[Bioperl-l] GFF to GTF
Filipe Garrett
fgarret at ub.edu
Wed Nov 9 12:05:00 EST 2005
Cook, Malcolm wrote:
>GFF as a format has a variety of versions. AFAIK, GTF is GFF 2.1 or 2.5
>
>The main differences have to do with format and semantics of GFF's
>column 9, the inclusion of sequence data itself in the file, and
>
>version reference
>1 & 2 http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
>2.1 http://genes.cs.wustl.edu/GTF21.html
>2.5 ref?
>3 http://song.sourceforge.net/gff3.shtml
>
>What is your source of GFF? It is possible that your GFF annotation
>already is GTF. What version is it? Look in the file. There may be a
>'##gff-version' directive in it. Or, if you see that column 9 looks
>like 'gene_id "381.000"; transcript_id "381.000.1";' (c.f. gff 2.1 docs)
>then it probably already is in GTF.
>
>If it is NOT already GTF (GFF 2.1 or 2.5), then you must provide example
>expected input and output to see if we (I) can help further.
>
>Cheers,
>
>Malcolm Cook - mec at stowers-institute.org - 816-926-4449
>Database Applications Manager - Bioinformatics
>Stowers Institute for Medical Research - Kansas City, MO USA
>
>
>
>-----Original Message-----
>From: bioperl-l-bounces at portal.open-bio.org
>[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Filipe
>Garrett
>Sent: Tuesday, November 08, 2005 8:18 AM
>To: Bioperl
>Subject: [Bioperl-l] GFF to GTF
>
>
>Hi all,
>
>I'm currently trying to use a software called Projector to predict
>genes. As input it needs two sequences and the anotation of one of them
>in GTF. As the info in GTF is included in the GFF I was thinking of
>getting a way to convert the GFF files into GTF. I thought of using the
>Bioperl module for GFF to parse the GFF and write the GTF fields to an
>output.
>
>Does anyone knows if there's any script already made? Or of a simple way
>
>to do it?
>
>Thanks in advance
>
>FG
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
Hi all,
I'm using GFF v3 from FlyBase.
I attached an example of input and how the output should come out..
Thanks in adv.
FG
-------------- next part --------------
##gff-version 3
##sequence-region 4 1 1281640
#organism dmel
#source FlyBase Chado DB r4.2.1
#date 20050807
#
4 . chromosome 1 1281640 . . . ID=4
4 . BAC 1 137841 . + . ID=BACR05L22-hsp;Name=BACR05L22
4 . scaffold 1 173874 . + . ID=AE003845;Dbxref=Gadfly:AE003845.4;dbxref_2nd=Gadfly:AE003845
4 . chromosome_arm 1 1281640 . . . ID=4;species=Drosophila_melanogaster
4 . repeat_region 2 347 . + . ID=:5142029
4 . transposable_element 2 611 . + . ID=TE62890;Name=ninja-Dsim-like{}4829;Dbxref=FlyBase:FBti0062890,Gadfly:TE62890;synonym=ninja-Dsim-like{}4829
4 . repeat_region 348 611 . + . ID=:5142030
4 sim4:na_transcript_dmel_r31 match 638 1719 . - . ID=:5141589
4 . transposable_element 638 1719 . - . ID=TE20395;Name=baggins{}1471;Dbxref=FlyBase:FBti0020395,Gadfly:TE20395;cyto_range=102A1-102A1;gbunit=AE003845;synonym=baggins{}1471,TE20395;synonym_2nd=baggins{}1471
4 . repeat_region 638 1723 . - . ID=:5142087
4 HDP match 661 4308 . - . ID=:5141724
4 . oligo 1483 1507 . - . ID=146637_at_149-hsp:196344;Name=146637_at_149
4 . oligo 1505 1529 . - . ID=146637_at_127-hsp:196343;Name=146637_at_127
4 . repeat_region 2022 2162 . + . ID=:5142031
4 . transposable_element 2022 2162 . + . ID=TE62886;Name=HMS-Beagle2{}4825;Dbxref=FlyBase:FBti0062886,Gadfly:TE62886;synonym=HMS-Beagle2{}4825
4 . transposable_element 2217 2505 . + . ID=TE62758;Name=gypsy{}4697;Dbxref=FlyBase:FBti0062758,Gadfly:TE62758;synonym=gypsy{}4697
4 . repeat_region 2496 2738 . - . ID=:5142088
4 . transposable_element 2506 4343 . - . ID=TE20396;Name=Rt1c{}1472;Dbxref=FlyBase:FBti0020396,Gadfly:TE20396;cyto_range=102A1-102A1;gbunit=AE003845;synonym=Rt1c{}1472,TE20396;synonym_2nd=Rt1c{}1472
4 sim4:na_transcript_dmel_r31 match 2554 4264 . - . ID=:5141588
4 . repeat_region 3692 4348 . - . ID=:5142089
4 . transposable_element 4364 13761 . - . ID=TE20400;Name=1360{}1476;Dbxref=FlyBase:FBti0020400,Gadfly:TE20400;cyto_range=102A1-102A1;gbunit=AE003845;synonym=1360{}1476,TE20400;synonym_2nd=1360{}1476
4 . repeat_region 4364 4611 . - . ID=:5142090
4 . transcription_start_site 4629 4630 . - . ID=:5140416
4 sim4:na_transcript_dmel_r31 match 4886 11664 . + . ID=:5141326
4 . repeat_region 4886 13244 . + . ID=:5142032
4 . transposable_element 4886 13244 . + . ID=TE59758;Name=GATE{}1697;Dbxref=FlyBase:FBti0059758,Gadfly:TE59758;synonym=GATE{}1697
4 . transcription_start_site 5031 5032 . + . ID=:5140355
4 sim4:na_dbEST.same.dmel match_part 5175 5627 . - . ID=8868228;Name=GH01459.5prime;Parent=88682278868229
4 sim4:na_dbEST.same.dmel match 5175 5627 . - . ID=88682278868229;Name=GH01459.5prime
4 . transcription_start_site 5996 5997 . - . ID=:5140417
4 . transcription_start_site 6231 6232 . + . ID=:5140356
4 sim4:na_dbEST.diff.dmel match_part 6312 6760 . + . ID=8868204;Name=EK241115.5prime;Parent=88682038868205
4 sim4:na_dbEST.diff.dmel match 6312 6760 . + . ID=88682038868205;Name=EK241115.5prime
4 HDP match 6597 6928 . + . ID=:5141702
4 sim4:na_dbEST.diff.dmel match_part 7095 7378 . + . ID=8868207;Name=CK00114.5prime.contig;Parent=88682068868208
4 sim4:na_dbEST.diff.dmel match 7095 7378 . + . ID=88682068868208;Name=CK00114.5prime.contig
4 sim4:na_dbEST.same.dmel match_part 7236 7740 . - . ID=8868231;Name=RH16086.5prime;Parent=88682308868232
4 sim4:na_dbEST.same.dmel match 7236 7740 . - . ID=88682308868232;Name=RH16086.5prime
4 sim4:na_dbEST.diff.dmel match_part 7431 7763 . + . ID=8868209;Name=CK00114.5prime.contig;Parent=88682068868208
4 HDP match 9305 10028 . - . ID=:5141722
4 . chromosome_band 9362 32056 . + . ID=band-101F1;cyto_range=101F1
4 sim4:na_dbEST.diff.dmel match_part 9485 9981 . - . ID=8868215;Name=SD08831.3prime;Parent=88682148868216
4 sim4:na_dbEST.diff.dmel match 9485 9981 . - . ID=88682148868216;Name=SD08831.3prime
4 sim4:na_dbEST.same.dmel match_part 9486 10040 . + . ID=8868234;Name=RH12136.5prime;Parent=88682338868235
4 sim4:na_dbEST.same.dmel match 9486 10040 . + . ID=88682338868235;Name=RH12136.5prime
4 sim4:na_dbEST.same.dmel match_part 9486 10058 . + . ID=8868237;Name=RH08968.5prime;Parent=88682368868238
4 sim4:na_dbEST.same.dmel match 9486 10058 . + . ID=88682368868238;Name=RH08968.5prime
4 sim4:na_dbEST.same.dmel match_part 9486 10105 . + . ID=8868240;Name=RH48040.5prime;Parent=88682398868241
4 sim4:na_dbEST.same.dmel match 9486 10105 . + . ID=88682398868241;Name=RH48040.5prime
4 sim4:na_dbEST.same.dmel match_part 9486 10133 . + . ID=8868243;Name=RH44242.5prime;Parent=88682428868244
4 sim4:na_dbEST.same.dmel match 9486 10133 . + . ID=88682428868244;Name=RH44242.5prime
4 sim4:na_dbEST.same.dmel match_part 9486 10134 . + . ID=8868246;Name=RH73307.5prime;Parent=88682459173144
4 sim4:na_dbEST.same.dmel match 9486 10134 . + . ID=88682459173144;Name=RH73307.5prime
4 sim4:na_dbEST.same.dmel match_part 9486 10149 . + . ID=9173146;Name=RH25961.5prime;Parent=91731459173147
4 sim4:na_dbEST.same.dmel match 9486 10149 . + . ID=91731459173147;Name=RH25961.5prime
4 sim4:na_dbEST.same.dmel match_part 9486 10169 . + . ID=9173149;Name=RH58061.5prime;Parent=91731489173150
4 sim4:na_dbEST.same.dmel match 9486 10169 . + . ID=91731489173150;Name=RH58061.5prime
4 sim4:na_dbEST.same.dmel match_part 9486 10189 . + . ID=9173152;Name=RH59867.5prime;Parent=91731519173153
4 sim4:na_dbEST.same.dmel match 9486 10189 . + . ID=91731519173153;Name=RH59867.5prime
4 sim4:na_dbEST.diff.dmel match_part 9885 10421 . + . ID=8868211;Name=SD22832.5prime;Parent=88682108868212
4 sim4:na_dbEST.diff.dmel match 9885 10421 . + . ID=88682108868212;Name=SD22832.5prime
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102383;Name=RH02591.5prime;Parent=101023829377562
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=9173155;Name=RH02741.5prime;Parent=91731549173156
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102379;Name=RH03564.5prime;Parent=101023789375809
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102399;Name=RH03774.5prime;Parent=101023989377570
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=9173160;Name=RH11163.5prime;Parent=91731599173161
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102371;Name=RH11216.5prime;Parent=101023709375805
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=9173165;Name=RH12703.5prime;Parent=91731649173166
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102391;Name=RH14480.5prime;Parent=101023909377554
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102375;Name=RH14757.5prime;Parent=101023749377558
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102407;Name=RH38788.5prime;Parent=101024069377578
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102415;Name=RH43241.5prime;Parent=101024149377586
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102411;Name=RH62973.5prime;Parent=101024109377582
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102403;Name=RH68715.5prime;Parent=101024029377574
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102387;Name=RH69115.5prime;Parent=101023869375816
4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102395;Name=RH74065.5prime;Parent=101023949377566
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023829377562;Name=RH02591.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=91731549173156;Name=RH02741.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023789375809;Name=RH03564.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023989377570;Name=RH03774.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=91731599173161;Name=RH11163.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023709375805;Name=RH11216.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=91731649173166;Name=RH12703.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023909377554;Name=RH14480.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023749377558;Name=RH14757.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101024069377578;Name=RH38788.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101024149377586;Name=RH43241.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101024109377582;Name=RH62973.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101024029377574;Name=RH68715.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023869375816;Name=RH69115.5prime
4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023949377566;Name=RH74065.5prime
4 sim4:na_dbEST.same.dmel match_part 9976 10015 . - . ID=10102420;Name=RH16541.5prime;Parent=101024189375793
4 sim4:na_dbEST.same.dmel match 9976 10015 . - . ID=101024189375793;Name=RH16541.5prime
4 HDP match 10103 10417 . - . ID=:5141721
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102384;Name=RH02591.5prime;Parent=101023829377562
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=9173157;Name=RH02741.5prime;Parent=91731549173156
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102380;Name=RH03564.5prime;Parent=101023789375809
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102400;Name=RH03774.5prime;Parent=101023989377570
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=9173162;Name=RH11163.5prime;Parent=91731599173161
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102372;Name=RH11216.5prime;Parent=101023709375805
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=9173167;Name=RH12703.5prime;Parent=91731649173166
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102392;Name=RH14480.5prime;Parent=101023909377554
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102376;Name=RH14757.5prime;Parent=101023749377558
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102408;Name=RH38788.5prime;Parent=101024069377578
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102416;Name=RH43241.5prime;Parent=101024149377586
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102412;Name=RH62973.5prime;Parent=101024109377582
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102404;Name=RH68715.5prime;Parent=101024029377574
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102388;Name=RH69115.5prime;Parent=101023869375816
4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102396;Name=RH74065.5prime;Parent=101023949377566
4 sim4:na_dbEST.same.dmel match_part 10114 10380 . - . ID=10102419;Name=RH16541.5prime;Parent=101024189375793
4 HDP match 10431 10936 . - . ID=:5141720
4 sim4:na_dbEST.diff.dmel match_part 10436 10499 . + . ID=8868213;Name=SD22832.5prime;Parent=88682108868212
4 sim4:na_dbEST.same.dmel match_part 10436 10514 . + . ID=9173158;Name=RH02741.5prime;Parent=91731549173156
4 sim4:na_dbEST.same.dmel match_part 10436 10623 . + . ID=9173163;Name=RH11163.5prime;Parent=91731599173161
4 sim4:na_dbEST.same.dmel match_part 10436 10624 . + . ID=9173168;Name=RH12703.5prime;Parent=91731649173166
4 sim4:na_dbEST.same.dmel match_part 10436 10636 . + . ID=10102373;Name=RH11216.5prime;Parent=101023709375805
4 sim4:na_dbEST.same.dmel match_part 10436 10638 . + . ID=10102377;Name=RH14757.5prime;Parent=101023749377558
4 sim4:na_dbEST.same.dmel match_part 10436 10639 . + . ID=10102381;Name=RH03564.5prime;Parent=101023789375809
4 sim4:na_dbEST.same.dmel match_part 10436 10669 . + . ID=10102385;Name=RH02591.5prime;Parent=101023829377562
4 sim4:na_dbEST.same.dmel match_part 10436 10675 . + . ID=10102393;Name=RH14480.5prime;Parent=101023909377554
4 sim4:na_dbEST.same.dmel match_part 10436 10675 . + . ID=10102389;Name=RH69115.5prime;Parent=101023869375816
4 sim4:na_dbEST.same.dmel match_part 10436 10734 . + . ID=10102397;Name=RH74065.5prime;Parent=101023949377566
4 sim4:na_dbEST.same.dmel match_part 10436 10739 . + . ID=10102401;Name=RH03774.5prime;Parent=101023989377570
4 sim4:na_dbEST.same.dmel match_part 10436 10774 . + . ID=10102405;Name=RH68715.5prime;Parent=101024029377574
4 sim4:na_dbEST.same.dmel match_part 10436 10775 . + . ID=10102409;Name=RH38788.5prime;Parent=101024069377578
4 sim4:na_dbEST.same.dmel match_part 10436 10777 . + . ID=10102413;Name=RH62973.5prime;Parent=101024109377582
4 sim4:na_dbEST.same.dmel match_part 10436 10779 . + . ID=10102417;Name=RH43241.5prime;Parent=101024149377586
4 HDP match 10968 12911 . - . ID=:5141719
4 HDP match 11351 12705 . - . ID=:5141723
4 sim4:na_dbEST.diff.dmel match_part 11561 12128 . - . ID=8868218;Name=SD14867.5prime;Parent=88682178868219
4 sim4:na_dbEST.diff.dmel match 11561 12128 . - . ID=88682178868219;Name=SD14867.5prime
4 sim4:na_transcript_dmel_r31 match 11691 12255 . - . ID=:5141587
4 . transposable_element 11691 12255 . - . ID=TE20398;Name=GATE{}1474;Dbxref=FlyBase:FBti0020398,Gadfly:TE20398;cyto_range=102A1-102A1;gbunit=AE003845;synonym=TE20398;synonym_2nd=GATE{}1474
4 sim4:na_dbEST.same.dmel match_part 12036 12645 . - . ID=10102426;Name=RH67006.5prime;Parent=101024259371916
4 sim4:na_dbEST.same.dmel match 12036 12645 . - . ID=101024259371916;Name=RH67006.5prime
4 sim4:na_dbEST.same.dmel match_part 12065 12680 . + . ID=10102422;Name=RH73606.3prime;Parent=101024219377304
4 sim4:na_dbEST.same.dmel match 12065 12680 . + . ID=101024219377304;Name=RH73606.3prime
4 sim4:na_dbEST.same.dmel match_part 12088 12645 . - . ID=10102428;Name=RH22614.5prime;Parent=101024279371908
4 sim4:na_dbEST.same.dmel match 12088 12645 . - . ID=101024279371908;Name=RH22614.5prime
4 sim4:na_dbEST.same.dmel match_part 12099 12645 . - . ID=10102430;Name=RH40331.5prime;Parent=101024299371892
4 sim4:na_dbEST.same.dmel match 12099 12645 . - . ID=101024299371892;Name=RH40331.5prime
4 sim4:na_transcript_dmel_r31 match 12291 13244 . + . ID=:5141327
4 sim4:na_dbEST.same.dmel match_part 12500 13159 . + . ID=10102424;Name=RE74714.3prime;Parent=101024239377301
4 sim4:na_dbEST.same.dmel match 12500 13159 . + . ID=101024239377301;Name=RE74714.3prime
4 sim4:na_dbEST.diff.dmel match_part 12654 13097 . - . ID=8868221;Name=SD03350.3prime;Parent=88682208868222
4 sim4:na_dbEST.diff.dmel match 12654 13097 . - . ID=88682208868222;Name=SD03350.3prime
4 sim4:na_transcript_dmel_r31 match 13288 13761 . - . ID=:5141586
4 . transcription_start_site 13733 13734 . + . ID=:5140357
4 . oligo 13735 13759 . + . ID=151319_at_40-hsp:196328;Name=151319_at_40
4 HDP match 13745 15728 . - . ID=:5141718
4 . repeat_region 13847 14009 . - . ID=:5142091
4 . transposable_element 13848 13898 . - . ID=TE62859;Name=R1{}4798;Dbxref=FlyBase:FBti0062859,Gadfly:TE62859;synonym=R1{}4798
4 . transposable_element 13913 16920 . - . ID=TE63397;Name=Rt1a{}5336;Dbxref=FlyBase:FBti0063397,Gadfly:TE63397;synonym=Rt1a{}5336
4 . repeat_region 14016 15300 . - . ID=:5142092
4 . repeat_region 15298 16140 . - . ID=:5142093
4 HDP match 16549 17324 . - . ID=:5141717
4 . transposable_element 17379 17472 . - . ID=TE62792;Name=Rt1b{}4731;Dbxref=FlyBase:FBti0062792,Gadfly:TE62792;synonym=Rt1b{}4731
4 . repeat_region 17379 17481 . - . ID=:5142094
4 sim4:na_transcript_dmel_r31 match 17702 18272 . - . ID=:5141585
4 . repeat_region 17702 18277 . - . ID=:5142095
4 . transposable_element 17702 24049 . - . ID=TE20401;Name=Rt1b{}1477;Dbxref=FlyBase:FBti0020401,Gadfly:TE20401;cyto_range=102A1-102A1;gbunit=AE003845;synonym=Rt1b{}1477,TE20401;synonym_2nd=Rt1b{}1477
4 HDP match 17946 19424 . - . ID=:5141716
4 . transposable_element 18281 23344 . + . ID=TE63368;Name=gypsy8{}5307;Dbxref=FlyBase:FBti0063368,Gadfly:TE63368;synonym=gypsy8{}5307
4 . repeat_region 18338 18730 . + . ID=:5142033
4 genscan match 18740 19127 . + . ID=:5141638
4 blastx:aa_SPTR.dmel match 18810 18941 . - . ID=:5142608
4 blastx:aa_SPTR.dmel match 19018 19188 . + . ID=:5142140
4 . repeat_region 19295 19668 . + . ID=:5142034
4 . transposable_element 19295 19668 . + . ID=TE62883;Name=Osvaldo-Dbuz-like{}4822;Dbxref=FlyBase:FBti0062883,Gadfly:TE62883;synonym=Osvaldo-Dbuz-like{}4822
4 . repeat_region 19753 20124 . + . ID=:5142035
4 . repeat_region 20125 20433 . + . ID=:5142036
4 HDP match 20207 21817 . + . ID=:5141703
4 sim4:na_dbEST.same.dmel match_part 21082 21535 . - . ID=10102434;Name=RH04454.3prime;Parent=1010243110102433
4 sim4:na_dbEST.same.dmel match 21082 21535 . - . ID=1010243110102433;Name=RH04454.3prime
4 . repeat_region 21236 21772 . + . ID=:5142037
4 sim4:na_dbEST.same.dmel match_part 21545 21617 . - . ID=10102432;Name=RH04454.3prime;Parent=1010243110102433
4 tblastx:na_dpse match 21774 21908 . + . ID=:5152554
4 tblastx:na_dpse match 21774 21908 . + . ID=:5152555
4 tblastx:na_dpse match 21774 21908 . + . ID=:5152556
4 tblastx:na_dpse match 21774 21908 . + . ID=:5152558
4 tblastx:na_dpse match 21774 21908 . + . ID=:5152559
4 tblastx:na_dpse match 21774 21908 . + . ID=:5152573
4 tblastx:na_dpse match 21783 21908 . + . ID=:5152572
4 genscan match 21806 21906 . + . ID=:5141639
4 genie match 21901 23205 . - . ID=:5154252
4 . repeat_region 21911 21956 . + . ID=:5142038
4 . repeat_region 21959 22348 . + . ID=:5142039
4 . exon 22335 22528 . - . ID=CG32013:2;Parent=CG32013-RA
4 sim4:na_transcript_dmel_r31 match 22335 22528 . - . ID=:5141584
4 sim4:na_transcript_dmel_r32 match 22335 22528 . - . ID=:5141970
4 . gene 22335 23205 . - . ID=CG32013;Dbxref=FlyBase:FBan0032013,FlyBase:FBgn0052013;cyto_range=102A1-102A1;gbunit=AE003845;synonym=CG32013
4 . mRNA 22335 23205 . - . ID=CG32013-RA;Dbxref=FlyBase:FBtr0089183,FlyBase:FBgn0052013;Parent=CG32013;dbxref_2nd=Gadfly:CG32013-RA;synonym=CG32013-RA
4 . CDS 22338 23205 . - . ID=CG32013-PA;Dbxref=FlyBase:FBpp0088247,GB_protein:AAN06536.1,FlyBase:FBgn0052013;Parent=CG32013-RA;dbxref_2nd=Gadfly:CG32013-PA;synonym=CG32013-PA
4 . repeat_region 22360 22514 . + . ID=:5142040
4 . oligo 22451 22475 . + . ID=146624_at_344-hsp:196340;Name=146624_at_344
4 . exon 22617 23205 . - . ID=CG32013:1;Parent=CG32013-RA
4 sim4:na_transcript_dmel_r31 match 22617 23205 . - . ID=:5141583
4 sim4:na_transcript_dmel_r32 match 22617 23205 . - . ID=:5141969
4 genscan match 22634 22812 . + . ID=:5141640
4 blastx:aa_SPTR.dmel match 22792 23205 . - . ID=:5142565
4 genscan match 22822 23043 . + . ID=:5141641
4 . repeat_region 23071 23164 . + . ID=:5142041
4 . repeat_region 23345 24049 . - . ID=:5142096
4 . oligo 23689 23713 . - . ID=146635_at_262-hsp:196342;Name=146635_at_262
4 . oligo 23915 23939 . - . ID=146635_at_58-hsp:196341;Name=146635_at_58
4 tblastx:na_dpse match 24050 24187 . + . ID=:5152560
4 tblastx:na_dpse match 24050 24211 . + . ID=:5152557
4 tblastx:na_agambiae match 24050 24211 . + . ID=:5151345
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4 FlyBase start_codon 23203 23205 . - 0 gene_id 1;transcript_id 1;exon_id 1
4 FlyBase exon 22617 23205 . - . gene_id 1;transcript_id 1;exon_id 1
4 FlyBase CDS 22617 23205 . - 0 gene_id 1;transcript_id 1;exon_id 1
4 FlyBase exon 22335 22528 . - . gene_id 1;transcript_id 1;exon_id 2
4 FlyBase CDS 22338 23528 . - 0 gene_id 1;transcript_id 1;exon_id 2
4 FlyBase stop_codon 22335 22337 . - 0 gene_id 1;transcript_id 1;exon_id 2
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