene_name "CG33054"; +chr3L refGene CDS 21190585 21190737 . - 0 gene_id "CG33054"; transcript_id "NM_176376"; exon_number "1"; exon_id "NM_176376.1"; gene_name "CG33054"; +chr2L refGene exon 4973719 4973852 . - . gene_id "l(2)05714"; transcript_id "NM_001273133"; exon_number "3"; exon_id "NM_001273133.3"; gene_name "l(2)05714"; +chr2L refGene 5UTR 4973719 4973852 . - . gene_id "l(2)05714"; transcript_id "NM_001273133"; exon_number "3"; exon_id "NM_001273133.3"; gene_name "l(2)05714"; +chr2R refGene exon 10755738 10756067 . - . gene_id "Inr-a"; transcript_id "NM_001202002"; exon_number "8"; exon_id "NM_001202002.8"; gene_name "Inr-a"; +chr2R refGene CDS 10755738 10756067 . - 0 gene_id "Inr-a"; transcript_id "NM_001202002"; exon_number "8"; exon_id "NM_001202002.8"; gene_name "Inr-a"; +chr2L refGene exon 2155753 2156790 . + . gene_id "CG15382"; transcript_id "NM_134806"; exon_number "1"; exon_id "NM_134806.1"; gene_name "CG15382"; +chr2L refGene 3UTR 2156257 2156790 . + . gene_id "CG15382"; transcript_id "NM_134806"; exon_number "1"; exon_id "NM_134806.1"; gene_name "CG15382"; +chr2L refGene exon 2226753 2227305 . - . gene_id "CR44114"; transcript_id "NR_073695"; exon_number "1"; exon_id "NR_073695.1"; gene_name "CR44114"; +chr3L refGene exon 15553826 15555783 . - . gene_id "CG7739"; transcript_id "NM_140519"; exon_number "1"; exon_id "NM_140519.1"; gene_name "CG7739"; +chr3L refGene 3UTR 15553826 15554185 . - . gene_id "CG7739"; transcript_id "NM_140519"; exon_number "1"; exon_id "NM_140519.1"; gene_name "CG7739"; +chr2L refGene exon 13177150 13178978 . + . gene_id "CG5439"; transcript_id "NM_135763"; exon_number "1"; exon_id "NM_135763.1"; gene_name "CG5439"; +chr2L refGene 5UTR 13177150 13177250 . + . gene_id "CG5439"; transcript_id "NM_135763"; exon_number "1"; exon_id "NM_135763.1"; gene_name "CG5439"; +chr2L refGene CDS 13177251 13178810 . + 0 gene_id "CG5439"; transcript_id "NM_135763"; exon_number "1"; exon_id "NM_135763.1"; gene_name "CG5439"; +chr2L refGene start_codon 13177251 13177253 . + 0 gene_id "CG5439"; transcript_id "NM_135763"; exon_number "1"; exon_id "NM_135763.1"; gene_name "CG5439"; +chr3L refGene exon 8717967 8718160 . + . gene_id "CG6511"; transcript_id "NM_001274668"; exon_number "5"; exon_id "NM_001274668.5"; gene_name "CG6511"; +chr3L refGene CDS 8717967 8718160 . + 1 gene_id "CG6511"; transcript_id "NM_001274668"; exon_number "5"; exon_id "NM_001274668.5"; gene_name "CG6511"; +chr3L refGene exon 8718226 8719208 . + . gene_id "CG6511"; transcript_id "NM_001274668"; exon_number "6"; exon_id "NM_001274668.6"; gene_name "CG6511"; +chr3L refGene 3UTR 8718612 8719208 . + . gene_id "CG6511"; transcript_id "NM_001274668"; exon_number "6"; exon_id "NM_001274668.6"; gene_name "CG6511"; +chr3L refGene exon 8717967 8718160 . + . gene_id "CG6511"; transcript_id "NM_139995"; exon_number "5"; exon_id "NM_139995.5"; gene_name "CG6511"; +chr3L refGene CDS 8717967 8718160 . + 1 gene_id "CG6511"; transcript_id "NM_139995"; exon_number "5"; exon_id "NM_139995.5"; gene_name "CG6511"; +chr3L refGene exon 8718226 8719208 . + . gene_id "CG6511"; transcript_id "NM_139995"; exon_number "6"; exon_id "NM_139995.6"; gene_name "CG6511"; +chr3L refGene 3UTR 8718612 8719208 . + . gene_id "CG6511"; transcript_id "NM_139995"; exon_number "6"; exon_id "NM_139995.6"; gene_name "CG6511"; +chr3R refGene exon 8252776 8253599 . + . gene_id "Sas"; transcript_id "NM_141938"; exon_number "2"; exon_id "NM_141938.2"; gene_name "Sas"; +chr3R refGene 3UTR 8253559 8253599 . + . gene_id "Sas"; transcript_id "NM_141938"; exon_number "2"; exon_id "NM_141938.2"; gene_name "Sas"; +chr2R refGene exon 12953476 12954959 . - . gene_id "CG30460"; transcript_id "NM_001103885"; exon_number "1"; exon_id "NM_001103885.1"; gene_name "CG30460"; +chr2R refGene 3UTR 12953476 12954286 . - . gene_id "CG30460"; transcript_id "NM_001103885"; exon_number "1"; exon_id "NM_001103885.1"; gene_name "CG30460"; +chr3L refGene exon 14035548 14036786 . + . gene_id "Hsc70Cb"; transcript_id "NM_001274893"; exon_number "6"; exon_id "NM_001274893.6"; gene_name "Hsc70Cb"; +chr3L refGene 3UTR 14036172 14036786 . + . gene_id "Hsc70Cb"; transcript_id "NM_001274893"; exon_number "6"; exon_id "NM_001274893.6"; gene_name "Hsc70Cb"; +chr2R refGene exon 13748834 13749096 . + . gene_id "CG14490"; transcript_id "NM_137430"; exon_number "2"; exon_id "NM_137430.2"; gene_name "CG14490"; +chr2R refGene 3UTR 13749019 13749096 . + . gene_id "CG14490"; transcript_id "NM_137430"; exon_number "2"; exon_id "NM_137430.2"; gene_name "CG14490"; +chr3R refGene exon 8822404 8822647 . + . gene_id "CG7488"; transcript_id "NM_141991"; exon_number "2"; exon_id "NM_141991.2"; gene_name "CG7488"; +chr3R refGene 3UTR 8822592 8822647 . + . gene_id "CG7488"; transcript_id "NM_141991"; exon_number "2"; exon_id "NM_141991.2"; gene_name "CG7488"; +chr3L refGene exon 22858978 22859060 . + . gene_id "CG33170"; transcript_id "NM_001275295"; exon_number "3"; exon_id "NM_001275295.3"; gene_name "CG33170"; +chr3L refGene CDS 22858978 22859060 . + 0 gene_id "CG33170"; transcript_id "NM_001275295"; exon_number "3"; exon_id "NM_001275295.3"; gene_name "CG33170"; +chr3L refGene exon 5132719 5133573 . + . gene_id "CHMP2B"; transcript_id "NM_139690"; exon_number "1"; exon_id "NM_139690.1"; gene_name "CHMP2B"; +chr3L refGene 3UTR 5133484 5133573 . + . gene_id "CHMP2B"; transcript_id "NM_139690"; exon_number "1"; exon_id "NM_139690.1"; gene_name "CHMP2B"; +chr3L refGene exon 5359905 5360481 . + . gene_id "membrin"; transcript_id "NM_139703"; exon_number "2"; exon_id "NM_139703.2"; gene_name "membrin"; +chr3L refGene 3UTR 5360419 5360481 . + . gene_id "membrin"; transcript_id "NM_139703"; exon_number "2"; exon_id "NM_139703.2"; gene_name "membrin"; +chr3L refGene exon 12498474 12499587 . - . gene_id "CG10654"; transcript_id "NM_001274838"; exon_number "1"; exon_id "NM_001274838.1"; gene_name "CG10654"; +chr3L refGene 3UTR 12498474 12498909 . - . gene_id "CG10654"; transcript_id "NM_001274838"; exon_number "1"; exon_id "NM_001274838.1"; gene_name "CG10654"; +chr3L refGene CDS 12498913 12499587 . - 0 gene_id "CG10654"; transcript_id "NM_001274838"; exon_number "1"; exon_id "NM_001274838.1"; gene_name "CG10654"; +chr3L refGene stop_codon 12498910 12498912 . - 0 gene_id "CG10654"; transcript_id "NM_001274838"; exon_number "1"; exon_id "NM_001274838.1"; gene_name "CG10654"; +chr3L refGene exon 12498864 12499587 . - . gene_id "CG10654"; transcript_id "NM_140326"; exon_number "1"; exon_id "NM_140326.1"; gene_name "CG10654"; +chr3L refGene 3UTR 12498864 12498909 . - . gene_id "CG10654"; transcript_id "NM_140326"; exon_number "1"; exon_id "NM_140326.1"; gene_name "CG10654"; +chr3L refGene CDS 12498913 12499587 . - 0 gene_id "CG10654"; transcript_id "NM_140326"; exon_number "1"; exon_id "NM_140326.1"; gene_name "CG10654"; +chr3L refGene stop_codon 12498910 12498912 . - 0 gene_id "CG10654"; transcript_id "NM_140326"; exon_number "1"; exon_id "NM_140326.1"; gene_name "CG10654"; +chr3L refGene exon 9363295 9363802 . - . gene_id "Fdxh"; transcript_id "NM_001202146"; exon_number "1"; exon_id "NM_001202146.1"; gene_name "Fdxh"; +chr3L refGene 3UTR 9363295 9363450 . - . gene_id "Fdxh"; transcript_id "NM_001202146"; exon_number "1"; exon_id "NM_001202146.1"; gene_name "Fdxh"; +chr3L refGene exon 7659266 7686955 . - . gene_id "Ank2"; transcript_id "NM_001202141"; exon_number "6"; exon_id "NM_001202141.6"; gene_name "Ank2"; +chr3L refGene CDS 7659266 7686955 . - 2 gene_id "Ank2"; transcript_id "NM_001202141"; exon_number "6"; exon_id "NM_001202141.6"; gene_name "Ank2"; +chr3L refGene exon 12395395 12397390 . - . gene_id "CG32103"; transcript_id "NM_206345"; exon_number "1"; exon_id "NM_206345.1"; gene_name "CG32103"; +chr3L refGene 3UTR 12395395 12397154 . - . gene_id "CG32103"; transcript_id "NM_206345"; exon_number "1"; exon_id "NM_206345.1"; gene_name "CG32103"; +chr3L refGene exon 19259573 19261560 . - . gene_id "CG9629"; transcript_id "NM_140842"; exon_number "1"; exon_id "NM_140842.1"; gene_name "CG9629"; +chr3L refGene 3UTR 19259573 19259936 . - . gene_id "CG9629"; transcript_id "NM_140842"; exon_number "1"; exon_id "NM_140842.1"; gene_name "CG9629"; +chr3L refGene exon 5805165 5805328 . + . gene_id "CG5537"; transcript_id "NM_001274522"; exon_number "3"; exon_id "NM_001274522.3"; gene_name "CG5537"; +chr3L refGene 3UTR 5805176 5805328 . + . gene_id "CG5537"; transcript_id "NM_001274522"; exon_number "3"; exon_id "NM_001274522.3"; gene_name "CG5537"; +chr3L refGene exon 5804486 5805328 . + . gene_id "CG5537"; transcript_id "NM_001274523"; exon_number "2"; exon_id "NM_001274523.2"; gene_name "CG5537"; +chr3L refGene 3UTR 5805030 5805328 . + . gene_id "CG5537"; transcript_id "NM_001274523"; exon_number "2"; exon_id "NM_001274523.2"; gene_name "CG5537"; +chr3L refGene exon 6584579 6587040 . + . gene_id "CG18769"; transcript_id "NM_144449"; exon_number "8"; exon_id "NM_144449.8"; gene_name "CG18769"; +chr3L refGene 3UTR 6584822 6587040 . + . gene_id "CG18769"; transcript_id "NM_144449"; exon_number "8"; exon_id "NM_144449.8"; gene_name "CG18769"; +chr3RHet refGene exon 1896444 1898929 . - . gene_id "Alg-2"; transcript_id "NM_001015400"; exon_number "1"; exon_id "NM_001015400.1"; gene_name "Alg-2"; +chr3RHet refGene 3UTR 1896444 1898328 . - . gene_id "Alg-2"; transcript_id "NM_001015400"; exon_number "1"; exon_id "NM_001015400.1"; gene_name "Alg-2"; +chr2LHet refGene exon 20723 21383 . - . gene_id "CG12567"; transcript_id "NM_001015383"; exon_number "2"; exon_id "NM_001015383.2"; gene_name "CG12567"; +chr2LHet refGene CDS 20723 21383 . - 0 gene_id "CG12567"; transcript_id "NM_001015383"; exon_number "2"; exon_id "NM_001015383.2"; gene_name "CG12567"; +chr2L refGene exon 18133588 18134826 . - . gene_id "kel"; transcript_id "NM_057241"; exon_number "4"; exon_id "NM_057241.4"; gene_name "kel"; +chr2L refGene CDS 18133588 18134826 . - 1 gene_id "kel"; transcript_id "NM_057241"; exon_number "4"; exon_id "NM_057241.4"; gene_name "kel"; +chr2R refGene exon 5475458 5475835 . - . gene_id "clos"; transcript_id "NM_001103776"; exon_number "1"; exon_id "NM_001103776.1"; gene_name "clos"; +chr2R refGene 3UTR 5475458 5475510 . - . gene_id "clos"; transcript_id "NM_001103776"; exon_number "1"; exon_id "NM_001103776.1"; gene_name "clos"; +chr3L refGene exon 9128809 9129001 . - . gene_id "Use1"; transcript_id "NM_140032"; exon_number "1"; exon_id "NM_140032.1"; gene_name "Use1"; +chr3L refGene 3UTR 9128809 9128957 . - . gene_id "Use1"; transcript_id "NM_140032"; exon_number "1"; exon_id "NM_140032.1"; gene_name "Use1"; +chr2R refGene exon 19696768 19698907 . + . gene_id "CG5543"; transcript_id "NM_137988"; exon_number "1"; exon_id "NM_137988.1"; gene_name "CG5543"; +chr2R refGene 3UTR 19698850 19698907 . + . gene_id "CG5543"; transcript_id "NM_137988"; exon_number "1"; exon_id "NM_137988.1"; gene_name "CG5543"; +chrX refGene exon 14476169 14476388 . - . gene_id "mRpS25"; transcript_id "NM_078598"; exon_number "1"; exon_id "NM_078598.1"; gene_name "mRpS25"; +chrX refGene 3UTR 14476169 14476216 . - . gene_id "mRpS25"; transcript_id "NM_078598"; exon_number "1"; exon_id "NM_078598.1"; gene_name "mRpS25"; +chrX refGene exon 8916051 8916272 . + . gene_id "rdgA"; transcript_id "NM_078537"; exon_number "12"; exon_id "NM_078537.12"; gene_name "rdgA"; +chrX refGene CDS 8916051 8916272 . + 2 gene_id "rdgA"; transcript_id "NM_078537"; exon_number "12"; exon_id "NM_078537.12"; gene_name "rdgA"; +chrX refGene exon 15360217 15361300 . - . gene_id "CG15642"; transcript_id "NM_132800"; exon_number "1"; exon_id "NM_132800.1"; gene_name "CG15642"; +chrX refGene 3UTR 15360217 15360865 . - . gene_id "CG15642"; transcript_id "NM_132800"; exon_number "1"; exon_id "NM_132800.1"; gene_name "CG15642"; +chrX refGene exon 14118058 14118761 . + . gene_id "l(1)G0007"; transcript_id "NM_132719"; exon_number "4"; exon_id "NM_132719.4"; gene_name "l(1)G0007"; +chrX refGene 3UTR 14118656 14118761 . + . gene_id "l(1)G0007"; transcript_id "NM_132719"; exon_number "4"; exon_id "NM_132719.4"; gene_name "l(1)G0007"; +chrX refGene exon 21217349 21217885 . + . gene_id "dod"; transcript_id "NM_078704"; exon_number "3"; exon_id "NM_078704.3"; gene_name "dod"; +chrX refGene 3UTR 21217459 21217885 . + . gene_id "dod"; transcript_id "NM_078704"; exon_number "3"; exon_id "NM_078704.3"; gene_name "dod"; +chr3LHet refGene exon 600380 601061 . - . gene_id "MED21"; transcript_id "NM_001015223"; exon_number "1"; exon_id "NM_001015223.1"; gene_name "MED21"; +chr3LHet refGene 3UTR 600380 600674 . - . gene_id "MED21"; transcript_id "NM_001015223"; exon_number "1"; exon_id "NM_001015223.1"; gene_name "MED21"; +chr3LHet refGene exon 600380 601061 . - . gene_id "MED21"; transcript_id "NM_001015224"; exon_number "1"; exon_id "NM_001015224.1"; gene_name "MED21"; +chr3LHet refGene 3UTR 600380 600674 . - . gene_id "MED21"; transcript_id "NM_001015224"; exon_number "1"; exon_id "NM_001015224.1"; gene_name "MED21"; +chr3L refGene exon 23777506 23780505 . + . gene_id "CG43968"; transcript_id "NM_001275309"; exon_number "2"; exon_id "NM_001275309.2"; gene_name "CG43968"; +chr3L refGene CDS 23777506 23780502 . + 0 gene_id "CG43968"; transcript_id "NM_001275309"; exon_number "2"; exon_id "NM_001275309.2"; gene_name "CG43968"; +chr3L refGene exon 10685630 10685908 . - . gene_id "CG33493"; transcript_id "NM_001274757"; exon_number "1"; exon_id "NM_001274757.1"; gene_name "CG33493"; +chr3L refGene 3UTR 10685630 10685858 . - . gene_id "CG33493"; transcript_id "NM_001274757"; exon_number "1"; exon_id "NM_001274757.1"; gene_name "CG33493"; +chr3L refGene exon 10685676 10686267 . - . gene_id "CG33493"; transcript_id "NM_206316"; exon_number "1"; exon_id "NM_206316.1"; gene_name "CG33493"; +chr3L refGene 3UTR 10685676 10685914 . - . gene_id "CG33493"; transcript_id "NM_206316"; exon_number "1"; exon_id "NM_206316.1"; gene_name "CG33493"; +chr3L refGene exon 20234367 20234640 . + . gene_id "CG6951"; transcript_id "NM_168838"; exon_number "1"; exon_id "NM_168838.1"; gene_name "CG6951"; +chr3L refGene 5UTR 20234367 20234640 . + . gene_id "CG6951"; transcript_id "NM_168838"; exon_number "1"; exon_id "NM_168838.1"; gene_name "CG6951"; +chr3L refGene exon 20308234 20308638 . - . gene_id "CR43875"; transcript_id "NR_073957"; exon_number "1"; exon_id "NR_073957.1"; gene_name "CR43875"; +chr2R refGene exon 18381802 18383903 . - . gene_id "px"; transcript_id "NM_001274207"; exon_number "1"; exon_id "NM_001274207.1"; gene_name "px"; +chr2R refGene 3UTR 18381802 18383835 . - . gene_id "px"; transcript_id "NM_001274207"; exon_number "1"; exon_id "NM_001274207.1"; gene_name "px"; +chr2R refGene exon 18775097 18775316 . - . gene_id "Gmer"; transcript_id "NM_137890"; exon_number "1"; exon_id "NM_137890.1"; gene_name "Gmer"; +chr2R refGene 3UTR 18775097 18775148 . - . gene_id "Gmer"; transcript_id "NM_137890"; exon_number "1"; exon_id "NM_137890.1"; gene_name "Gmer"; +chr2L refGene exon 6125879 6126595 . - . gene_id "WDR79"; transcript_id "NM_135153"; exon_number "1"; exon_id "NM_135153.1"; gene_name "WDR79"; +chr2L refGene 3UTR 6125879 6125931 . - . gene_id "WDR79"; transcript_id "NM_135153"; exon_number "1"; exon_id "NM_135153.1"; gene_name "WDR79"; +chr3L refGene exon 4281116 4281585 . + . gene_id "CG1311"; transcript_id "NM_001274482"; exon_number "9"; exon_id "NM_001274482.9"; gene_name "CG1311"; +chr3L refGene 3UTR 4281347 4281585 . + . gene_id "CG1311"; transcript_id "NM_001274482"; exon_number "9"; exon_id "NM_001274482.9"; gene_name "CG1311"; +chr3L refGene exon 4281116 4281585 . + . gene_id "CG1311"; transcript_id "NM_139627"; exon_number "9"; exon_id "NM_139627.9"; gene_name "CG1311"; +chr3L refGene 3UTR 4281347 4281585 . + . gene_id "CG1311"; transcript_id "NM_139627"; exon_number "9"; exon_id "NM_139627.9"; gene_name "CG1311"; +chr3L refGene exon 4261038 4261305 . + . gene_id "CG1309"; transcript_id "NM_139623"; exon_number "5"; exon_id "NM_139623.5"; gene_name "CG1309"; +chr3L refGene CDS 4261038 4261305 . + 1 gene_id "CG1309"; transcript_id "NM_139623"; exon_number "5"; exon_id "NM_139623.5"; gene_name "CG1309"; +chr3R refGene exon 9094859 9095551 . - . gene_id "CG8449"; transcript_id "NM_169499"; exon_number "1"; exon_id "NM_169499.1"; gene_name "CG8449"; +chr3R refGene 3UTR 9094859 9095041 . - . gene_id "CG8449"; transcript_id "NM_169499"; exon_number "1"; exon_id "NM_169499.1"; gene_name "CG8449"; +chr2R refGene exon 17205298 17207308 . - . gene_id "CG33655"; transcript_id "NM_001169765"; exon_number "1"; exon_id "NM_001169765.1"; gene_name "CG33655"; +chr2R refGene 3UTR 17205298 17207083 . - . gene_id "CG33655"; transcript_id "NM_001169765"; exon_number "1"; exon_id "NM_001169765.1"; gene_name "CG33655"; +chr2R refGene exon 19792186 19792792 . + . gene_id "CG13562"; transcript_id "NM_138005"; exon_number "4"; exon_id "NM_138005.4"; gene_name "CG13562"; +chr2R refGene 3UTR 19792617 19792792 . + . gene_id "CG13562"; transcript_id "NM_138005"; exon_number "4"; exon_id "NM_138005.4"; gene_name "CG13562"; +chr2R refGene exon 17546261 17546980 . - . gene_id "Rae1"; transcript_id "NM_137753"; exon_number "1"; exon_id "NM_137753.1"; gene_name "Rae1"; +chr2R refGene 3UTR 17546261 17546347 . - . gene_id "Rae1"; transcript_id "NM_137753"; exon_number "1"; exon_id "NM_137753.1"; gene_name "Rae1"; +chr2R refGene exon 17181907 17182715 . - . gene_id "CG9752"; transcript_id "NM_137729"; exon_number "1"; exon_id "NM_137729.1"; gene_name "CG9752"; +chr2R refGene 3UTR 17181907 17181939 . - . gene_id "CG9752"; transcript_id "NM_137729"; exon_number "1"; exon_id "NM_137729.1"; gene_name "CG9752"; +chr3R refGene exon 9949885 9950584 . - . gene_id "140up"; transcript_id "NM_001275632"; exon_number "1"; exon_id "NM_001275632.1"; gene_name "140up"; +chr3R refGene 3UTR 9949885 9950226 . - . gene_id "140up"; transcript_id "NM_001275632"; exon_number "1"; exon_id "NM_001275632.1"; gene_name "140up"; +chr2L refGene exon 20064261 20064572 . - . gene_id "vls"; transcript_id "NM_136175"; exon_number "1"; exon_id "NM_136175.1"; gene_name "vls"; +chr2L refGene 3UTR 20064261 20064385 . - . gene_id "vls"; transcript_id "NM_136175"; exon_number "1"; exon_id "NM_136175.1"; gene_name "vls"; +chr2L refGene exon 21102586 21103970 . - . gene_id "CR43809"; transcript_id "NR_073816"; exon_number "1"; exon_id "NR_073816.1"; gene_name "CR43809"; +chr2LHet refGene exon 20723 21383 . - . gene_id "CG12567"; transcript_id "NM_001015384"; exon_number "2"; exon_id "NM_001015384.2"; gene_name "CG12567"; +chr2LHet refGene CDS 20723 21383 . - 0 gene_id "CG12567"; transcript_id "NM_001015384"; exon_number "2"; exon_id "NM_001015384.2"; gene_name "CG12567"; +chr2LHet refGene exon 20723 21373 . - . gene_id "CG12567"; transcript_id "NM_001110861"; exon_number "2"; exon_id "NM_001110861.2"; gene_name "CG12567"; +chr2LHet refGene 3UTR 20723 21367 . - . gene_id "CG12567"; transcript_id "NM_001110861"; exon_number "2"; exon_id "NM_001110861.2"; gene_name "CG12567"; +chr2LHet refGene exon 20723 21569 . - . gene_id "CG12567"; transcript_id "NM_001170363"; exon_number "2"; exon_id "NM_001170363.2"; gene_name "CG12567"; +chr2LHet refGene 3UTR 20723 21414 . - . gene_id "CG12567"; transcript_id "NM_001170363"; exon_number "2"; exon_id "NM_001170363.2"; gene_name "CG12567"; +chr2R refGene exon 402893 403824 . - . gene_id "RpL38"; transcript_id "NM_001273771"; exon_number "1"; exon_id "NM_001273771.1"; gene_name "RpL38"; +chr2R refGene CDS 403615 403824 . - 0 gene_id "RpL38"; transcript_id "NM_001273771"; exon_number "1"; exon_id "NM_001273771.1"; gene_name "RpL38"; +chr2R refGene exon 403505 403824 . - . gene_id "RpL38"; transcript_id "NM_001042975"; exon_number "1"; exon_id "NM_001042975.1"; gene_name "RpL38"; +chr2R refGene CDS 403615 403824 . - 0 gene_id "RpL38"; transcript_id "NM_001042975"; exon_number "1"; exon_id "NM_001042975.1"; gene_name "RpL38"; +chr3L refGene exon 20382951 20384487 . - . gene_id "CR43944"; transcript_id "NR_073958"; exon_number "1"; exon_id "NR_073958.1"; gene_name "CR43944"; +chrX refGene exon 8916051 8916272 . + . gene_id "rdgA"; transcript_id "NM_001042799"; exon_number "12"; exon_id "NM_001042799.12"; gene_name "rdgA"; +chrX refGene CDS 8916051 8916272 . + 2 gene_id "rdgA"; transcript_id "NM_001042799"; exon_number "12"; exon_id "NM_001042799.12"; gene_name "rdgA"; +chrX refGene exon 3465577 3466033 . + . gene_id "CG32792"; transcript_id "NM_001042795"; exon_number "5"; exon_id "NM_001042795.5"; gene_name "CG32792"; +chrX refGene CDS 3465577 3465830 . + 2 gene_id "CG32792"; transcript_id "NM_001042795"; exon_number "5"; exon_id "NM_001042795.5"; gene_name "CG32792"; +chrX refGene exon 10031932 10032746 . + . gene_id "CG34104"; transcript_id "NM_001042802"; exon_number "7"; exon_id "NM_001042802.7"; gene_name "CG34104"; +chrX refGene 3UTR 10031937 10032746 . + . gene_id "CG34104"; transcript_id "NM_001042802"; exon_number "7"; exon_id "NM_001042802.7"; gene_name "CG34104"; +chr2R refGene exon 20758822 20759032 . + . gene_id "Atf-2"; transcript_id "NM_001038884"; exon_number "2"; exon_id "NM_001038884.2"; gene_name "Atf-2"; +chr2R refGene 3UTR 20758932 20759032 . + . gene_id "Atf-2"; transcript_id "NM_001038884"; exon_number "2"; exon_id "NM_001038884.2"; gene_name "Atf-2"; +chr3R refGene exon 4808454 4809273 . - . gene_id "RagA"; transcript_id "NM_141593"; exon_number "1"; exon_id "NM_141593.1"; gene_name "RagA"; +chr3R refGene 3UTR 4808454 4808834 . - . gene_id "RagA"; transcript_id "NM_141593"; exon_number "1"; exon_id "NM_141593.1"; gene_name "RagA"; +chr3R refGene exon 4760735 4761009 . - . gene_id "CR44020"; transcript_id "NR_073991"; exon_number "2"; exon_id "NR_073991.2"; gene_name "CR44020"; +chr3R refGene exon 4769187 4770620 . - . gene_id "CG11964"; transcript_id "NM_141590"; exon_number "3"; exon_id "NM_141590.3"; gene_name "CG11964"; +chr3R refGene CDS 4769187 4770620 . - 0 gene_id "CG11964"; transcript_id "NM_141590"; exon_number "3"; exon_id "NM_141590.3"; gene_name "CG11964"; +chr3R refGene exon 4830231 4831053 . + . gene_id "CG11980"; transcript_id "NM_141600"; exon_number "3"; exon_id "NM_141600.3"; gene_name "CG11980"; +chr3R refGene 3UTR 4830973 4831053 . + . gene_id "CG11980"; transcript_id "NM_141600"; exon_number "3"; exon_id "NM_141600.3"; gene_name "CG11980"; +chr3R refGene exon 4830231 4831053 . + . gene_id "CG11980"; transcript_id "NM_169250"; exon_number "3"; exon_id "NM_169250.3"; gene_name "CG11980"; +chr3R refGene 3UTR 4830973 4831053 . + . gene_id "CG11980"; transcript_id "NM_169250"; exon_number "3"; exon_id "NM_169250.3"; gene_name "CG11980"; +chr2R refGene exon 14296516 14297340 . + . gene_id "GstE9"; transcript_id "NM_166279"; exon_number "1"; exon_id "NM_166279.1"; gene_name "GstE9"; +chr2R refGene 3UTR 14297262 14297340 . + . gene_id "GstE9"; transcript_id "NM_166279"; exon_number "1"; exon_id "NM_166279.1"; gene_name "GstE9"; +chr3L refGene exon 8975312 8976573 . - . gene_id "Galk"; transcript_id "NM_168307"; exon_number "1"; exon_id "NM_168307.1"; gene_name "Galk"; +chr3L refGene 3UTR 8975312 8976386 . - . gene_id "Galk"; transcript_id "NM_168307"; exon_number "1"; exon_id "NM_168307.1"; gene_name "Galk"; +chr2R refGene exon 19780589 19780941 . - . gene_id "Upf3"; transcript_id "NM_166629"; exon_number "1"; exon_id "NM_166629.1"; gene_name "Upf3"; +chr2R refGene 3UTR 19780589 19780698 . - . gene_id "Upf3"; transcript_id "NM_166629"; exon_number "1"; exon_id "NM_166629.1"; gene_name "Upf3"; +chr2R refGene stop_codon 19780699 19780701 . - 0 gene_id "Upf3"; transcript_id "NM_166629"; exon_number "1"; exon_id "NM_166629.1"; gene_name "Upf3"; +chr2R refGene exon 17554252 17555099 . + . gene_id "CG42365"; transcript_id "NM_166469"; exon_number "1"; exon_id "NM_166469.1"; gene_name "CG42365"; +chr2R refGene 3UTR 17555004 17555099 . + . gene_id "CG42365"; transcript_id "NM_166469"; exon_number "1"; exon_id "NM_166469.1"; gene_name "CG42365"; +chr2R refGene exon 3461391 3461663 . + . gene_id "Vps13"; transcript_id "NM_001273852"; exon_number "15"; exon_id "NM_001273852.15"; gene_name "Vps13"; +chr2R refGene CDS 3461391 3461663 . + 2 gene_id "Vps13"; transcript_id "NM_001273852"; exon_number "15"; exon_id "NM_001273852.15"; gene_name "Vps13"; +chr2R refGene exon 3461391 3461663 . + . gene_id "Vps13"; transcript_id "NM_136455"; exon_number "15"; exon_id "NM_136455.15"; gene_name "Vps13"; +chr2R refGene CDS 3461391 3461663 . + 2 gene_id "Vps13"; transcript_id "NM_136455"; exon_number "15"; exon_id "NM_136455.15"; gene_name "Vps13"; +chr2R refGene exon 16445897 16447458 . + . gene_id "lms"; transcript_id "NM_137647"; exon_number "3"; exon_id "NM_137647.3"; gene_name "lms"; +chr2R refGene 3UTR 16446647 16447458 . + . gene_id "lms"; transcript_id "NM_137647"; exon_number "3"; exon_id "NM_137647.3"; gene_name "lms"; +chr2R refGene exon 13453284 13454499 . - . gene_id "ns2"; transcript_id "NM_137388"; exon_number "1"; exon_id "NM_137388.1"; gene_name "ns2"; +chr2R refGene 3UTR 13453284 13453363 . - . gene_id "ns2"; transcript_id "NM_137388"; exon_number "1"; exon_id "NM_137388.1"; gene_name "ns2"; +chr2R refGene exon 12953476 12954959 . - . gene_id "CG30460"; transcript_id "NM_137342"; exon_number "1"; exon_id "NM_137342.1"; gene_name "CG30460"; +chr2R refGene 3UTR 12953476 12954286 . - . gene_id "CG30460"; transcript_id "NM_137342"; exon_number "1"; exon_id "NM_137342.1"; gene_name "CG30460"; +chr2R refGene exon 11900178 11901329 . + . gene_id "CG8389"; transcript_id "NM_137232"; exon_number "4"; exon_id "NM_137232.4"; gene_name "CG8389"; +chr2R refGene 3UTR 11901042 11901329 . + . gene_id "CG8389"; transcript_id "NM_137232"; exon_number "4"; exon_id "NM_137232.4"; gene_name "CG8389"; +chr2R refGene exon 8041411 8041768 . + . gene_id "CG8407"; transcript_id "NM_001169653"; exon_number "4"; exon_id "NM_001169653.4"; gene_name "CG8407"; +chr2R refGene 3UTR 8041576 8041768 . + . gene_id "CG8407"; transcript_id "NM_001169653"; exon_number "4"; exon_id "NM_001169653.4"; gene_name "CG8407"; +chr2R refGene exon 8041411 8041768 . + . gene_id "CG8407"; transcript_id "NM_136890"; exon_number "3"; exon_id "NM_136890.3"; gene_name "CG8407"; +chr2R refGene 3UTR 8041576 8041768 . + . gene_id "CG8407"; transcript_id "NM_136890"; exon_number "3"; exon_id "NM_136890.3"; gene_name "CG8407"; +chr2R refGene exon 8521671 8523187 . - . gene_id "CG33671"; transcript_id "NM_001273993"; exon_number "1"; exon_id "NM_001273993.1"; gene_name "CG33671"; +chr2R refGene 3UTR 8521671 8521758 . - . gene_id "CG33671"; transcript_id "NM_001273993"; exon_number "1"; exon_id "NM_001273993.1"; gene_name "CG33671"; +chr2R refGene exon 8521671 8523646 . - . gene_id "CG33671"; transcript_id "NM_001032241"; exon_number "1"; exon_id "NM_001032241.1"; gene_name "CG33671"; +chr2R refGene 3UTR 8521671 8521758 . - . gene_id "CG33671"; transcript_id "NM_001032241"; exon_number "1"; exon_id "NM_001032241.1"; gene_name "CG33671"; +chr2R refGene exon 8521671 8523646 . - . gene_id "CG33672"; transcript_id "NM_001032242"; exon_number "1"; exon_id "NM_001032242.1"; gene_name "CG33672"; +chr2R refGene 3UTR 8521671 8523328 . - . gene_id "CG33672"; transcript_id "NM_001032242"; exon_number "1"; exon_id "NM_001032242.1"; gene_name "CG33672"; +chr2R refGene exon 9108444 9108881 . - . gene_id "Fsn"; transcript_id "NM_165973"; exon_number "1"; exon_id "NM_165973.1"; gene_name "Fsn"; +chr2R refGene 3UTR 9108444 9108786 . - . gene_id "Fsn"; transcript_id "NM_165973"; exon_number "1"; exon_id "NM_165973.1"; gene_name "Fsn"; +chr2R refGene exon 9108444 9108881 . - . gene_id "Fsn"; transcript_id "NM_137005"; exon_number "1"; exon_id "NM_137005.1"; gene_name "Fsn"; +chr2R refGene 3UTR 9108444 9108786 . - . gene_id "Fsn"; transcript_id "NM_137005"; exon_number "1"; exon_id "NM_137005.1"; gene_name "Fsn"; +chr2R refGene exon 4984436 4985641 . - . gene_id "CG8078"; transcript_id "NM_136607"; exon_number "1"; exon_id "NM_136607.1"; gene_name "CG8078"; +chr2R refGene 3UTR 4984436 4984815 . - . gene_id "CG8078"; transcript_id "NM_136607"; exon_number "1"; exon_id "NM_136607.1"; gene_name "CG8078"; +chr2R refGene exon 4972167 4972827 . + . gene_id "CNT1"; transcript_id "NM_136603"; exon_number "6"; exon_id "NM_136603.6"; gene_name "CNT1"; +chr2R refGene 3UTR 4972205 4972827 . + . gene_id "CNT1"; transcript_id "NM_136603"; exon_number "6"; exon_id "NM_136603.6"; gene_name "CNT1"; +chr2R refGene exon 11900178 11901329 . + . gene_id "CG8389"; transcript_id "NM_166132"; exon_number "4"; exon_id "NM_166132.4"; gene_name "CG8389"; +chr2R refGene 3UTR 11901042 11901329 . + . gene_id "CG8389"; transcript_id "NM_166132"; exon_number "4"; exon_id "NM_166132.4"; gene_name "CG8389"; +chr2R refGene exon 10755738 10756067 . - . gene_id "Inr-a"; transcript_id "NM_137155"; exon_number "8"; exon_id "NM_137155.8"; gene_name "Inr-a"; +chr2R refGene CDS 10755738 10756067 . - 0 gene_id "Inr-a"; transcript_id "NM_137155"; exon_number "8"; exon_id "NM_137155.8"; gene_name "Inr-a"; +chr2R refGene exon 9747854 9748795 . - . gene_id "CG16935"; transcript_id "NM_137070"; exon_number "1"; exon_id "NM_137070.1"; gene_name "CG16935"; +chr2R refGene 3UTR 9747854 9747935 . - . gene_id "CG16935"; transcript_id "NM_137070"; exon_number "1"; exon_id "NM_137070.1"; gene_name "CG16935"; +chr2R refGene exon 8374314 8375491 . + . gene_id "Dh44-R2"; transcript_id "NM_136945"; exon_number "11"; exon_id "NM_136945.11"; gene_name "Dh44-R2"; +chr2R refGene 3UTR 8374411 8375491 . + . gene_id "Dh44-R2"; transcript_id "NM_136945"; exon_number "11"; exon_id "NM_136945.11"; gene_name "Dh44-R2"; +chr2R refGene exon 8064935 8066035 . - . gene_id "EndoG"; transcript_id "NM_136893"; exon_number "1"; exon_id "NM_136893.1"; gene_name "EndoG"; +chr2R refGene 3UTR 8064935 8065045 . - . gene_id "EndoG"; transcript_id "NM_136893"; exon_number "1"; exon_id "NM_136893.1"; gene_name "EndoG"; +chr2R refGene exon 6714934 6716361 . - . gene_id "CG12344"; transcript_id "NM_136775"; exon_number "1"; exon_id "NM_136775.1"; gene_name "CG12344"; +chr2R refGene 3UTR 6714934 6716160 . - . gene_id "CG12344"; transcript_id "NM_136775"; exon_number "1"; exon_id "NM_136775.1"; gene_name "CG12344"; +chr2R refGene exon 6709744 6710826 . - . gene_id "CG12343"; transcript_id "NM_136773"; exon_number "1"; exon_id "NM_136773.1"; gene_name "CG12343"; +chr2R refGene 3UTR 6709744 6710087 . - . gene_id "CG12343"; transcript_id "NM_136773"; exon_number "1"; exon_id "NM_136773.1"; gene_name "CG12343"; +chr2R refGene exon 3856756 3857013 . + . gene_id "nito"; transcript_id "NM_136495"; exon_number "4"; exon_id "NM_136495.4"; gene_name "nito"; +chr2R refGene 3UTR 3856756 3857013 . + . gene_id "nito"; transcript_id "NM_136495"; exon_number "4"; exon_id "NM_136495.4"; gene_name "nito"; +chr2L refGene exon 21159272 21160783 . + . gene_id "CG9248"; transcript_id "NM_136249"; exon_number "3"; exon_id "NM_136249.3"; gene_name "CG9248"; +chr2L refGene 3UTR 21160568 21160783 . + . gene_id "CG9248"; transcript_id "NM_136249"; exon_number "3"; exon_id "NM_136249.3"; gene_name "CG9248"; +chr2L refGene exon 21157433 21158243 . - . gene_id "CG9249"; transcript_id "NM_136248"; exon_number "1"; exon_id "NM_136248.1"; gene_name "CG9249"; +chr2L refGene CDS 21157520 21158243 . - 1 gene_id "CG9249"; transcript_id "NM_136248"; exon_number "1"; exon_id "NM_136248.1"; gene_name "CG9249"; +chr3L refGene exon 19860588 19861745 . - . gene_id "Rab8"; transcript_id "NM_079448"; exon_number "1"; exon_id "NM_079448.1"; gene_name "Rab8"; +chr3L refGene 3UTR 19860588 19861652 . - . gene_id "Rab8"; transcript_id "NM_079448"; exon_number "1"; exon_id "NM_079448.1"; gene_name "Rab8"; +chr3L refGene exon 19860808 19861745 . - . gene_id "Rab8"; transcript_id "NM_001259908"; exon_number "1"; exon_id "NM_001259908.1"; gene_name "Rab8"; +chr3L refGene 3UTR 19860808 19861652 . - . gene_id "Rab8"; transcript_id "NM_001259908"; exon_number "1"; exon_id "NM_001259908.1"; gene_name "Rab8"; +chr2L refGene exon 18711071 18711733 . - . gene_id "Irk3"; transcript_id "NM_001144363"; exon_number "1"; exon_id "NM_001144363.1"; gene_name "Irk3"; +chr2L refGene 3UTR 18711071 18711336 . - . gene_id "Irk3"; transcript_id "NM_001144363"; exon_number "1"; exon_id "NM_001144363.1"; gene_name "Irk3"; +chr3L refGene exon 8905410 8905771 . - . gene_id "mfr"; transcript_id "NM_001144444"; exon_number "14"; exon_id "NM_001144444.14"; gene_name "mfr"; +chr3L refGene 5UTR 8905410 8905771 . - . gene_id "mfr"; transcript_id "NM_001144444"; exon_number "14"; exon_id "NM_001144444.14"; gene_name "mfr"; +chr3L refGene exon 22858978 22859060 . + . gene_id "CG33170"; transcript_id "NM_001144528"; exon_number "3"; exon_id "NM_001144528.3"; gene_name "CG33170"; +chr3L refGene CDS 22858978 22859060 . + 0 gene_id "CG33170"; transcript_id "NM_001144528"; exon_number "3"; exon_id "NM_001144528.3"; gene_name "CG33170"; +chr3R refGene exon 6234340 6234597 . - . gene_id "Irp-1B"; transcript_id "NM_079579"; exon_number "1"; exon_id "NM_079579.1"; gene_name "Irp-1B"; +chr3R refGene 3UTR 6234340 6234486 . - . gene_id "Irp-1B"; transcript_id "NM_079579"; exon_number "1"; exon_id "NM_079579.1"; gene_name "Irp-1B"; +chr3R refGene exon 7447188 7447666 . - . gene_id "CG6808"; transcript_id "NM_169411"; exon_number "1"; exon_id "NM_169411.1"; gene_name "CG6808"; +chr3R refGene 3UTR 7447188 7447446 . - . gene_id "CG6808"; transcript_id "NM_169411"; exon_number "1"; exon_id "NM_169411.1"; gene_name "CG6808"; +chr3R refGene exon 9502271 9502666 . + . gene_id "lkb1"; transcript_id "NM_169544"; exon_number "1"; exon_id "NM_169544.1"; gene_name "lkb1"; +chr3R refGene 5UTR 9502271 9502666 . + . gene_id "lkb1"; transcript_id "NM_169544"; exon_number "1"; exon_id "NM_169544.1"; gene_name "lkb1"; +chr3R refGene exon 9223557 9224305 . + . gene_id "CG14377"; transcript_id "NM_169524"; exon_number "1"; exon_id "NM_169524.1"; gene_name "CG14377"; +chr3R refGene 3UTR 9223907 9224305 . + . gene_id "CG14377"; transcript_id "NM_169524"; exon_number "1"; exon_id "NM_169524.1"; gene_name "CG14377"; +chrX refGene exon 19036145 19037801 . - . gene_id "RhoGAP18B"; transcript_id "NM_001144748"; exon_number "1"; exon_id "NM_001144748.1"; gene_name "RhoGAP18B"; +chrX refGene 3UTR 19036145 19037617 . - . gene_id "RhoGAP18B"; transcript_id "NM_001144748"; exon_number "1"; exon_id "NM_001144748.1"; gene_name "RhoGAP18B"; +chr3L refGene exon 22858978 22859134 . + . gene_id "CG33170"; transcript_id "NM_176391"; exon_number "3"; exon_id "NM_176391.3"; gene_name "CG33170"; +chr3L refGene CDS 22858978 22859061 . + 0 gene_id "CG33170"; transcript_id "NM_176391"; exon_number "3"; exon_id "NM_176391.3"; gene_name "CG33170"; +chr3L refGene 3UTR 22859065 22859134 . + . gene_id "CG33170"; transcript_id "NM_176391"; exon_number "3"; exon_id "NM_176391.3"; gene_name "CG33170"; +chr3L refGene stop_codon 22859062 22859064 . + 0 gene_id "CG33170"; transcript_id "NM_176391"; exon_number "1"; exon_id "NM_176391.1"; gene_name "CG33170"; +chrX refGene exon 6898793 6899011 . - . gene_id "Inx7"; transcript_id "NM_176698"; exon_number "3"; exon_id "NM_176698.3"; gene_name "Inx7"; +chrX refGene 5UTR 6898796 6899011 . - . gene_id "Inx7"; transcript_id "NM_176698"; exon_number "3"; exon_id "NM_176698.3"; gene_name "Inx7"; +chr2R refGene exon 12953476 12954959 . - . gene_id "CG30460"; transcript_id "NM_206149"; exon_number "1"; exon_id "NM_206149.1"; gene_name "CG30460"; +chr2R refGene 3UTR 12953476 12954286 . - . gene_id "CG30460"; transcript_id "NM_206149"; exon_number "1"; exon_id "NM_206149.1"; gene_name "CG30460"; +chr2R refGene exon 12953476 12954959 . - . gene_id "CG30460"; transcript_id "NM_206150"; exon_number "1"; exon_id "NM_206150.1"; gene_name "CG30460"; +chr2R refGene 3UTR 12953476 12954286 . - . gene_id "CG30460"; transcript_id "NM_206150"; exon_number "1"; exon_id "NM_206150.1"; gene_name "CG30460"; +chr2R refGene exon 12953476 12954959 . - . gene_id "CG30460"; transcript_id "NM_206148"; exon_number "1"; exon_id "NM_206148.1"; gene_name "CG30460"; +chr2R refGene 3UTR 12953476 12954286 . - . gene_id "CG30460"; transcript_id "NM_206148"; exon_number "1"; exon_id "NM_206148.1"; gene_name "CG30460"; +chr2L refGene exon 9959248 9961617 . - . gene_id "CG5850"; transcript_id "NM_001259026"; exon_number "1"; exon_id "NM_001259026.1"; gene_name "CG5850"; +chr2L refGene 3UTR 9959248 9961354 . - . gene_id "CG5850"; transcript_id "NM_001259026"; exon_number "1"; exon_id "NM_001259026.1"; gene_name "CG5850"; +chr2L refGene exon 9787352 9788499 . + . gene_id "IP3K1"; transcript_id "NM_001259025"; exon_number "4"; exon_id "NM_001259025.4"; gene_name "IP3K1"; +chr2L refGene CDS 9787352 9788168 . + 1 gene_id "IP3K1"; transcript_id "NM_001259025"; exon_number "4"; exon_id "NM_001259025.4"; gene_name "IP3K1"; +chr3R refGene exon 7447188 7447666 . - . gene_id "CG6808"; transcript_id "NM_001260126"; exon_number "1"; exon_id "NM_001260126.1"; gene_name "CG6808"; +chr3R refGene 3UTR 7447188 7447446 . - . gene_id "CG6808"; transcript_id "NM_001260126"; exon_number "1"; exon_id "NM_001260126.1"; gene_name "CG6808"; +chr3R refGene exon 3836629 3836956 . - . gene_id "CG10435"; transcript_id "NM_141502"; exon_number "1"; exon_id "NM_141502.1"; gene_name "CG10435"; +chr3R refGene 3UTR 3836629 3836830 . - . gene_id "CG10435"; transcript_id "NM_141502"; exon_number "1"; exon_id "NM_141502.1"; gene_name "CG10435"; +chr3R refGene exon 13621717 13622039 . + . gene_id "CG7713"; transcript_id "NM_001260230"; exon_number "4"; exon_id "NM_001260230.4"; gene_name "CG7713"; +chr3R refGene 3UTR 13621801 13622039 . + . gene_id "CG7713"; transcript_id "NM_001260230"; exon_number "4"; exon_id "NM_001260230.4"; gene_name "CG7713"; +chr3R refGene exon 13621717 13622039 . + . gene_id "CG7713"; transcript_id "NM_001260229"; exon_number "5"; exon_id "NM_001260229.5"; gene_name "CG7713"; +chr3R refGene 3UTR 13621801 13622039 . + . gene_id "CG7713"; transcript_id "NM_001260229"; exon_number "5"; exon_id "NM_001260229.5"; gene_name "CG7713"; +chr3R refGene exon 7462899 7463460 . + . gene_id "CR44137"; transcript_id "NR_073997"; exon_number "1"; exon_id "NR_073997.1"; gene_name "CR44137"; +chr3R refGene exon 20680218 20681667 . - . gene_id "HdacX"; transcript_id "NM_001260367"; exon_number "1"; exon_id "NM_001260367.1"; gene_name "HdacX"; +chr3R refGene 3UTR 20680218 20680824 . - . gene_id "HdacX"; transcript_id "NM_001260367"; exon_number "1"; exon_id "NM_001260367.1"; gene_name "HdacX"; +chr3R refGene exon 4576502 4578463 . - . gene_id "CG34135"; transcript_id "NM_001043224"; exon_number "2"; exon_id "NM_001043224.2"; gene_name "CG34135"; +chr3R refGene 5UTR 4576638 4578463 . - . gene_id "CG34135"; transcript_id "NM_001043224"; exon_number "2"; exon_id "NM_001043224.2"; gene_name "CG34135"; +chr3R refGene exon 4576502 4580132 . - . gene_id "CG34135"; transcript_id "NM_001043223"; exon_number "2"; exon_id "NM_001043223.2"; gene_name "CG34135"; +chr3R refGene 5UTR 4576638 4580132 . - . gene_id "CG34135"; transcript_id "NM_001043223"; exon_number "2"; exon_id "NM_001043223.2"; gene_name "CG34135"; +chrX refGene exon 8329051 8330244 . - . gene_id "CG12125"; transcript_id "NM_001169231"; exon_number "2"; exon_id "NM_001169231.2"; gene_name "CG12125"; +chrX refGene CDS 8329051 8330244 . - 0 gene_id "CG12125"; transcript_id "NM_001169231"; exon_number "2"; exon_id "NM_001169231.2"; gene_name "CG12125"; +chr3R refGene exon 16416746 16417333 . - . gene_id "CG4159"; transcript_id "NM_001170193"; exon_number "1"; exon_id "NM_001170193.1"; gene_name "CG4159"; +chr3R refGene 3UTR 16416746 16416807 . - . gene_id "CG4159"; transcript_id "NM_001170193"; exon_number "1"; exon_id "NM_001170193.1"; gene_name "CG4159"; +chrX refGene exon 3465577 3466033 . + . gene_id "CG32792"; transcript_id "NM_001144679"; exon_number "6"; exon_id "NM_001144679.6"; gene_name "CG32792"; +chrX refGene CDS 3465577 3465830 . + 2 gene_id "CG32792"; transcript_id "NM_001144679"; exon_number "6"; exon_id "NM_001144679.6"; gene_name "CG32792"; +chr2R refGene exon 19792186 19792792 . + . gene_id "CG13562"; transcript_id "NM_001259555"; exon_number "5"; exon_id "NM_001259555.5"; gene_name "CG13562"; +chr2R refGene 3UTR 19792617 19792792 . + . gene_id "CG13562"; transcript_id "NM_001259555"; exon_number "5"; exon_id "NM_001259555.5"; gene_name "CG13562"; +chr3L refGene exon 19861136 19861745 . - . gene_id "Rab8"; transcript_id "NM_001259907"; exon_number "1"; exon_id "NM_001259907.1"; gene_name "Rab8"; +chr3L refGene 3UTR 19861136 19861652 . - . gene_id "Rab8"; transcript_id "NM_001259907"; exon_number "1"; exon_id "NM_001259907.1"; gene_name "Rab8"; +chr3L refGene exon 16837668 16837962 . - . gene_id "CG9669"; transcript_id "NM_001259878"; exon_number "1"; exon_id "NM_001259878.1"; gene_name "CG9669"; +chr3L refGene 3UTR 16837668 16837724 . - . gene_id "CG9669"; transcript_id "NM_001259878"; exon_number "1"; exon_id "NM_001259878.1"; gene_name "CG9669"; +chr3R refGene exon 3714818 3715872 . + . gene_id "CG10092"; transcript_id "NM_001275422"; exon_number "5"; exon_id "NM_001275422.5"; gene_name "CG10092"; +chr3R refGene 3UTR 3714972 3715872 . + . gene_id "CG10092"; transcript_id "NM_001275422"; exon_number "5"; exon_id "NM_001275422.5"; gene_name "CG10092"; +chr3R refGene exon 8302987 8303989 . - . gene_id "alphagamma-element:CR32865"; transcript_id "NR_002020"; exon_number "2"; exon_id "NR_002020.2"; gene_name "alphagamma-element:CR32865"; +chr3R refGene exon 1433980 1435042 . + . gene_id "CR43628"; transcript_id "NR_048327"; exon_number "3"; exon_id "NR_048327.3"; gene_name "CR43628"; +chr2R refGene exon 15287274 15288840 . + . gene_id "CR43430"; transcript_id "NR_048145"; exon_number "1"; exon_id "NR_048145.1"; gene_name "CR43430"; +chr2R refGene exon 8763587 8764785 . + . gene_id "CR43468"; transcript_id "NR_048099"; exon_number "2"; exon_id "NR_048099.2"; gene_name "CR43468"; +chrX refGene exon 12864509 12865007 . - . gene_id "CR43636"; transcript_id "NR_047800"; exon_number "1"; exon_id "NR_047800.1"; gene_name "CR43636"; +chrX refGene exon 7766860 7767673 . + . gene_id "CR43615"; transcript_id "NR_047779"; exon_number "1"; exon_id "NR_047779.1"; gene_name "CR43615"; +chrUextra refGene exon 21314107 21314290 . - . gene_id "Su(Ste):CR42422"; transcript_id "NR_026616"; exon_number "4"; exon_id "NR_026616.4"; gene_name "Su(Ste):CR42422"; +chrUextra refGene exon 14493536 14493887 . - . gene_id "CR41583"; transcript_id "NR_003998"; exon_number "4"; exon_id "NR_003998.4"; gene_name "CR41583"; +chrUextra refGene exon 16450512 16450821 . - . gene_id "CR41583"; transcript_id "NR_003998_2"; exon_number "5"; exon_id "NR_003998_2.5"; gene_name "CR41583"; +chrUextra refGene exon 21242017 21242310 . + . gene_id "CR41583"; transcript_id "NR_003998_5"; exon_number "1"; exon_id "NR_003998_5.1"; gene_name "CR41583"; +chrUextra refGene exon 21598582 21599121 . + . gene_id "CR41583"; transcript_id "NR_003998_5"; exon_number "2"; exon_id "NR_003998_5.2"; gene_name "CR41583"; +chrX refGene exon 18880 19093 . + . gene_id "CR40469"; transcript_id "NR_003723"; exon_number "1"; exon_id "NR_003723.1"; gene_name "CR40469"; +chr3R refGene exon 7048136 7048564 . - . gene_id "CR31144"; transcript_id "NR_037759"; exon_number "1"; exon_id "NR_037759.1"; gene_name "CR31144"; +chr3R refGene exon 5605241 5608415 . - . gene_id "CR31514"; transcript_id "NR_037757"; exon_number "1"; exon_id "NR_037757.1"; gene_name "CR31514"; +chr3R refGene exon 27594101 27595145 . + . gene_id "pncr017:3R"; transcript_id "NR_002507"; exon_number "2"; exon_id "NR_002507.2"; gene_name "pncr017:3R"; +chr3R refGene exon 27043086 27043384 . - . gene_id "RNaseP:RNA"; transcript_id "NR_002092"; exon_number "1"; exon_id "NR_002092.1"; gene_name "RNaseP:RNA"; +chr3R refGene exon 2902612 2903703 . + . gene_id "CG1943"; transcript_id "NM_001275397"; exon_number "2"; exon_id "NM_001275397.2"; gene_name "CG1943"; +chr3R refGene 3UTR 2902998 2903703 . + . gene_id "CG1943"; transcript_id "NM_001275397"; exon_number "2"; exon_id "NM_001275397.2"; gene_name "CG1943"; +chr3R refGene exon 2951993 2953194 . - . gene_id "CG10068"; transcript_id "NM_141438"; exon_number "1"; exon_id "NM_141438.1"; gene_name "CG10068"; +chr3R refGene 3UTR 2951993 2952493 . - . gene_id "CG10068"; transcript_id "NM_141438"; exon_number "1"; exon_id "NM_141438.1"; gene_name "CG10068"; +chr3R refGene exon 11102162 11103292 . - . gene_id "MRG15"; transcript_id "NM_001275659"; exon_number "1"; exon_id "NM_001275659.1"; gene_name "MRG15"; +chr3R refGene 3UTR 11102162 11102306 . - . gene_id "MRG15"; transcript_id "NM_001275659"; exon_number "1"; exon_id "NM_001275659.1"; gene_name "MRG15"; +chr3R refGene exon 11143217 11144007 . + . gene_id "CG14866"; transcript_id "NM_001144585"; exon_number "3"; exon_id "NM_001144585.3"; gene_name "CG14866"; +chr3R refGene 3UTR 11143861 11144007 . + . gene_id "CG14866"; transcript_id "NM_001144585"; exon_number "3"; exon_id "NM_001144585.3"; gene_name "CG14866"; +chr3R refGene exon 11143217 11144007 . + . gene_id "CG14866"; transcript_id "NM_142187"; exon_number "2"; exon_id "NM_142187.2"; gene_name "CG14866"; +chr3R refGene 3UTR 11143861 11144007 . + . gene_id "CG14866"; transcript_id "NM_142187"; exon_number "2"; exon_id "NM_142187.2"; gene_name "CG14866"; +chr3R refGene exon 11157306 11158270 . - . gene_id "FK506-bp1"; transcript_id "NM_079640"; exon_number "1"; exon_id "NM_079640.1"; gene_name "FK506-bp1"; +chr3R refGene CDS 11157429 11158270 . - 2 gene_id "FK506-bp1"; transcript_id "NM_079640"; exon_number "1"; exon_id "NM_079640.1"; gene_name "FK506-bp1"; +chr3R refGene exon 11196340 11197934 . - . gene_id "CG6136"; transcript_id "NM_001275671"; exon_number "3"; exon_id "NM_001275671.3"; gene_name "CG6136"; +chr3R refGene 5UTR 11197536 11197934 . - . gene_id "CG6136"; transcript_id "NM_001275671"; exon_number "3"; exon_id "NM_001275671.3"; gene_name "CG6136"; +chr3R refGene exon 11195758 11197934 . - . gene_id "CG6136"; transcript_id "NM_142203"; exon_number "1"; exon_id "NM_142203.1"; gene_name "CG6136"; +chr3R refGene 5UTR 11197536 11197934 . - . gene_id "CG6136"; transcript_id "NM_142203"; exon_number "1"; exon_id "NM_142203.1"; gene_name "CG6136"; +chr3R refGene exon 11196537 11197934 . - . gene_id "CG6136"; transcript_id "NM_001202295"; exon_number "1"; exon_id "NM_001202295.1"; gene_name "CG6136"; +chr3R refGene 5UTR 11197536 11197934 . - . gene_id "CG6136"; transcript_id "NM_001202295"; exon_number "1"; exon_id "NM_001202295.1"; gene_name "CG6136"; +chr3R refGene exon 12470794 12471668 . - . gene_id "CG10324"; transcript_id "NM_142314"; exon_number "1"; exon_id "NM_142314.1"; gene_name "CG10324"; +chr3R refGene 3UTR 12470794 12470895 . - . gene_id "CG10324"; transcript_id "NM_142314"; exon_number "1"; exon_id "NM_142314.1"; gene_name "CG10324"; +chr3R refGene exon 12825833 12827295 . - . gene_id "CG16941"; transcript_id "NM_142326"; exon_number "4"; exon_id "NM_142326.4"; gene_name "CG16941"; +chr3R refGene CDS 12825833 12827295 . - 1 gene_id "CG16941"; transcript_id "NM_142326"; exon_number "4"; exon_id "NM_142326.4"; gene_name "CG16941"; +chr3R refGene exon 13511411 13512083 . - . gene_id "CG31249"; transcript_id "NM_169774"; exon_number "1"; exon_id "NM_169774.1"; gene_name "CG31249"; +chr3R refGene CDS 13511731 13512083 . - 2 gene_id "CG31249"; transcript_id "NM_169774"; exon_number "1"; exon_id "NM_169774.1"; gene_name "CG31249"; +chr3R refGene exon 14012095 14013597 . + . gene_id "Arp5"; transcript_id "NM_142427"; exon_number "2"; exon_id "NM_142427.2"; gene_name "Arp5"; +chr3R refGene 3UTR 14013547 14013597 . + . gene_id "Arp5"; transcript_id "NM_142427"; exon_number "2"; exon_id "NM_142427.2"; gene_name "Arp5"; +chr3R refGene exon 14012095 14013597 . + . gene_id "Arp5"; transcript_id "NM_001275768"; exon_number "2"; exon_id "NM_001275768.2"; gene_name "Arp5"; +chr3R refGene 3UTR 14013547 14013597 . + . gene_id "Arp5"; transcript_id "NM_001275768"; exon_number "2"; exon_id "NM_001275768.2"; gene_name "Arp5"; +chr3R refGene exon 14985821 14986385 . - . gene_id "CG42358"; transcript_id "NM_142530"; exon_number "1"; exon_id "NM_142530.1"; gene_name "CG42358"; +chr3R refGene 3UTR 14985821 14985954 . - . gene_id "CG42358"; transcript_id "NM_142530"; exon_number "1"; exon_id "NM_142530.1"; gene_name "CG42358"; +chr3R refGene exon 15691139 15694492 . - . gene_id "CG4562"; transcript_id "NM_001275816"; exon_number "1"; exon_id "NM_001275816.1"; gene_name "CG4562"; +chr3R refGene 3UTR 15691139 15693191 . - . gene_id "CG4562"; transcript_id "NM_001275816"; exon_number "1"; exon_id "NM_001275816.1"; gene_name "CG4562"; +chr3R refGene exon 16436973 16438411 . - . gene_id "CG15923"; transcript_id "NM_001104376"; exon_number "1"; exon_id "NM_001104376.1"; gene_name "CG15923"; +chr3R refGene 3UTR 16436973 16438330 . - . gene_id "CG15923"; transcript_id "NM_001104376"; exon_number "1"; exon_id "NM_001104376.1"; gene_name "CG15923"; +chr3R refGene exon 16436973 16438411 . - . gene_id "CG15923"; transcript_id "NM_001275840"; exon_number "1"; exon_id "NM_001275840.1"; gene_name "CG15923"; +chr3R refGene 3UTR 16436973 16438279 . - . gene_id "CG15923"; transcript_id "NM_001275840"; exon_number "1"; exon_id "NM_001275840.1"; gene_name "CG15923"; +chr3R refGene exon 16648854 16649078 . + . gene_id "RpS20"; transcript_id "NM_079697"; exon_number "4"; exon_id "NM_079697.4"; gene_name "RpS20"; +chr3R refGene 3UTR 16648968 16649078 . + . gene_id "RpS20"; transcript_id "NM_079697"; exon_number "4"; exon_id "NM_079697.4"; gene_name "RpS20"; +chr3R refGene exon 16649035 16649461 . - . gene_id "CG17272"; transcript_id "NM_142660"; exon_number "1"; exon_id "NM_142660.1"; gene_name "CG17272"; +chr3R refGene 3UTR 16649035 16649110 . - . gene_id "CG17272"; transcript_id "NM_142660"; exon_number "1"; exon_id "NM_142660.1"; gene_name "CG17272"; +chr3R refGene exon 16738144 16738591 . + . gene_id "CR44106"; transcript_id "NR_074034"; exon_number "2"; exon_id "NR_074034.2"; gene_name "CR44106"; +chr3R refGene exon 16930768 16932293 . - . gene_id "sec15"; transcript_id "NM_142685"; exon_number "1"; exon_id "NM_142685.1"; gene_name "sec15"; +chr3R refGene 3UTR 16930768 16931186 . - . gene_id "sec15"; transcript_id "NM_142685"; exon_number "1"; exon_id "NM_142685.1"; gene_name "sec15"; +chr3R refGene exon 16942839 16943266 . + . gene_id "ppan"; transcript_id "NM_057631"; exon_number "3"; exon_id "NM_057631.3"; gene_name "ppan"; +chr3R refGene CDS 16942839 16943266 . + 1 gene_id "ppan"; transcript_id "NM_057631"; exon_number "3"; exon_id "NM_057631.3"; gene_name "ppan"; +chr3R refGene exon 17849419 17850063 . + . gene_id "mRpL35"; transcript_id "NM_142744"; exon_number "2"; exon_id "NM_142744.2"; gene_name "mRpL35"; +chr3R refGene 3UTR 17849931 17850063 . + . gene_id "mRpL35"; transcript_id "NM_142744"; exon_number "2"; exon_id "NM_142744.2"; gene_name "mRpL35"; +chr3R refGene exon 17855162 17855801 . - . gene_id "CG13409"; transcript_id "NM_142747"; exon_number "1"; exon_id "NM_142747.1"; gene_name "CG13409"; +chr3R refGene 3UTR 17855162 17855427 . - . gene_id "CG13409"; transcript_id "NM_142747"; exon_number "1"; exon_id "NM_142747.1"; gene_name "CG13409"; +chr3R refGene exon 19080792 19081345 . - . gene_id "wda"; transcript_id "NM_142879"; exon_number "1"; exon_id "NM_142879.1"; gene_name "wda"; +chr3R refGene 3UTR 19080792 19081215 . - . gene_id "wda"; transcript_id "NM_142879"; exon_number "1"; exon_id "NM_142879.1"; gene_name "wda"; +chr3R refGene exon 19585205 19585645 . - . gene_id "CG10219"; transcript_id "NM_142924"; exon_number "1"; exon_id "NM_142924.1"; gene_name "CG10219"; +chr3R refGene 3UTR 19585205 19585443 . - . gene_id "CG10219"; transcript_id "NM_142924"; exon_number "1"; exon_id "NM_142924.1"; gene_name "CG10219"; +chr3R refGene exon 19988551 19988882 . - . gene_id "mRpS24"; transcript_id "NM_079752"; exon_number "1"; exon_id "NM_079752.1"; gene_name "mRpS24"; +chr3R refGene CDS 19988596 19988882 . - 2 gene_id "mRpS24"; transcript_id "NM_079752"; exon_number "1"; exon_id "NM_079752.1"; gene_name "mRpS24"; +chr3R refGene exon 20046825 20047348 . + . gene_id "cav"; transcript_id "NM_170134"; exon_number "1"; exon_id "NM_170134.1"; gene_name "cav"; +chr3R refGene 5UTR 20046825 20047348 . + . gene_id "cav"; transcript_id "NM_170134"; exon_number "1"; exon_id "NM_170134.1"; gene_name "cav"; +chr3R refGene exon 20046825 20047475 . + . gene_id "cav"; transcript_id "NM_170135"; exon_number "1"; exon_id "NM_170135.1"; gene_name "cav"; +chr3R refGene 5UTR 20046825 20047463 . + . gene_id "cav"; transcript_id "NM_170135"; exon_number "1"; exon_id "NM_170135.1"; gene_name "cav"; +chr3R refGene exon 20047253 20047647 . + . gene_id "cav"; transcript_id "NM_079753"; exon_number "1"; exon_id "NM_079753.1"; gene_name "cav"; +chr3R refGene 5UTR 20047253 20047629 . + . gene_id "cav"; transcript_id "NM_079753"; exon_number "1"; exon_id "NM_079753.1"; gene_name "cav"; +chr3R refGene exon 20345347 20345800 . - . gene_id "CR44021"; transcript_id "NR_074058"; exon_number "1"; exon_id "NR_074058.1"; gene_name "CR44021"; +chr3R refGene exon 20707188 20707554 . - . gene_id "CG31121"; transcript_id "NM_170180"; exon_number "1"; exon_id "NM_170180.1"; gene_name "CG31121"; +chr3R refGene 3UTR 20707188 20707323 . - . gene_id "CG31121"; transcript_id "NM_170180"; exon_number "1"; exon_id "NM_170180.1"; gene_name "CG31121"; +chr3R refGene exon 20707188 20707554 . - . gene_id "CG31121"; transcript_id "NM_170179"; exon_number "1"; exon_id "NM_170179.1"; gene_name "CG31121"; +chr3R refGene 3UTR 20707188 20707323 . - . gene_id "CG31121"; transcript_id "NM_170179"; exon_number "1"; exon_id "NM_170179.1"; gene_name "CG31121"; +chr3R refGene exon 21317007 21318979 . - . gene_id "CR44179"; transcript_id "NR_074059"; exon_number "1"; exon_id "NR_074059.1"; gene_name "CR44179"; +chr3R refGene exon 21509345 21510238 . - . gene_id "RpL27"; transcript_id "NM_001276039"; exon_number "1"; exon_id "NM_001276039.1"; gene_name "RpL27"; +chr3R refGene 3UTR 21509345 21509816 . - . gene_id "RpL27"; transcript_id "NM_001276039"; exon_number "1"; exon_id "NM_001276039.1"; gene_name "RpL27"; +chr3R refGene exon 22810427 22811428 . + . gene_id "CG14253"; transcript_id "NM_143260"; exon_number "5"; exon_id "NM_143260.5"; gene_name "CG14253"; +chr3R refGene 3UTR 22810980 22811428 . + . gene_id "CG14253"; transcript_id "NM_143260"; exon_number "5"; exon_id "NM_143260.5"; gene_name "CG14253"; +chr3R refGene exon 22810427 22811428 . + . gene_id "CG14253"; transcript_id "NM_001276074"; exon_number "7"; exon_id "NM_001276074.7"; gene_name "CG14253"; +chr3R refGene 3UTR 22810980 22811428 . + . gene_id "CG14253"; transcript_id "NM_001276074"; exon_number "7"; exon_id "NM_001276074.7"; gene_name "CG14253"; +chr3R refGene exon 22810427 22811428 . + . gene_id "CG14253"; transcript_id "NM_170300"; exon_number "6"; exon_id "NM_170300.6"; gene_name "CG14253"; +chr3R refGene 3UTR 22810980 22811428 . + . gene_id "CG14253"; transcript_id "NM_170300"; exon_number "6"; exon_id "NM_170300.6"; gene_name "CG14253"; +chr3R refGene exon 22810427 22811428 . + . gene_id "CG14253"; transcript_id "NM_170301"; exon_number "6"; exon_id "NM_170301.6"; gene_name "CG14253"; +chr3R refGene 3UTR 22810980 22811428 . + . gene_id "CG14253"; transcript_id "NM_170301"; exon_number "6"; exon_id "NM_170301.6"; gene_name "CG14253"; +chr3R refGene exon 22810427 22811428 . + . gene_id "CG14253"; transcript_id "NM_170302"; exon_number "6"; exon_id "NM_170302.6"; gene_name "CG14253"; +chr3R refGene 3UTR 22810980 22811428 . + . gene_id "CG14253"; transcript_id "NM_170302"; exon_number "6"; exon_id "NM_170302.6"; gene_name "CG14253"; +chr3R refGene exon 22810427 22811428 . + . gene_id "CG14253"; transcript_id "NM_170303"; exon_number "6"; exon_id "NM_170303.6"; gene_name "CG14253"; +chr3R refGene 3UTR 22810980 22811428 . + . gene_id "CG14253"; transcript_id "NM_170303"; exon_number "6"; exon_id "NM_170303.6"; gene_name "CG14253"; +chr3R refGene exon 23085772 23086137 . + . gene_id "CR44049"; transcript_id "NR_074063"; exon_number "1"; exon_id "NR_074063.1"; gene_name "CR44049"; +chr3R refGene exon 23086189 23087670 . + . gene_id "CR44049"; transcript_id "NR_074063"; exon_number "2"; exon_id "NR_074063.2"; gene_name "CR44049"; +chr3R refGene exon 23111808 23113170 . + . gene_id "CG3368"; transcript_id "NM_143298"; exon_number "3"; exon_id "NM_143298.3"; gene_name "CG3368"; +chr3R refGene 3UTR 23113038 23113170 . + . gene_id "CG3368"; transcript_id "NM_143298"; exon_number "3"; exon_id "NM_143298.3"; gene_name "CG3368"; +chr3R refGene exon 23117257 23117715 . - . gene_id "CG3348"; transcript_id "NM_144004"; exon_number "1"; exon_id "NM_144004.1"; gene_name "CG3348"; +chr3R refGene 3UTR 23117257 23117381 . - . gene_id "CG3348"; transcript_id "NM_144004"; exon_number "1"; exon_id "NM_144004.1"; gene_name "CG3348"; +chr3R refGene exon 25698263 25698986 . + . gene_id "CG34133"; transcript_id "NM_001043308"; exon_number "6"; exon_id "NM_001043308.6"; gene_name "CG34133"; +chr3R refGene CDS 25698263 25698986 . + 1 gene_id "CG34133"; transcript_id "NM_001043308"; exon_number "6"; exon_id "NM_001043308.6"; gene_name "CG34133"; +chr3R refGene exon 25698263 25698986 . + . gene_id "CG34133"; transcript_id "NM_001043307"; exon_number "7"; exon_id "NM_001043307.7"; gene_name "CG34133"; +chr3R refGene CDS 25698263 25698986 . + 1 gene_id "CG34133"; transcript_id "NM_001043307"; exon_number "7"; exon_id "NM_001043307.7"; gene_name "CG34133"; +chr3R refGene exon 25698427 25698986 . + . gene_id "CG34133"; transcript_id "NM_143485"; exon_number "8"; exon_id "NM_143485.8"; gene_name "CG34133"; +chr3R refGene CDS 25698427 25698986 . + 2 gene_id "CG34133"; transcript_id "NM_143485"; exon_number "8"; exon_id "NM_143485.8"; gene_name "CG34133"; +chr3R refGene exon 25860262 25860461 . - . gene_id "CR44045"; transcript_id "NR_074065"; exon_number "1"; exon_id "NR_074065.1"; gene_name "CR44045"; +chr3R refGene exon 27039536 27040506 . + . gene_id "CG1542"; transcript_id "NM_143593"; exon_number "3"; exon_id "NM_143593.3"; gene_name "CG1542"; +chr3R refGene 3UTR 27040310 27040506 . + . gene_id "CG1542"; transcript_id "NM_143593"; exon_number "3"; exon_id "NM_143593.3"; gene_name "CG1542"; +chr3R refGene exon 27420514 27421323 . - . gene_id "RpL6"; transcript_id "NM_143619"; exon_number "1"; exon_id "NM_143619.1"; gene_name "RpL6"; +chr3R refGene CDS 27420649 27421323 . - 0 gene_id "RpL6"; transcript_id "NM_143619"; exon_number "1"; exon_id "NM_143619.1"; gene_name "RpL6"; +chr3R refGene exon 27420514 27421185 . - . gene_id "RpL6"; transcript_id "NM_170554"; exon_number "1"; exon_id "NM_170554.1"; gene_name "RpL6"; +chr3R refGene CDS 27420649 27421185 . - 0 gene_id "RpL6"; transcript_id "NM_170554"; exon_number "1"; exon_id "NM_170554.1"; gene_name "RpL6"; +chr4 refGene exon 348791 352013 . + . gene_id "CG32850"; transcript_id "NM_001272124"; exon_number "4"; exon_id "NM_001272124.4"; gene_name "CG32850"; +chr4 refGene 3UTR 348791 352013 . + . gene_id "CG32850"; transcript_id "NM_001272124"; exon_number "4"; exon_id "NM_001272124.4"; gene_name "CG32850"; +chr4 refGene exon 473598 474573 . + . gene_id "CaMKI"; transcript_id "NM_079883"; exon_number "9"; exon_id "NM_079883.9"; gene_name "CaMKI"; +chr4 refGene CDS 473598 473822 . + 0 gene_id "CaMKI"; transcript_id "NM_079883"; exon_number "9"; exon_id "NM_079883.9"; gene_name "CaMKI"; +chr4 refGene exon 473598 474573 . + . gene_id "CaMKI"; transcript_id "NM_166764"; exon_number "8"; exon_id "NM_166764.8"; gene_name "CaMKI"; +chr4 refGene CDS 473598 473822 . + 0 gene_id "CaMKI"; transcript_id "NM_166764"; exon_number "8"; exon_id "NM_166764.8"; gene_name "CaMKI"; +chr4 refGene exon 473598 474573 . + . gene_id "CaMKI"; transcript_id "NM_166760"; exon_number "11"; exon_id "NM_166760.11"; gene_name "CaMKI"; +chr4 refGene CDS 473598 473822 . + 0 gene_id "CaMKI"; transcript_id "NM_166760"; exon_number "11"; exon_id "NM_166760.11"; gene_name "CaMKI"; +chr4 refGene exon 473598 474573 . + . gene_id "CaMKI"; transcript_id "NM_166761"; exon_number "9"; exon_id "NM_166761.9"; gene_name "CaMKI"; +chr4 refGene CDS 473598 473822 . + 0 gene_id "CaMKI"; transcript_id "NM_166761"; exon_number "9"; exon_id "NM_166761.9"; gene_name "CaMKI"; +chr4 refGene exon 473598 474573 . + . gene_id "CaMKI"; transcript_id "NM_166759"; exon_number "10"; exon_id "NM_166759.10"; gene_name "CaMKI"; +chr4 refGene CDS 473598 473822 . + 0 gene_id "CaMKI"; transcript_id "NM_166759"; exon_number "10"; exon_id "NM_166759.10"; gene_name "CaMKI"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_001169361"; exon_number "1"; exon_id "NM_001169361.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_001169361"; exon_number "1"; exon_id "NM_001169361.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_166810"; exon_number "1"; exon_id "NM_166810.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_166810"; exon_number "1"; exon_id "NM_166810.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_166811"; exon_number "1"; exon_id "NM_166811.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_166811"; exon_number "1"; exon_id "NM_166811.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_001014696"; exon_number "1"; exon_id "NM_001014696.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_001014696"; exon_number "1"; exon_id "NM_001014696.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_001272153"; exon_number "1"; exon_id "NM_001272153.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_001272153"; exon_number "1"; exon_id "NM_001272153.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_001272154"; exon_number "1"; exon_id "NM_001272154.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_001272154"; exon_number "1"; exon_id "NM_001272154.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_001272155"; exon_number "1"; exon_id "NM_001272155.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_001272155"; exon_number "1"; exon_id "NM_001272155.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_079896"; exon_number "1"; exon_id "NM_079896.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_079896"; exon_number "1"; exon_id "NM_079896.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_166812"; exon_number "1"; exon_id "NM_166812.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_166812"; exon_number "1"; exon_id "NM_166812.1"; gene_name "CaMKII"; +chr4 refGene exon 1055914 1058048 . - . gene_id "CaMKII"; transcript_id "NM_166813"; exon_number "1"; exon_id "NM_166813.1"; gene_name "CaMKII"; +chr4 refGene 3UTR 1055914 1057903 . - . gene_id "CaMKII"; transcript_id "NM_166813"; exon_number "1"; exon_id "NM_166813.1"; gene_name "CaMKII"; +chr4 refGene exon 1212983 1213163 . + . gene_id "CG33521"; transcript_id "NM_001014703"; exon_number "11"; exon_id "NM_001014703.11"; gene_name "CG33521"; +chr4 refGene 3UTR 1212986 1213163 . + . gene_id "CG33521"; transcript_id "NM_001014703"; exon_number "11"; exon_id "NM_001014703.11"; gene_name "CG33521"; +chr4 refGene exon 1212983 1213163 . + . gene_id "CG33521"; transcript_id "NM_001258506"; exon_number "11"; exon_id "NM_001258506.11"; gene_name "CG33521"; +chr4 refGene 3UTR 1212986 1213163 . + . gene_id "CG33521"; transcript_id "NM_001258506"; exon_number "11"; exon_id "NM_001258506.11"; gene_name "CG33521"; +chr4 refGene exon 1212983 1213320 . + . gene_id "CG33521"; transcript_id "NM_001014705"; exon_number "11"; exon_id "NM_001014705.11"; gene_name "CG33521"; +chr4 refGene 3UTR 1212986 1213320 . + . gene_id "CG33521"; transcript_id "NM_001014705"; exon_number "11"; exon_id "NM_001014705.11"; gene_name "CG33521"; +chr4 refGene exon 1212983 1213482 . + . gene_id "CG33521"; transcript_id "NM_001014702"; exon_number "11"; exon_id "NM_001014702.11"; gene_name "CG33521"; +chr4 refGene 3UTR 1212986 1213482 . + . gene_id "CG33521"; transcript_id "NM_001014702"; exon_number "11"; exon_id "NM_001014702.11"; gene_name "CG33521"; +chrX refGene exon 518440 518798 . + . gene_id "CG13369"; transcript_id "NM_130494"; exon_number "3"; exon_id "NM_130494.3"; gene_name "CG13369"; +chrX refGene 3UTR 518753 518798 . + . gene_id "CG13369"; transcript_id "NM_130494"; exon_number "3"; exon_id "NM_130494.3"; gene_name "CG13369"; +chrX refGene exon 1587418 1587876 . + . gene_id "CG14798"; transcript_id "NM_130582"; exon_number "3"; exon_id "NM_130582.3"; gene_name "CG14798"; +chrX refGene CDS 1587418 1587727 . + 1 gene_id "CG14798"; transcript_id "NM_130582"; exon_number "3"; exon_id "NM_130582.3"; gene_name "CG14798"; +chrX refGene exon 1784646 1785515 . + . gene_id "mRpL16"; transcript_id "NM_001272219"; exon_number "3"; exon_id "NM_001272219.3"; gene_name "mRpL16"; +chrX refGene 3UTR 1785263 1785515 . + . gene_id "mRpL16"; transcript_id "NM_001272219"; exon_number "3"; exon_id "NM_001272219.3"; gene_name "mRpL16"; +chrX refGene exon 8303696 8305691 . - . gene_id "lawc"; transcript_id "NM_001258650"; exon_number "4"; exon_id "NM_001258650.4"; gene_name "lawc"; +chrX refGene 5UTR 8304008 8305691 . - . gene_id "lawc"; transcript_id "NM_001258650"; exon_number "4"; exon_id "NM_001258650.4"; gene_name "lawc"; +chrX refGene exon 8582660 8582935 . - . gene_id "Ppt1"; transcript_id "NM_167166"; exon_number "1"; exon_id "NM_167166.1"; gene_name "Ppt1"; +chrX refGene 3UTR 8582660 8582812 . - . gene_id "Ppt1"; transcript_id "NM_167166"; exon_number "1"; exon_id "NM_167166.1"; gene_name "Ppt1"; +chrX refGene exon 8916051 8916272 . + . gene_id "rdgA"; transcript_id "NM_001272437"; exon_number "12"; exon_id "NM_001272437.12"; gene_name "rdgA"; +chrX refGene CDS 8916051 8916272 . + 2 gene_id "rdgA"; transcript_id "NM_001272437"; exon_number "12"; exon_id "NM_001272437.12"; gene_name "rdgA"; +chrX refGene exon 8918657 8921648 . + . gene_id "rdgA"; transcript_id "NM_001272437"; exon_number "16"; exon_id "NM_001272437.16"; gene_name "rdgA"; +chrX refGene 3UTR 8918865 8921648 . + . gene_id "rdgA"; transcript_id "NM_001272437"; exon_number "16"; exon_id "NM_001272437.16"; gene_name "rdgA"; +chrX refGene exon 8916051 8916272 . + . gene_id "rdgA"; transcript_id "NM_001272438"; exon_number "12"; exon_id "NM_001272438.12"; gene_name "rdgA"; +chrX refGene CDS 8916051 8916272 . + 2 gene_id "rdgA"; transcript_id "NM_001272438"; exon_number "12"; exon_id "NM_001272438.12"; gene_name "rdgA"; +chrX refGene exon 8918657 8923509 . + . gene_id "rdgA"; transcript_id "NM_001272438"; exon_number "16"; exon_id "NM_001272438.16"; gene_name "rdgA"; +chrX refGene 3UTR 8918865 8923509 . + . gene_id "rdgA"; transcript_id "NM_001272438"; exon_number "16"; exon_id "NM_001272438.16"; gene_name "rdgA"; +chrX refGene exon 8916051 8916272 . + . gene_id "rdgA"; transcript_id "NM_001103447"; exon_number "10"; exon_id "NM_001103447.10"; gene_name "rdgA"; +chrX refGene CDS 8916051 8916272 . + 2 gene_id "rdgA"; transcript_id "NM_001103447"; exon_number "10"; exon_id "NM_001103447.10"; gene_name "rdgA"; +chrX refGene exon 9046556 9048273 . - . gene_id "His3.3B"; transcript_id "NM_001272445"; exon_number "1"; exon_id "NM_001272445.1"; gene_name "His3.3B"; +chrX refGene 3UTR 9046556 9048144 . - . gene_id "His3.3B"; transcript_id "NM_001272445"; exon_number "1"; exon_id "NM_001272445.1"; gene_name "His3.3B"; +chrX refGene exon 9088305 9089366 . + . gene_id "CG12106"; transcript_id "NM_132308"; exon_number "2"; exon_id "NM_132308.2"; gene_name "CG12106"; +chrX refGene 3UTR 9088769 9089366 . + . gene_id "CG12106"; transcript_id "NM_132308"; exon_number "2"; exon_id "NM_132308.2"; gene_name "CG12106"; +chrX refGene exon 9088783 9089254 . - . gene_id "CG12118"; transcript_id "NM_001272451"; exon_number "1"; exon_id "NM_001272451.1"; gene_name "CG12118"; +chrX refGene CDS 9088955 9089254 . - 0 gene_id "CG12118"; transcript_id "NM_001272451"; exon_number "1"; exon_id "NM_001272451.1"; gene_name "CG12118"; +chrX refGene exon 9088783 9089254 . - . gene_id "CG12118"; transcript_id "NM_132309"; exon_number "1"; exon_id "NM_132309.1"; gene_name "CG12118"; +chrX refGene CDS 9088955 9089254 . - 0 gene_id "CG12118"; transcript_id "NM_132309"; exon_number "1"; exon_id "NM_132309.1"; gene_name "CG12118"; +chrX refGene exon 9088783 9089254 . - . gene_id "CG12118"; transcript_id "NM_176720"; exon_number "1"; exon_id "NM_176720.1"; gene_name "CG12118"; +chrX refGene CDS 9088955 9089254 . - 0 gene_id "CG12118"; transcript_id "NM_176720"; exon_number "1"; exon_id "NM_176720.1"; gene_name "CG12118"; +chrX refGene exon 10674926 10676128 . - . gene_id "sesB"; transcript_id "NM_167247"; exon_number "1"; exon_id "NM_167247.1"; gene_name "sesB"; +chrX refGene 3UTR 10674926 10675653 . - . gene_id "sesB"; transcript_id "NM_167247"; exon_number "1"; exon_id "NM_167247.1"; gene_name "sesB"; +chrX refGene exon 10675026 10676128 . - . gene_id "sesB"; transcript_id "NM_167248"; exon_number "1"; exon_id "NM_167248.1"; gene_name "sesB"; +chrX refGene 3UTR 10675026 10675653 . - . gene_id "sesB"; transcript_id "NM_167248"; exon_number "1"; exon_id "NM_167248.1"; gene_name "sesB"; +chrX refGene exon 10675026 10676128 . - . gene_id "sesB"; transcript_id "NM_078554"; exon_number "1"; exon_id "NM_078554.1"; gene_name "sesB"; +chrX refGene 3UTR 10675026 10675653 . - . gene_id "sesB"; transcript_id "NM_078554"; exon_number "1"; exon_id "NM_078554.1"; gene_name "sesB"; +chrX refGene exon 10675026 10676128 . - . gene_id "sesB"; transcript_id "NM_167246"; exon_number "1"; exon_id "NM_167246.1"; gene_name "sesB"; +chrX refGene 3UTR 10675026 10675653 . - . gene_id "sesB"; transcript_id "NM_167246"; exon_number "1"; exon_id "NM_167246.1"; gene_name "sesB"; +chrX refGene exon 12607694 12609320 . - . gene_id "Smr"; transcript_id "NM_001272562"; exon_number "8"; exon_id "NM_001272562.8"; gene_name "Smr"; +chrX refGene CDS 12607694 12609320 . - 1 gene_id "Smr"; transcript_id "NM_001272562"; exon_number "8"; exon_id "NM_001272562.8"; gene_name "Smr"; +chrX refGene exon 12607694 12609302 . - . gene_id "Smr"; transcript_id "NM_167334"; exon_number "8"; exon_id "NM_167334.8"; gene_name "Smr"; +chrX refGene CDS 12607694 12609302 . - 1 gene_id "Smr"; transcript_id "NM_167334"; exon_number "8"; exon_id "NM_167334.8"; gene_name "Smr"; +chrX refGene exon 12607694 12609302 . - . gene_id "Smr"; transcript_id "NM_167335"; exon_number "8"; exon_id "NM_167335.8"; gene_name "Smr"; +chrX refGene CDS 12607694 12609302 . - 1 gene_id "Smr"; transcript_id "NM_167335"; exon_number "8"; exon_id "NM_167335.8"; gene_name "Smr"; +chrX refGene exon 12607694 12609302 . - . gene_id "Smr"; transcript_id "NM_080536"; exon_number "8"; exon_id "NM_080536.8"; gene_name "Smr"; +chrX refGene CDS 12607694 12609302 . - 1 gene_id "Smr"; transcript_id "NM_080536"; exon_number "8"; exon_id "NM_080536.8"; gene_name "Smr"; +chrX refGene exon 16199192 16201410 . + . gene_id "CG3679"; transcript_id "NM_001272674"; exon_number "3"; exon_id "NM_001272674.3"; gene_name "CG3679"; +chrX refGene 3UTR 16200248 16201410 . + . gene_id "CG3679"; transcript_id "NM_001272674"; exon_number "3"; exon_id "NM_001272674.3"; gene_name "CG3679"; +chrX refGene exon 16779109 16779892 . + . gene_id "Rcp"; transcript_id "NM_132947"; exon_number "3"; exon_id "NM_132947.3"; gene_name "Rcp"; +chrX refGene 3UTR 16779550 16779892 . + . gene_id "Rcp"; transcript_id "NM_132947"; exon_number "3"; exon_id "NM_132947.3"; gene_name "Rcp"; +chrX refGene exon 16779109 16779892 . + . gene_id "Rcp"; transcript_id "NM_206770"; exon_number "4"; exon_id "NM_206770.4"; gene_name "Rcp"; +chrX refGene 3UTR 16779550 16779892 . + . gene_id "Rcp"; transcript_id "NM_206770"; exon_number "4"; exon_id "NM_206770.4"; gene_name "Rcp"; +chrX refGene exon 19510696 19511958 . - . gene_id "CG12788"; transcript_id "NM_001272782"; exon_number "1"; exon_id "NM_001272782.1"; gene_name "CG12788"; +chrX refGene 3UTR 19510696 19510942 . - . gene_id "CG12788"; transcript_id "NM_001272782"; exon_number "1"; exon_id "NM_001272782.1"; gene_name "CG12788"; +chrX refGene exon 19510696 19512220 . - . gene_id "Tim9b"; transcript_id "NM_001031903"; exon_number "1"; exon_id "NM_001031903.1"; gene_name "Tim9b"; +chrX refGene 3UTR 19510696 19511983 . - . gene_id "Tim9b"; transcript_id "NM_001031903"; exon_number "1"; exon_id "NM_001031903.1"; gene_name "Tim9b"; +chrX refGene exon 19510696 19512220 . - . gene_id "CG12788"; transcript_id "NM_001272783"; exon_number "1"; exon_id "NM_001272783.1"; gene_name "CG12788"; +chrX refGene 3UTR 19510696 19510942 . - . gene_id "CG12788"; transcript_id "NM_001272783"; exon_number "1"; exon_id "NM_001272783.1"; gene_name "CG12788"; +chrX refGene exon 19510696 19512220 . - . gene_id "CG12788"; transcript_id "NM_134485"; exon_number "1"; exon_id "NM_134485.1"; gene_name "CG12788"; +chrX refGene 3UTR 19510696 19510942 . - . gene_id "CG12788"; transcript_id "NM_134485"; exon_number "1"; exon_id "NM_134485.1"; gene_name "CG12788";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/te.gtf Wed May 13 12:57:29 2020 -0400 @@ -0,0 +1,866 @@ +chr4 dm3_rmsk exon 343119 348355 . + . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup2"; family_id "Gypsy"; class_id "LTR"; +chr4 dm3_rmsk exon 954243 955152 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup25"; family_id "CR1"; class_id "LINE"; +chr4 dm3_rmsk exon 1281301 1285200 . - . gene_id "TART"; transcript_id "TART_dup3"; family_id "telomeric"; class_id "LINE"; +chr4 dm3_rmsk exon 1298748 1302519 . - . gene_id "HETA"; transcript_id "HETA_dup2"; family_id "telomeric"; class_id "LINE"; +chr4 dm3_rmsk exon 1325146 1336223 . - . gene_id "TART"; transcript_id "TART_dup10"; family_id "telomeric"; class_id "LINE"; +chr4 dm3_rmsk exon 1338128 1349150 . - . gene_id "TART"; transcript_id "TART_dup15"; family_id "telomeric"; class_id "LINE"; +chrU dm3_rmsk exon 191398 191854 . + . gene_id "BURDOCK_I"; transcript_id "BURDOCK_I_dup3"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 276311 276724 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup5"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 276725 281011 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup7"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 357869 358422 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup58"; family_id "CR1"; class_id "LINE"; +chrU dm3_rmsk exon 444361 445162 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup10"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 445163 445576 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup8"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 560147 564265 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup5"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 585727 586749 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup7"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 923349 923833 . - . gene_id "T412LTR"; transcript_id "T412LTR"; family_id "LTR"; class_id "LTR"; +chrU dm3_rmsk exon 923724 930674 . - . gene_id "DM412"; transcript_id "DM412_dup20"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 930358 930842 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup1"; family_id "LTR"; class_id "LTR"; +chrU dm3_rmsk exon 977434 977847 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup9"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 977848 984017 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup11"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1068318 1074427 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup12"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1145421 1151606 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup14"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1183521 1184031 . - . gene_id "DNAREP1_DM"; transcript_id "DNAREP1_DM_dup737"; family_id "Penelope"; class_id "LINE"; +chrU dm3_rmsk exon 1210262 1212598 . - . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup7"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1217990 1220370 . - . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup8"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1223765 1226146 . - . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup9"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1293346 1293758 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup12"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1293759 1298196 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup15"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1308708 1311586 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup17"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1420117 1423754 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup22"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1443400 1449972 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup15"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1572762 1573180 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup24"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1722014 1722692 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup27"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1781498 1782154 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup10"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1805831 1807913 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup29"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1881961 1886692 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup29"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1886693 1887052 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup16"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1896226 1896818 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup28"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 1902819 1903411 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup29"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 2048219 2050481 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup35"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 2051056 2057160 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup36"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 2092493 2094999 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup152"; family_id "CR1"; class_id "LINE"; +chrU dm3_rmsk exon 2247039 2253619 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup25"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 2328705 2329297 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup30"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 2472019 2472186 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup48"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 2581052 2581507 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup31"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 2691771 2694411 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup51"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 3096181 3099337 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup53"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 3312718 3313508 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup27"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 3371327 3372261 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup61"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 3503665 3504199 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup69"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 3578157 3578336 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup4"; family_id "Copia"; class_id "LTR"; +chrU dm3_rmsk exon 3625425 3626082 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup20"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 3770053 3770709 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup22"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 3777432 3777737 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup40"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 3837334 3839552 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup76"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 4015850 4017758 . + . gene_id "TART_B1"; transcript_id "TART_B1_dup3"; family_id "telomeric"; class_id "LINE"; +chrU dm3_rmsk exon 4116367 4117555 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup48"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 4126825 4127440 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup28"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 4236892 4237987 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup83"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 4345607 4346049 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup83"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 4838081 4838523 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup59"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 5189745 5189910 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup237"; family_id "CR1"; class_id "LINE"; +chrU dm3_rmsk exon 5190657 5191171 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup93"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 5475097 5476840 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup62"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 5524199 5524856 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup36"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 5553424 5553622 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup8"; family_id "Copia"; class_id "LTR"; +chrU dm3_rmsk exon 5690556 5690753 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup9"; family_id "Copia"; class_id "LTR"; +chrU dm3_rmsk exon 5767489 5772171 . + . gene_id "TART_B1"; transcript_id "TART_B1_dup7"; family_id "telomeric"; class_id "LINE"; +chrU dm3_rmsk exon 5951132 5951685 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup99"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 5977542 5978155 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup4"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 6001421 6002602 . - . gene_id "DOC3_DM"; transcript_id "DOC3_DM_dup51"; family_id "Jockey"; class_id "LINE"; +chrU dm3_rmsk exon 6086408 6086991 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup45"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 6179002 6180525 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup103"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 6224902 6228880 . + . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup42"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 6309683 6309880 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup12"; family_id "Copia"; class_id "LTR"; +chrU dm3_rmsk exon 6473514 6473693 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup13"; family_id "Copia"; class_id "LTR"; +chrU dm3_rmsk exon 6628271 6628930 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup41"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 6677331 6677601 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup70"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 6731465 6734022 . + . gene_id "TART_B1"; transcript_id "TART_B1_dup11"; family_id "telomeric"; class_id "LINE"; +chrU dm3_rmsk exon 6945365 6947093 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup111"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 6987604 6988260 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup42"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7126511 7127835 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup114"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7264880 7267505 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup116"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7308561 7309535 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup119"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7329574 7329736 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup81"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7332248 7332896 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup122"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7332960 7334528 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup124"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7487018 7487473 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup111"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7519432 7520276 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup127"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7748631 7750155 . + . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup78"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7828761 7829083 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup132"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7881322 7881911 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup48"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 7907279 7907794 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup135"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8033433 8034022 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup51"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8137658 8137976 . + . gene_id "TIRANT_I"; transcript_id "TIRANT_I_dup20"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8244488 8244933 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup113"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8371984 8372439 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup115"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8374715 8375214 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup144"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8427074 8427271 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup15"; family_id "Copia"; class_id "LTR"; +chrU dm3_rmsk exon 8523917 8524479 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup55"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8639171 8640550 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup91"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8647157 8647861 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup306"; family_id "CR1"; class_id "LINE"; +chrU dm3_rmsk exon 8711610 8712130 . + . gene_id "Gypsy_DS"; transcript_id "Gypsy_DS_dup11"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8720854 8721046 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup107"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8721047 8721460 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup29"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8731513 8731702 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup17"; family_id "Copia"; class_id "LTR"; +chrU dm3_rmsk exon 8772055 8772757 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup157"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8809472 8809792 . - . gene_id "TIRANT_I"; transcript_id "TIRANT_I_dup23"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 8899308 8899741 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup62"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9007353 9007909 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup42"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9013996 9014409 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup30"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9014410 9014542 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup110"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9043750 9044112 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup31"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9044113 9044332 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup111"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9194346 9194700 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup63"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9280618 9281548 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup176"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9409569 9410084 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup4"; family_id "LTR"; class_id "LTR"; +chrU dm3_rmsk exon 9409769 9410183 . + . gene_id "DM412"; transcript_id "DM412_dup60"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9423981 9424974 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup181"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9466785 9467907 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup183"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9476659 9477397 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup68"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9480221 9480307 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup69"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9549357 9549872 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup7"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9693207 9693297 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup120"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9693298 9693711 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup32"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9841738 9842180 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup125"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9890510 9891080 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup9"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9917593 9917947 . - . gene_id "DM412"; transcript_id "DM412_dup62"; family_id "Gypsy"; class_id "LTR"; +chrU dm3_rmsk exon 9917630 9918110 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup5"; family_id "LTR"; class_id "LTR"; +chrU dm3_rmsk exon 9931601 9932153 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup196"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 10820 12794 . + . gene_id "TAHRE"; transcript_id "TAHRE_dup104"; family_id "telomeric"; class_id "LINE"; +chrX dm3_rmsk exon 19112 19196 . + . gene_id "TAHRE"; transcript_id "TAHRE_dup105"; family_id "telomeric"; class_id "LINE"; +chrX dm3_rmsk exon 189895 197508 . - . gene_id "DM412"; transcript_id "DM412_dup64"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 445510 453014 . + . gene_id "DM412"; transcript_id "DM412_dup65"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 706355 706755 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup33"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 706756 710761 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup122"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 927440 935019 . + . gene_id "DM412"; transcript_id "DM412_dup66"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 1251868 1253278 . - . gene_id "IVK_DM"; transcript_id "IVK_DM_dup17"; family_id "I"; class_id "LINE"; +chrX dm3_rmsk exon 1825142 1831621 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup57"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 1849398 1854645 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup49"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 3073073 3079644 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup58"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 3387608 3395852 . - . gene_id "ROO_I"; transcript_id "ROO_I_dup129"; family_id "Pao"; class_id "LTR"; +chrX dm3_rmsk exon 3395853 3396280 . - . gene_id "ROO_LTR"; transcript_id "ROO_LTR_dup45"; family_id "Pao"; class_id "LTR"; +chrX dm3_rmsk exon 3495547 3495974 . - . gene_id "ROO_LTR"; transcript_id "ROO_LTR_dup47"; family_id "Pao"; class_id "LTR"; +chrX dm3_rmsk exon 3508115 3508542 . - . gene_id "ROO_LTR"; transcript_id "ROO_LTR_dup49"; family_id "Pao"; class_id "LTR"; +chrX dm3_rmsk exon 3880951 3881464 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup6"; family_id "LTR"; class_id "LTR"; +chrX dm3_rmsk exon 3881355 3888326 . - . gene_id "DM412"; transcript_id "DM412_dup67"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 3888013 3888526 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup7"; family_id "LTR"; class_id "LTR"; +chrX dm3_rmsk exon 4051980 4052393 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup36"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 4052394 4058543 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup124"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 4722487 4728965 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup197"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 5285684 5286482 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup126"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 5286483 5286896 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup39"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 5418929 5420968 . + . gene_id "DM412"; transcript_id "DM412_dup68"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 5420945 5422734 . + . gene_id "DM412"; transcript_id "DM412_dup69"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 6065672 6066329 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup74"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 6066330 6072388 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup125"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 6072389 6073046 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup75"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 6340461 6344677 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup128"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 6344678 6345091 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup41"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 9693025 9699191 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup129"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 9699192 9699605 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup43"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 9989251 9989664 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup44"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 9989665 9994170 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup130"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 10032303 10032783 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup8"; family_id "LTR"; class_id "LTR"; +chrX dm3_rmsk exon 10032470 10039372 . + . gene_id "DM412"; transcript_id "DM412_dup70"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 10039263 10039743 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup9"; family_id "LTR"; class_id "LTR"; +chrX dm3_rmsk exon 10419160 10419572 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup46"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 10419573 10425740 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup132"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 11206576 11213009 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup51"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 11527919 11534087 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup133"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 11534088 11534501 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup50"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 12608970 12609026 . - . gene_id "ROO_I"; transcript_id "ROO_I_dup330"; family_id "Pao"; class_id "LTR"; +chrX dm3_rmsk exon 14052861 14056866 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup135"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 14056867 14057280 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup52"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 14446249 14452816 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup59"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 19030640 19031120 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup10"; family_id "LTR"; class_id "LTR"; +chrX dm3_rmsk exon 19030807 19035865 . + . gene_id "DM412"; transcript_id "DM412_dup71"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 19037021 19037501 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup11"; family_id "LTR"; class_id "LTR"; +chrX dm3_rmsk exon 19691843 19698056 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup198"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 19927404 19927817 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup57"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 19927818 19929771 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup140"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21329782 21335151 . - . gene_id "IVK_DM"; transcript_id "IVK_DM_dup19"; family_id "I"; class_id "LINE"; +chrX dm3_rmsk exon 21395076 21395730 . - . gene_id "ROO_I"; transcript_id "ROO_I_dup450"; family_id "Pao"; class_id "LTR"; +chrX dm3_rmsk exon 21421820 21423555 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup146"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21423556 21423969 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup60"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21512181 21519806 . - . gene_id "DM412"; transcript_id "DM412_dup74"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21519811 21524347 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup54"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21547758 21549716 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup201"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21549795 21551471 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup202"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21552015 21558368 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup204"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21580844 21582367 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup207"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21586806 21587822 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup208"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21604473 21610607 . - . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup71"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21615912 21617588 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup210"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21642451 21643491 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup213"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 21644907 21645298 . - . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup76"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 22022378 22022791 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup62"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 22022792 22027540 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup147"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 22175530 22176216 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup150"; family_id "Gypsy"; class_id "LTR"; +chrX dm3_rmsk exon 22176217 22176630 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup66"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 2112686 2119254 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup63"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 2565593 2566006 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup74"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 2566007 2569028 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup159"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 2772653 2773066 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup76"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 2773067 2776969 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup161"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 4662398 4668884 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup64"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 4973719 4973842 . - . gene_id "S2_DM"; transcript_id "S2_DM_dup7"; family_id "Tc1"; class_id "DNA"; +chr2L dm3_rmsk exon 4973823 4973927 . - . gene_id "S2_DM"; transcript_id "S2_DM_dup8"; family_id "Tc1"; class_id "DNA"; +chr2L dm3_rmsk exon 7977135 7977547 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup78"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 7977548 7983640 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup164"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 8594934 8601102 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup165"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 8601103 8601516 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup81"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 10593415 10599983 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup65"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 10876598 10877011 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup82"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 10877012 10883182 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup166"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 12067385 12067798 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup84"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 12067799 12073965 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup167"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 12781859 12782516 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup77"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 12782517 12788586 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup128"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 12788587 12789244 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup78"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 13449518 13450176 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup79"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 13450177 13456236 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup129"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 13456237 13456895 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup80"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 14984971 14991457 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup66"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 15586465 15586878 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup86"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 15586879 15593045 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup168"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 15683783 15684440 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup81"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 15684441 15686758 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup130"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 15718780 15719437 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup82"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 15719438 15721755 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup131"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 15726912 15727569 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup83"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 16154206 16160372 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup169"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 16160373 16160787 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup89"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 17144903 17151477 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup67"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 19147425 19147838 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup90"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 19147839 19153988 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup170"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 19658198 19664770 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup68"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 20156132 20156835 . - . gene_id "POGO"; transcript_id "POGO_dup19"; family_id "Pogo"; class_id "DNA"; +chr2L dm3_rmsk exon 20157736 20158439 . - . gene_id "POGO"; transcript_id "POGO_dup20"; family_id "Pogo"; class_id "DNA"; +chr2L dm3_rmsk exon 20835864 20836522 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup84"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 21406236 21406838 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup123"; family_id "Gypsy"; class_id "LTR"; +chr2L dm3_rmsk exon 22786818 22788162 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup218"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 29494 29691 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup23"; family_id "Copia"; class_id "LTR"; +chr2R dm3_rmsk exon 33561 33757 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup24"; family_id "Copia"; class_id "LTR"; +chr2R dm3_rmsk exon 37627 37795 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup25"; family_id "Copia"; class_id "LTR"; +chr2R dm3_rmsk exon 62686 66864 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup221"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 290249 291158 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup460"; family_id "CR1"; class_id "LINE"; +chr2R dm3_rmsk exon 320405 321649 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup138"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 333623 334869 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup142"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 352453 354318 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup144"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 1208416 1208645 . - . gene_id "DNAREP1_DM"; transcript_id "DNAREP1_DM_dup2748"; family_id "Penelope"; class_id "LINE"; +chr2R dm3_rmsk exon 1268080 1274651 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup84"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 1275172 1281362 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup63"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 1316559 1318957 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup536"; family_id "CR1"; class_id "LINE"; +chr2R dm3_rmsk exon 1469711 1470864 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup547"; family_id "CR1"; class_id "LINE"; +chr2R dm3_rmsk exon 2204690 2208130 . - . gene_id "Copia2_I"; transcript_id "Copia2_I_dup101"; family_id "Copia"; class_id "LTR"; +chr2R dm3_rmsk exon 2218252 2224794 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup227"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 2254749 2254934 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup27"; family_id "Copia"; class_id "LTR"; +chr2R dm3_rmsk exon 2261767 2261952 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup28"; family_id "Copia"; class_id "LTR"; +chr2R dm3_rmsk exon 2840244 2846730 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup86"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 3150161 3156328 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup210"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 3156329 3156741 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup106"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 3994550 3994963 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup107"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 3994964 3998866 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup211"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 7304683 7305764 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup88"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 9616211 9622776 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup89"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 10972539 10972952 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup110"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 10972953 10979116 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup215"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 15957285 15958055 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup90"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 17039987 17040847 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup94"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 19417152 19424670 . - . gene_id "DM412"; transcript_id "DM412_dup82"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 19801877 19809443 . - . gene_id "DM412"; transcript_id "DM412_dup83"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 20034646 20035128 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup13"; family_id "LTR"; class_id "LTR"; +chr2R dm3_rmsk exon 20035019 20041999 . - . gene_id "DM412"; transcript_id "DM412_dup84"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 20041684 20042166 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup14"; family_id "LTR"; class_id "LTR"; +chr2R dm3_rmsk exon 20064814 20072241 . - . gene_id "DM412"; transcript_id "DM412_dup85"; family_id "Gypsy"; class_id "LTR"; +chr2R dm3_rmsk exon 20535163 20542666 . - . gene_id "DM412"; transcript_id "DM412_dup86"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 403154 409321 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup216"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 409322 409735 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup115"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 1047407 1054568 . - . gene_id "DM412"; transcript_id "DM412_dup87"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 1054555 1055161 . - . gene_id "DM412"; transcript_id "DM412_dup88"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 1219647 1220216 . + . gene_id "DM412"; transcript_id "DM412_dup89"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 1220203 1227326 . + . gene_id "DM412"; transcript_id "DM412_dup90"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 4328954 4335856 . + . gene_id "DM412"; transcript_id "DM412_dup91"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 5292308 5292965 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup97"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 5292966 5299027 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup149"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 5299028 5299685 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup98"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 7370471 7370884 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup117"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 7370885 7371685 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup217"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 7787281 7793447 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup219"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 7793448 7793861 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup120"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 7880360 7881722 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup228"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 9070082 9070595 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup17"; family_id "LTR"; class_id "LTR"; +chr3L dm3_rmsk exon 9070282 9077180 . + . gene_id "DM412"; transcript_id "DM412_dup92"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 9077071 9077584 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup18"; family_id "LTR"; class_id "LTR"; +chr3L dm3_rmsk exon 9123704 9127416 . - . gene_id "DM412"; transcript_id "DM412_dup93"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 9526908 9534410 . + . gene_id "DM412"; transcript_id "DM412_dup94"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 11557936 11565503 . + . gene_id "DM412"; transcript_id "DM412_dup95"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 13260258 13260342 . - . gene_id "ROO_I"; transcript_id "ROO_I_dup1029"; family_id "Pao"; class_id "LTR"; +chr3L dm3_rmsk exon 14818714 14825517 . + . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup66"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 15418565 15419184 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup96"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 16609665 16610078 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup121"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 16610079 16614098 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup220"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 17510135 17517635 . - . gene_id "DM412"; transcript_id "DM412_dup96"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 17912044 17912904 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup97"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 18704339 18709588 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup67"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 19813441 19813921 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup19"; family_id "LTR"; class_id "LTR"; +chr3L dm3_rmsk exon 19813812 19820779 . - . gene_id "DM412"; transcript_id "DM412_dup97"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 19820466 19820946 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup20"; family_id "LTR"; class_id "LTR"; +chr3L dm3_rmsk exon 20327933 20328517 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup132"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 20334190 20334783 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup133"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 20583219 20583700 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup12"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 21236884 21244408 . + . gene_id "DM412"; transcript_id "DM412_dup98"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 22754546 22759914 . + . gene_id "IVK_DM"; transcript_id "IVK_DM_dup40"; family_id "I"; class_id "LINE"; +chr3L dm3_rmsk exon 22797386 22803956 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup99"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 22806024 22812083 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup158"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 22983017 22983430 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup124"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 22983431 22989521 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup228"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23150298 23150955 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup106"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23150956 23157025 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup159"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23157026 23157683 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup107"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23159066 23159723 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup108"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23159724 23165793 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup160"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23165794 23166451 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup109"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23296135 23297324 . - . gene_id "DMRT1B"; transcript_id "DMRT1B_dup239"; family_id "R1"; class_id "LINE"; +chr3L dm3_rmsk exon 23309691 23310346 . - . gene_id "PROTOP_B"; transcript_id "PROTOP_B_dup304"; family_id "P"; class_id "DNA"; +chr3L dm3_rmsk exon 23365825 23372408 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup100"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23378792 23385373 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup101"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23415043 23418949 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup230"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23464990 23466103 . + . gene_id "Gypsy3_I"; transcript_id "Gypsy3_I_dup62"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23492288 23496191 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup235"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23566127 23571153 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup236"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23665822 23667053 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup239"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23667051 23667540 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup240"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23771950 23772323 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup171"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 23800784 23802508 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup669"; family_id "CR1"; class_id "LINE"; +chr3L dm3_rmsk exon 23877394 23877591 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup29"; family_id "Copia"; class_id "LTR"; +chr3L dm3_rmsk exon 23881877 23882073 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup30"; family_id "Copia"; class_id "LTR"; +chr3L dm3_rmsk exon 23906997 23908404 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup691"; family_id "CR1"; class_id "LINE"; +chr3L dm3_rmsk exon 23968584 23969241 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup115"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 24131239 24137265 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup168"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 24190735 24191392 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup119"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 24195937 24196594 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup120"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 24265766 24272339 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup111"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 24402882 24408921 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup174"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 24467900 24472283 . + . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup114"; family_id "Gypsy"; class_id "LTR"; +chr3L dm3_rmsk exon 24512256 24513726 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup746"; family_id "CR1"; class_id "LINE"; +chr3R dm3_rmsk exon 85005 91064 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup175"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 3557455 3562699 . + . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup82"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 3917683 3919320 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup276"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 3919321 3919734 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup135"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 4694573 4694985 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup136"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 4694986 4697176 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup277"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 4723998 4724411 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup138"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 4724412 4724498 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup279"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 5130941 5137128 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup243"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 6022729 6023142 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup140"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 6023143 6027676 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup283"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 6167799 6173891 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup285"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 6173892 6174304 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup143"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 6892543 6896548 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup287"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 6896549 6896962 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup145"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 8294200 8294397 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup31"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8295389 8295558 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup32"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8299366 8299535 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup35"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8300958 8301127 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup37"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8302550 8302719 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup39"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8303884 8304053 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup40"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8305497 8305666 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup42"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8308326 8308495 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup45"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8313462 8313631 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup48"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8316291 8316460 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup51"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 8325323 8325492 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup53"; family_id "Copia"; class_id "LTR"; +chr3R dm3_rmsk exon 10928275 10928755 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup21"; family_id "LTR"; class_id "LTR"; +chr3R dm3_rmsk exon 10934859 10935305 . - . gene_id "DM412"; transcript_id "DM412_dup107"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 10934992 10935472 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup22"; family_id "LTR"; class_id "LTR"; +chr3R dm3_rmsk exon 11426941 11427422 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup23"; family_id "LTR"; class_id "LTR"; +chr3R dm3_rmsk exon 11427313 11434238 . - . gene_id "DM412"; transcript_id "DM412_dup108"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 11433924 11434405 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup24"; family_id "LTR"; class_id "LTR"; +chr3R dm3_rmsk exon 13334998 13342488 . + . gene_id "DM412"; transcript_id "DM412_dup109"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 13859073 13865652 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup114"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 16340057 16340908 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup116"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 19677352 19683927 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup117"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 22043124 22047018 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup289"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 22047019 22047431 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup147"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 22384740 22390952 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup245"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 22966292 22973844 . + . gene_id "DM412"; transcript_id "DM412_dup110"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 23701891 23708060 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup290"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 24425799 24425915 . - . gene_id "LINEJ1_DM"; transcript_id "LINEJ1_DM_dup144"; family_id "Jockey"; class_id "LINE"; +chr3R dm3_rmsk exon 24590095 24596647 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup246"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 26201316 26208883 . + . gene_id "DM412"; transcript_id "DM412_dup111"; family_id "Gypsy"; class_id "LTR"; +chr3R dm3_rmsk exon 27495986 27496134 . - . gene_id "DNAREP1_DM"; transcript_id "DNAREP1_DM_dup4623"; family_id "Penelope"; class_id "LINE"; +chrXHet dm3_rmsk exon 92917 93113 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup55"; family_id "Copia"; class_id "LTR"; +chrXHet dm3_rmsk exon 98805 99001 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup56"; family_id "Copia"; class_id "LTR"; +chrXHet dm3_rmsk exon 104691 104887 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup57"; family_id "Copia"; class_id "LTR"; +chrXHet dm3_rmsk exon 110576 110772 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup58"; family_id "Copia"; class_id "LTR"; +chrXHet dm3_rmsk exon 116461 116657 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup59"; family_id "Copia"; class_id "LTR"; +chrXHet dm3_rmsk exon 122349 122545 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup60"; family_id "Copia"; class_id "LTR"; +chrXHet dm3_rmsk exon 128221 128417 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup61"; family_id "Copia"; class_id "LTR"; +chrXHet dm3_rmsk exon 132522 132719 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup62"; family_id "Copia"; class_id "LTR"; +chrYHet dm3_rmsk exon 79707 80691 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup771"; family_id "CR1"; class_id "LINE"; +chrYHet dm3_rmsk exon 181984 182181 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup64"; family_id "Copia"; class_id "LTR"; +chrYHet dm3_rmsk exon 314592 317225 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup252"; family_id "Gypsy"; class_id "LTR"; +chrYHet dm3_rmsk exon 321875 324507 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup254"; family_id "Gypsy"; class_id "LTR"; +chrYHet dm3_rmsk exon 338562 339218 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup134"; family_id "Gypsy"; class_id "LTR"; +chr2LHet dm3_rmsk exon 22078 22201 . + . gene_id "DNAREP1_DM"; transcript_id "DNAREP1_DM_dup4748"; family_id "Penelope"; class_id "LINE"; +chr2LHet dm3_rmsk exon 237708 243077 . + . gene_id "IVK_DM"; transcript_id "IVK_DM_dup49"; family_id "I"; class_id "LINE"; +chr2LHet dm3_rmsk exon 319022 322935 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup263"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 321363 324230 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup266"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 396896 397012 . - . gene_id "HELENA"; transcript_id "HELENA_dup3"; family_id "Jockey"; class_id "LINE"; +chr2RHet dm3_rmsk exon 401410 401722 . + . gene_id "Gypsy_I"; transcript_id "Gypsy_I_dup117"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 412537 413738 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup825"; family_id "CR1"; class_id "LINE"; +chr2RHet dm3_rmsk exon 422796 423997 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup827"; family_id "CR1"; class_id "LINE"; +chr2RHet dm3_rmsk exon 579626 585667 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup272"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 711188 717988 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup87"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 845370 850300 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup278"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 906168 912510 . + . gene_id "TABOR_I"; transcript_id "TABOR_I_dup14"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1070316 1070759 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup200"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1096471 1097123 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup138"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1097124 1102831 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup193"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1103201 1103853 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup139"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1103854 1109562 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup195"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1109932 1110584 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup140"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1430601 1435981 . - . gene_id "IVK_DM"; transcript_id "IVK_DM_dup57"; family_id "I"; class_id "LINE"; +chr2RHet dm3_rmsk exon 1578556 1579063 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup142"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1595646 1595867 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup143"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1662407 1663532 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup925"; family_id "CR1"; class_id "LINE"; +chr2RHet dm3_rmsk exon 1671374 1671829 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup207"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1732318 1732515 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup66"; family_id "Copia"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1756050 1757426 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup931"; family_id "CR1"; class_id "LINE"; +chr2RHet dm3_rmsk exon 1759026 1763079 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup283"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1766744 1767869 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup934"; family_id "CR1"; class_id "LINE"; +chr2RHet dm3_rmsk exon 1829805 1830461 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup148"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 1937252 1938427 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup287"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2126851 2127507 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup150"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2205238 2211812 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup155"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2266184 2266380 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup959"; family_id "CR1"; class_id "LINE"; +chr2RHet dm3_rmsk exon 2266388 2267371 . - . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup172"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2271200 2271396 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup960"; family_id "CR1"; class_id "LINE"; +chr2RHet dm3_rmsk exon 2576017 2576497 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup29"; family_id "LTR"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2576388 2583339 . - . gene_id "DM412"; transcript_id "DM412_dup120"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2583026 2583506 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup30"; family_id "LTR"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2620135 2626569 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup294"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2649149 2649806 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup151"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 2876877 2877347 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup214"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 3240766 3242314 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup353"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 3242315 3242729 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup169"; family_id "Gypsy"; class_id "LTR"; +chr2RHet dm3_rmsk exon 3277824 3279072 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup223"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 354910 357822 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup220"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 483329 484050 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1079"; family_id "CR1"; class_id "LINE"; +chr3LHet dm3_rmsk exon 509933 513445 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup302"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 549647 552049 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup223"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 792236 794266 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1098"; family_id "CR1"; class_id "LINE"; +chr3LHet dm3_rmsk exon 823538 825639 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1102"; family_id "CR1"; class_id "LINE"; +chr3LHet dm3_rmsk exon 956253 956909 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup163"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 957266 962595 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup240"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 983668 986473 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup315"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1030809 1031465 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup167"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1151071 1155572 . + . gene_id "Gypsy_I"; transcript_id "Gypsy_I_dup153"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1160221 1165073 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup319"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1373023 1377857 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup320"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1538514 1544203 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup323"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1683469 1684123 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup173"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1690175 1690811 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup174"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1737851 1738507 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup175"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1744573 1744770 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup67"; family_id "Copia"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1774179 1777159 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup106"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 1923212 1923837 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup177"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 2034838 2037212 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup329"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 2119474 2126010 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup330"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 2197643 2198319 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1188"; family_id "CR1"; class_id "LINE"; +chr3LHet dm3_rmsk exon 2228211 2230060 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup332"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 2388150 2391546 . - . gene_id "IVK_DM"; transcript_id "IVK_DM_dup87"; family_id "I"; class_id "LINE"; +chr3LHet dm3_rmsk exon 2493951 2500000 . - . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup178"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 2501208 2501456 . - . gene_id "ACCORD2_I"; transcript_id "ACCORD2_I_dup230"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 2523539 2528337 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup334"; family_id "Gypsy"; class_id "LTR"; +chr3LHet dm3_rmsk exon 2529719 2534595 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup336"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 103505 104162 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup181"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 115978 118430 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1232"; family_id "CR1"; class_id "LINE"; +chr3RHet dm3_rmsk exon 168333 168746 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup185"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 168747 173788 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup414"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 174269 174682 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup186"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 174683 177140 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup416"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 235339 236750 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1237"; family_id "CR1"; class_id "LINE"; +chr3RHet dm3_rmsk exon 391520 393355 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup345"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 621179 625027 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1258"; family_id "CR1"; class_id "LINE"; +chr3RHet dm3_rmsk exon 708787 710560 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup266"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 714932 715949 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup269"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 735903 736888 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1270"; family_id "CR1"; class_id "LINE"; +chr3RHet dm3_rmsk exon 1048132 1048714 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup201"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 1274333 1279708 . + . gene_id "IVK_DM"; transcript_id "IVK_DM_dup92"; family_id "I"; class_id "LINE"; +chr3RHet dm3_rmsk exon 1391501 1397669 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup430"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 1397670 1398083 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup194"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 1725207 1725866 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup189"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 1969336 1971537 . - . gene_id "Gypsy_I"; transcript_id "Gypsy_I_dup201"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 1976195 1976261 . - . gene_id "DM176_I"; transcript_id "DM176_I_dup171"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 1976257 1976371 . - . gene_id "DM176_I"; transcript_id "DM176_I_dup172"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 2012595 2015484 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup357"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 2132247 2132697 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup294"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 2137589 2140535 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1362"; family_id "CR1"; class_id "LINE"; +chr3RHet dm3_rmsk exon 2152093 2154363 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1364"; family_id "CR1"; class_id "LINE"; +chr3RHet dm3_rmsk exon 2162807 2163464 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup191"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 2166224 2169074 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup287"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 2174172 2174747 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup193"; family_id "Gypsy"; class_id "LTR"; +chr3RHet dm3_rmsk exon 2502594 2502988 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup217"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 263872 264250 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup197"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 417914 418576 . - . gene_id "Baggins1"; transcript_id "Baggins1_dup329"; family_id "LOA"; class_id "LINE"; +chrUextra dm3_rmsk exon 490459 490644 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup69"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 534429 535172 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup455"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 558971 559475 . + . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup207"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 561513 561682 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup70"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 632088 632637 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup219"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 666562 666767 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup456"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 748847 750174 . + . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup193"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 781576 782842 . + . gene_id "TART"; transcript_id "TART_dup264"; family_id "telomeric"; class_id "LINE"; +chrUextra dm3_rmsk exon 1105430 1106023 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup207"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1136603 1137798 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup295"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1206989 1207411 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup382"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1207512 1207872 . - . gene_id "DM412"; transcript_id "DM412_dup150"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1207558 1208072 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup34"; family_id "LTR"; class_id "LTR"; +chrUextra dm3_rmsk exon 1214193 1214388 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup71"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 1263999 1264196 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup72"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 1283624 1283793 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup74"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 1337297 1338164 . + . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup199"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1479272 1479814 . + . gene_id "IVK_DM"; transcript_id "IVK_DM_dup115"; family_id "I"; class_id "LINE"; +chrUextra dm3_rmsk exon 1491307 1491476 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup76"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 1553696 1553892 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1507"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 1558560 1558972 . + . gene_id "Baggins1"; transcript_id "Baggins1_dup350"; family_id "LOA"; class_id "LINE"; +chrUextra dm3_rmsk exon 1566550 1567649 . - . gene_id "TART"; transcript_id "TART_dup297"; family_id "telomeric"; class_id "LINE"; +chrUextra dm3_rmsk exon 1634074 1634271 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup77"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 1674843 1675634 . + . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup206"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1682961 1683896 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup339"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1802357 1803441 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup392"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1874696 1875287 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup224"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 1943630 1944699 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup398"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2168853 2169605 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup404"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2169603 2169894 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup405"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2270032 2270229 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup80"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 2275702 2275899 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup81"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 2295331 2295528 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup82"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 2329835 2330219 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup227"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2548657 2549227 . + . gene_id "TART_B1"; transcript_id "TART_B1_dup92"; family_id "telomeric"; class_id "LINE"; +chrUextra dm3_rmsk exon 2553740 2553861 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup218"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2559253 2560254 . + . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup229"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2623068 2624066 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup427"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2821009 2821596 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup436"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2822098 2822482 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup438"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2826450 2827057 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup440"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 2892734 2893715 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup443"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 3035810 3036529 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1570"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 3052810 3053324 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup237"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 3058643 3059056 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup209"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 3059057 3059176 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup495"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 3129560 3129757 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup84"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 3203233 3203707 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup26"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 3343187 3343846 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup226"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 3457873 3458356 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup227"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 3535293 3536032 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1586"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 3577563 3578217 . + . gene_id "IVK_DM"; transcript_id "IVK_DM_dup124"; family_id "I"; class_id "LINE"; +chrUextra dm3_rmsk exon 3619388 3619704 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup228"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 3922644 3923216 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup350"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4113357 4113963 . - . gene_id "POGO"; transcript_id "POGO_dup58"; family_id "Pogo"; class_id "DNA"; +chrUextra dm3_rmsk exon 4221101 4221566 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup379"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4268697 4269186 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup497"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4308781 4308977 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1604"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 4331740 4332657 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup499"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4344371 4344921 . - . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup265"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4362616 4363106 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup380"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4372298 4372494 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1605"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 4506984 4507430 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup237"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4534961 4535282 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup509"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4643605 4644074 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup239"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4649981 4650177 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1615"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 4667366 4667714 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup513"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4743405 4743601 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup86"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 4770443 4770927 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup240"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4799955 4800151 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1616"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 4806564 4807465 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup517"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4834620 4835060 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup518"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 4903649 4904547 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup520"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5002630 5003323 . + . gene_id "DM412"; transcript_id "DM412_dup163"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5199146 5199460 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup255"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5410456 5410970 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup35"; family_id "LTR"; class_id "LTR"; +chrUextra dm3_rmsk exon 5419739 5420020 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup258"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5467623 5467819 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup87"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 5468267 5469145 . + . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup157"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5525509 5525875 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup249"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5566323 5566520 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup88"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 5639085 5639356 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup27"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5645896 5646768 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1631"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 5871695 5872156 . - . gene_id "ROVER-I_DM"; transcript_id "ROVER-I_DM_dup287"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5894742 5895604 . - . gene_id "TART"; transcript_id "TART_dup471"; family_id "telomeric"; class_id "LINE"; +chrUextra dm3_rmsk exon 5939997 5940317 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup256"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5968183 5968380 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup90"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 5973645 5974503 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup551"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 5989011 5989803 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup552"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6006291 6007150 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup553"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6057681 6057850 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup91"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 6214785 6215147 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup28"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6275627 6276474 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup556"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6356315 6356488 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup92"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 6415169 6415678 . + . gene_id "TIRANT_I"; transcript_id "TIRANT_I_dup109"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6477616 6478058 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup259"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6596063 6596902 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup566"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6726414 6727249 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup574"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6731093 6731592 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1651"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 6777120 6777571 . - . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup257"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6817033 6817865 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup411"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6841514 6842113 . - . gene_id "Stalker2_I"; transcript_id "Stalker2_I_dup170"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6903682 6904071 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup261"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6907402 6907941 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup584"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6920422 6921251 . + . gene_id "DM412"; transcript_id "DM412_dup170"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 6992859 6993661 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup412"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7102128 7102952 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup593"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7150450 7150988 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup30"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7235015 7235497 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup263"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7315986 7316645 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup600"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7334043 7334240 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup95"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 7370695 7370891 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1665"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 7446279 7446798 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup606"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7507585 7508242 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup265"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7588853 7588998 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup267"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7616213 7617024 . + . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup342"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7702096 7702404 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup269"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7734930 7735285 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup31"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7900550 7901354 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup428"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 7922267 7922830 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup272"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8078372 8078451 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1684"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 8250902 8251698 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup550"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8271783 8272323 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup636"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8290345 8291138 . - . gene_id "TART_B1"; transcript_id "TART_B1_dup139"; family_id "telomeric"; class_id "LINE"; +chrUextra dm3_rmsk exon 8314031 8314435 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup260"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8459459 8459943 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup39"; family_id "LTR"; class_id "LTR"; +chrUextra dm3_rmsk exon 8459627 8460144 . + . gene_id "DM412"; transcript_id "DM412_dup172"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8478977 8479082 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup553"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8479083 8479496 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup219"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8532787 8533222 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup435"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8560978 8561767 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup645"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8590054 8590223 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup100"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 8734305 8735091 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup557"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8806116 8806901 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup654"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8833870 8834362 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup276"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8872012 8872417 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup277"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 8926762 8926958 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1699"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 9061442 9062185 . - . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup356"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9101936 9102517 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup659"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9118656 9118814 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup559"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9118815 9119228 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup222"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9136851 9137035 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup101"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 9250524 9251301 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup662"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9351400 9351889 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1706"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 9487421 9487729 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup282"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9580526 9581298 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup669"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9771332 9772101 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup672"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9849567 9849768 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup281"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9856519 9856717 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup286"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9861728 9862489 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup673"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9899335 9899815 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup33"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9935491 9935857 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup34"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9935858 9935990 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup35"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 9994442 9995207 . - . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup282"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 10381383 10382143 . - . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup286"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 10486351 10487110 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup697"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 10539624 10540301 . + . gene_id "DM412"; transcript_id "DM412_dup184"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 10543476 10543672 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup107"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 10619983 10620180 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup108"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 11073586 11074338 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup714"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11164747 11165497 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup574"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11167300 11168050 . + . gene_id "IVK_DM"; transcript_id "IVK_DM_dup143"; family_id "I"; class_id "LINE"; +chrUextra dm3_rmsk exon 11320396 11321145 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup721"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11379012 11379760 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup725"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11560510 11560996 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup298"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11582535 11583278 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup733"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11648555 11649291 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup735"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11729718 11730462 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup740"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11747463 11748207 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup580"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11766055 11766797 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup490"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11916285 11917027 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup747"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 11919657 11920399 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup748"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12017406 12018147 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup752"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12023632 12023801 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup109"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 12084875 12085287 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup228"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12085288 12085501 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup582"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12111673 12112413 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup758"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12170543 12170736 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup110"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 12210874 12211613 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup759"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12320847 12321585 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup585"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12392963 12393700 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup765"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12445757 12446494 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup766"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12468359 12469095 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup768"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12502676 12503268 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup772"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12574033 12574537 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup494"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12608080 12608347 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup229"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12608348 12608815 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup586"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12746217 12746386 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup111"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 12761216 12761385 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup112"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 12762629 12763363 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup781"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12791845 12792001 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup588"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12792002 12792415 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup230"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 12801853 12802586 . - . gene_id "DM412"; transcript_id "DM412_dup191"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13003552 13003917 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup231"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13003918 13004284 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup590"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13012838 13013035 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup113"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 13031417 13031757 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup301"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13090101 13090449 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup41"; family_id "LTR"; class_id "LTR"; +chrUextra dm3_rmsk exon 13095090 13095821 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup790"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13145823 13146552 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup792"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13195854 13196413 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup304"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13203200 13203369 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup114"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 13359258 13359976 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup527"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13368369 13369097 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup801"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13513532 13514102 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup38"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13568026 13568291 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup232"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13568292 13568753 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup593"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13689617 13690340 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup811"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13699538 13700264 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup596"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13863890 13864605 . + . gene_id "DM412"; transcript_id "DM412_dup198"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13898531 13898702 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup309"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 13912672 13913280 . + . gene_id "Gypsy6_I"; transcript_id "Gypsy6_I_dup312"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14161352 14162074 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup545"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14234569 14235290 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup835"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14420512 14420954 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup39"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14429265 14429985 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup839"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14480972 14481691 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup841"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14585098 14585815 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup555"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14641608 14642326 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup844"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14643246 14643964 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup845"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14801198 14801911 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup40"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 14918063 14918779 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup853"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15010326 15011041 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup564"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15128635 15129292 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup317"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15145715 15146429 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup860"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15182390 15182946 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup319"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15320001 15320714 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup867"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15336281 15336994 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup869"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15411173 15411820 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup322"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15612583 15612802 . + . gene_id "POGO"; transcript_id "POGO_dup66"; family_id "Pogo"; class_id "DNA"; +chrUextra dm3_rmsk exon 15640191 15640901 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup883"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15724535 15725245 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup884"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 15812893 15813373 . + . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup278"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 16121328 16121525 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup120"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 16144641 16144838 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup121"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 16219727 16220433 . - . gene_id "NOMAD_I"; transcript_id "NOMAD_I_dup280"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 16354882 16355051 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup122"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 16419763 16420468 . + . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup41"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 16443943 16444408 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup42"; family_id "LTR"; class_id "LTR"; +chrUextra dm3_rmsk exon 16450018 16450214 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1790"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 16453089 16453509 . + . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup544"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 16529332 16529408 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup237"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 16529409 16530033 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup622"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 16837298 16837913 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup42"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 16862996 16863696 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup915"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 16992168 16992869 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup920"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 17001792 17002493 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup922"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 17027456 17028157 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup43"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 17221404 17221817 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup238"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 17221818 17221904 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup626"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 17530604 17530896 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup316"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 17768434 17768846 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup240"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 17768847 17768942 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup630"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 17786236 17786432 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1803"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 17913642 17913836 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup334"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 18148886 18149054 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup123"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 18492386 18493072 . + . gene_id "Copia2_I"; transcript_id "Copia2_I_dup423"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 18536680 18537370 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup636"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 18578603 18579293 . - . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup637"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 18870829 18871517 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup974"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 18899228 18899915 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup977"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 18907108 18907779 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup642"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19142583 19143269 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup989"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19144944 19145630 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup990"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19208740 19209153 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup242"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19209154 19209331 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup644"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19226168 19226623 . + . gene_id "T412LTR"; transcript_id "T412LTR_dup43"; family_id "LTR"; class_id "LTR"; +chrUextra dm3_rmsk exon 19328097 19328776 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup997"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19335638 19335834 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1810"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 19460722 19460965 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup322"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19573658 19574297 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup344"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19604935 19605408 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup345"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19610833 19611098 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup323"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19663660 19664337 . - . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1813"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 19695763 19696445 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1009"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19749726 19750030 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup347"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19824016 19824697 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1015"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19851352 19852032 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1017"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 19870877 19871557 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup656"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20052745 20053274 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1021"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20105098 20105612 . - . gene_id "T412LTR"; transcript_id "T412LTR_dup44"; family_id "LTR"; class_id "LTR"; +chrUextra dm3_rmsk exon 20323731 20324408 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1032"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20430184 20430860 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1042"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20446501 20447177 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1043"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20459710 20460257 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup354"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20463595 20464152 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup355"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20573012 20573133 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup652"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20573134 20573546 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup244"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20694709 20694754 . + . gene_id "POGO"; transcript_id "POGO_dup68"; family_id "Pogo"; class_id "DNA"; +chrUextra dm3_rmsk exon 20737713 20737995 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup357"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20784536 20785205 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1053"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20898322 20898891 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup45"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20977865 20978433 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup363"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20980680 20980850 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup328"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 20984041 20984712 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup676"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21106789 21107460 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1063"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21131266 21131362 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup364"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21377241 21377401 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1839"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 21461959 21462128 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup126"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 21528691 21529097 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1078"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21631573 21631769 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup332"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21636942 21637608 . + . gene_id "IVK_DM"; transcript_id "IVK_DM_dup163"; family_id "I"; class_id "LINE"; +chrUextra dm3_rmsk exon 21640777 21641443 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1082"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21664856 21665217 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup333"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21711341 21711989 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1086"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21758994 21759541 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup369"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21826284 21826949 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1088"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21882187 21882851 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1090"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21885247 21885911 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1091"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 21912022 21912686 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup689"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22126822 22127485 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1101"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22131406 22131601 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup375"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22207714 22208376 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1105"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22239760 22240422 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1106"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22596021 22596680 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup46"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22630198 22630856 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1112"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22784344 22784756 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup251"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22784757 22784859 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup668"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22831953 22832331 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup380"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 22994621 22995276 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1122"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 23057337 23057991 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1124"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 23066397 23066815 . - . gene_id "DM412B_LTR"; transcript_id "DM412B_LTR_dup47"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 23173643 23174205 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1132"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 23303172 23303787 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup383"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 23336267 23336919 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1135"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 23443874 23444070 . + . gene_id "DMCR1A"; transcript_id "DMCR1A_dup1862"; family_id "CR1"; class_id "LINE"; +chrUextra dm3_rmsk exon 23444078 23444448 . - . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup536"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 23847780 23847903 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup385"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 23991993 23992531 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup386"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 24009236 24009433 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup128"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 24345996 24346636 . + . gene_id "Gypsy12_LTR"; transcript_id "Gypsy12_LTR_dup545"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 24360836 24361477 . + . gene_id "QUASIMODO_I"; transcript_id "QUASIMODO_I_dup723"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 24576989 24577527 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup341"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 24811648 24812150 . + . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup391"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 25197241 25197870 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1185"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 25294542 25294915 . + . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup342"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 25304648 25305061 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup253"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 25305062 25305121 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup679"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 25319135 25319332 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup129"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 25431843 25432469 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1194"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 25722607 25722945 . + . gene_id "TIRANT_I"; transcript_id "TIRANT_I_dup139"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 25919521 25919667 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup130"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 26246267 26246681 . + . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup255"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 26246682 26246789 . + . gene_id "DM297_I"; transcript_id "DM297_I_dup682"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 26305984 26306164 . - . gene_id "QUASIMODO_LTR"; transcript_id "QUASIMODO_LTR_dup396"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 26399753 26400360 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1224"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 26779758 26780354 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1237"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 26821013 26821485 . - . gene_id "Gypsy4_I"; transcript_id "Gypsy4_I_dup648"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 27117304 27117501 . - . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup132"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 27229943 27230524 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1247"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 27234053 27234637 . + . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1248"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 27886616 27886879 . - . gene_id "IDEFIX_LTR"; transcript_id "IDEFIX_LTR_dup350"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 27905485 27905571 . - . gene_id "DM297_I"; transcript_id "DM297_I_dup690"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 27905572 27905891 . - . gene_id "DM297_LTR"; transcript_id "DM297_LTR_dup262"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 28209068 28209265 . + . gene_id "Copia2_LTR_DM"; transcript_id "Copia2_LTR_DM_dup133"; family_id "Copia"; class_id "LTR"; +chrUextra dm3_rmsk exon 28715167 28715519 . + . gene_id "TABOR_I"; transcript_id "TABOR_I_dup112"; family_id "Gypsy"; class_id "LTR"; +chrUextra dm3_rmsk exon 28866030 28866253 . + . gene_id "SAR_DM"; transcript_id "SAR_DM_dup7047"; family_id "Satellite"; class_id "Satellite"; +chrUextra dm3_rmsk exon 28961580 28961826 . - . gene_id "STALKER4_I"; transcript_id "STALKER4_I_dup1265"; family_id "Gypsy"; class_id "LTR";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tetranscript.xml Wed May 13 12:57:29 2020 -0400 @@ -0,0 +1,299 @@ +<?xml version="1.0"?> +<tool id="tetoolkit_tetranscripts" name="TEtranscripts" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> + <description>annotates reads to genes and transposable elements</description> + <macros> + <token name="@TOOL_VERSION@">2.1.4</token> + <token name="@WRAPPER_VERSION@">galaxy0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">tetranscripts</requirement> + </requirements> + <version_command>TEtranscripts --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ## initialize + ## file extension is required + ln -s '$GTF' 'gene_annotation.gtf' && + ln -s '$TE' 'transposable_annotation.gtf' && + + ## run + TEtranscripts + ## required + -t + #for $s in $sample_rep + '${s.t}' + #end for + -c + #for $s in $sample_rep + '${s.c}' + #end for + --GTF 'gene_annotation.gtf' + --TE 'transposable_annotation.gtf' + ## optional + --stranded '$io.stranded' + $io.sortByPos + --project 'result' + --mode '$ap.mode' + --minread $ap.minread + #if $ap.fragmentLength + --fragmentLength $ap.fragmentLength + #end if + --iteration $ap.iteration + --padj $ap.padj + --foldchange $ap.foldchange + #if 'log' in $ap.out + --verbose 3 + |& tee log.txt + #end if + ]]></command> + <inputs> + <repeat name="sample_rep" min="2" title="Select input data"> + <param argument="-t" type="data" format="bam" label="Treatment sample file"/> + <param argument="-c" type="data" format="bam" label="Control sample file"/> + </repeat> + <param argument="--GTF" type="data" format="gtf" label="Select GTF file for gene annotations"/> + <param argument="--TE" type="data" format="gtf" label="Select GTF file for transposable element annotations"/> + <section name="io" title="Input options"> + <param argument="--stranded" type="select" label="Select library type"> + <option value="no">Library is unstranded (no)</option> + <option value="forward">Second-strand cDNA library e.g. QIAseq stranded (forward)</option> + <option value="reverse">First-strand cDNA library e.g. Illumina TruSeq stranded (reverse)</option> + </param> + <param argument="--sortByPos" type="boolean" truevalue="--sortByPos" falsevalue="" label="Are input files sorted by chromosome position?"/> + </section> + <section name="ap" title="Advanced parameters"> + <param argument="--mode" type="select" label="Set TE counting mode"> + <option value="multi">Distribute among all alignments (multi)</option> + <option value="uniq">Unique mappers only (uniq)</option> + </param> + <param argument="--minread" type="integer" value="1" min="0" label="Set read count cutoff"/> + <param argument="--fragmentLength" type="integer" min="0" optional="true" label="Set average length of fragment used for single-end sequencing" help="For paired-end, estimated from the input alignment file. For single-end, ignored by default."/> + <param argument="--iteration" type="integer" value="100" min="0" label="Set maximum number of iterations used to optimize multi-reads assignment"/> + <param argument="--padj" type="float" value="0.05" min="0.0" max="1.0" label="Set FDR cutoff for significance"/> + <param argument="--foldchange" type="float" value="1.0" min="0.0" label="Set fold-change ratio (absolute) cutoff for differential expression"/> + <param name="out" type="select" multiple="true" label="Select output file(s)" help="Result files for gene TE analysis and sigDiff gene TE will be created if more than one dataset is applied."> + <option value="cnttable" selected="true">cntTable</option> + <option value="deseq2" selected="true">DESeq2.R</option> + <option value="gta" selected="true">Gene TE Analysis</option> + <option value="sgt" selected="true">SigDiff Gene TE</option> + <option value="log">Log</option> + </param> + </section> + </inputs> + <outputs> + <data name="out_cnt" format="tabular" from_work_dir="result.cntTable" label="${tool.name} on ${on_string}: cntTable"> + <filter>'cnttable' in ap['out']</filter> + </data> + <data name="out_deseq2" format="txt" from_work_dir="result_DESeq2.R" label="${tool.name} on ${on_string}: DESeq2.R"> + <filter>'deseq2' in ap['out']</filter> + </data> + <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log"> + <filter>'log' in ap['out']</filter> + </data> + <data name="out_gta" format="txt" from_work_dir="result_gene_TE_analysis.txt" label="${tool.name} on ${on_string}: Gene TE analysis"> + <filter>'gta' in ap['out']</filter> + </data> + <data name="out_sgt" format="txt" from_work_dir="result_sigdiff_gene_TE.txt" label="${tool.name} on ${on_string}: SigDiff Gene TE"> + <filter>'sgt' in ap['out']</filter> + </data> + </outputs> + <tests> + <!-- + sources for test data: + https://github.com/mhammell-laboratory/tetoolkit-test-data + https://github.com/mhammell-laboratory/TEtranscripts/issues/66 + --> + + <!-- #1: default --> + <test expect_num_outputs="5"> + <repeat name="sample_rep"> + <param name="t" value="treatment1.bam"/> + <param name="c" value="control1.bam"/> + </repeat> + <repeat name="sample_rep"> + <param name="t" value="treatment2.bam"/> + <param name="c" value="control2.bam"/> + </repeat> + <param name="GTF" value="gtf.gtf"/> + <param name="TE" value="te.gtf"/> + <section name="ap"> + <param name="out" value="cnttable,deseq2,gta,sgt,log"/> + </section> + <output name="out_cnt"> + <assert_contents> + <has_n_lines n="295"/> + <!-- depends on sample names --> + <has_text_matching expression="gene.+"/> + <!-- order changes --> + <has_text_matching expression="TIRANT.+"/> + </assert_contents> + </output> + <output name="out_deseq2"> + <assert_contents> + <has_n_lines n="14"/> + <has_text_matching expression="data.+"/> + </assert_contents> + </output> + <output name="out_log"> + <assert_contents> + <has_text_matching expression="INFO"/> + <has_text_matching expression=".+Done"/> + </assert_contents> + </output> + <output name="out_gta"> + <assert_contents> + <has_n_lines n="71"/> + <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> + <!-- order changes --> + <has_text_matching expression="TIRANT.+"/> + </assert_contents> + </output> + <!-- no content, test dataset to small --> + <output name="out_sgt"> + <assert_contents> + <has_n_lines n="1"/> + <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> + </assert_contents> + </output> + </test> + <!-- #2 --> + <test expect_num_outputs="5"> + <repeat name="sample_rep"> + <param name="t" value="treatment1.bam"/> + <param name="c" value="control1.bam"/> + </repeat> + <repeat name="sample_rep"> + <param name="t" value="treatment2.bam"/> + <param name="c" value="control2.bam"/> + </repeat> + <param name="GTF" value="gtf.gtf"/> + <param name="TE" value="te.gtf"/> + <section name="io"> + <param name="stranded" value="forward"/> + <param name="sortByPos" value="true"/> + </section> + <section name="ap"> + <param name="mode" value="uniq"/> + <param name="minread" value="2"/> + <param name="fragmentLength" value="10"/> + <param name="iteration" value="90"/> + <param name="padj" value="0.06"/> + <param name="foldchange" value="2.0"/> + <param name="out" value="cnttable,deseq2,gta,sgt,log"/> + </section> + <output name="out_cnt"> + <assert_contents> + <has_n_lines n="295"/> + <!-- depends on sample names --> + <has_text_matching expression="gene.+"/> + <!-- order changes --> + <has_text_matching expression="TIRANT.+"/> + </assert_contents> + </output> + <output name="out_deseq2"> + <assert_contents> + <has_n_lines n="14"/> + <has_text_matching expression="data.+"/> + </assert_contents> + </output> + <output name="out_log"> + <assert_contents> + <has_text_matching expression="INFO.+"/> + </assert_contents> + </output> + <output name="out_gta"> + <assert_contents> + <has_n_lines n="3"/> + <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> + <!-- order changes --> + <has_text_matching expression="DNAREP1.+"/> + </assert_contents> + </output> + <!-- no content, test dataset to small --> + <output name="out_sgt"> + <assert_contents> + <has_n_lines n="1"/> + <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> + </assert_contents> + </output> + </test> + <!-- #3 --> + <test expect_num_outputs="5"> + <repeat name="sample_rep"> + <param name="t" value="treatment1.bam"/> + <param name="c" value="control1.bam"/> + </repeat> + <repeat name="sample_rep"> + <param name="t" value="treatment2.bam"/> + <param name="c" value="control2.bam"/> + </repeat> + <param name="GTF" value="gtf.gtf"/> + <param name="TE" value="te.gtf"/> + <section name="io"> + <param name="stranded" value="reverse"/> + </section> + <section name="ap"> + <param name="out" value="cnttable,deseq2,gta,sgt,log"/> + </section> + <output name="out_cnt"> + <assert_contents> + <has_n_lines n="295"/> + <!-- depends on sample names --> + <has_text_matching expression="gene.+"/> + <!-- order changes --> + <has_text_matching expression="TIRANT.+"/> + </assert_contents> + </output> + <output name="out_deseq2"> + <assert_contents> + <has_n_lines n="14"/> + <has_text_matching expression="data.+"/> + </assert_contents> + </output> + <output name="out_log"> + <assert_contents> + <has_text_matching expression="INFO.+"/> + </assert_contents> + </output> + <output name="out_gta"> + <assert_contents> + <has_n_lines n="23"/> + <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> + <!-- order changes --> + <has_text_matching expression="TART.+"/> + </assert_contents> + </output> + <output name="out_sgt"> + <assert_contents> + <has_n_lines n="2"/> + <has_line line="baseMean	log2FoldChange	lfcSE	stat	pvalue	padj"/> + <has_text_matching expression="Gypsy12.+"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +TEtranscripts is a software package that utilizes both unambiguously (uniquely) and ambiguously (multi-) mapped reads to perform differential enrichment analyses from high throughput sequencing experiments. Currently, most expression analysis software packates are not optimized for handling the complexities involved in quantifying highly repetitive regions of the genome, especially transposable elements (TE), from short sequencing reads. Although transposon elements make up between 20 to 80% of many eukaryotic genomes and contribute significantly to the cellular transcriptome output, the difficulty in quantifying their abundances from high throughput sequencing experiments has led them to be largely ignored in most studies. The TEtranscripts provides a noticeable improvement in the recovery of TE transcripts from RNA-Seq experiments and identification of peaks associated with repetitive regions of the genome. + +**Input** + +GTF files for gene annotation can be obtained from `UCSC RefSeq <http://genome.ucsc.edu/cgi-bin/hgTables>`_, Ensembl, `iGenomes <http://support.illumina.com/sequencing/sequencing_software/igenome.html>`_ or other annotation databases. GTF files for TE annotations are customly generated from `UCSC RepeatMasker <http://genome.ucsc.edu/cgi-bin/hgTables>`_ or other annotation database. They contain two custom attributes, class_id and family_id, corresponding to the class (e.g. LINE) and family (e.g. L1) of the corresponding transposable element. A unique ID (e.g. L1Md_Gf_dup1) is also assigned for each TE annotation in the transcript_id attribute. + +**Output** + +TEtranscripts quantifies both gene and transposable element (TE) transcript abundances from RNA-Seq experiments, utilizing both uniquely and ambiguously mapped short read sequences. It processes the short reads alignments (BAM files) and proportionally assigns read counts to the corresponding gene or TE based on the user-provided annotation files (GTF files). In addition, TEtranscripts combines multiple libraries and perform differential analysis using DESeq2. + +.. class:: infomark + +**References** + +More information are available on the `project website <http://hammelllab.labsites.cshl.edu/software/#TEtranscripts>`_ and `github <https://github.com/mhammell-laboratory/TEtranscripts>`_. + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btv422</citation> + <citation type="doi">10.1007/978-1-4939-7710-9_11</citation> + </citations> +</tool> \ No newline at end of file