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/test-data/5.gff3

https://bitbucket.org/cistrome/cistrome-harvard/
Unknown | 150 lines | 150 code | 0 blank | 0 comment | 0 complexity | 2656dc5596913557f33e4578072c69b8 MD5 | raw file
  1##gff-version 3
  2##date Tue Jun 26 10:48:17 2007
  3##sequence-region ctgA 1 50000
  4##source gbrowse GFFToGalaxyDumper plugin
  5##NOTE: All features dumped.
  6ctgA	example	my_feature	22132	24633	.	+	.	ID=My_feature:f15
  7ctgA	example	my_feature	46990	48410	.	-	.	ID=My_feature:f11
  8ctgA	example	my_feature	44705	47713	.	-	.	ID=My_feature:f01
  9ctgA	example	my_feature	36649	40440	.	-	.	ID=My_feature:f03
 10ctgA	example	my_feature	23072	23185	.	+	.	ID=My_feature:f14
 11ctgA	example	my_feature	37242	38653	.	+	.	ID=My_feature:f04
 12ctgA	example	motif	37497	40559	.	-	.	ID=Motif:m15;Note=7-transmembrane
 13ctgA	example	my_feature	36034	38167	.	+	.	ID=My_feature:f09
 14ctgA	example	motif	28332	30033	.	-	.	ID=Motif:m02;Note=HOX
 15ctgA	example	my_feature	4715	5968	.	-	.	ID=My_feature:f05
 16ctgA	example	motif	48253	48366	.	+	.	ID=Motif:m01;Note=WD40
 17ctgA	example	BAC	1000	20000	.	.	.	ID=BAC:b101.2;Note=Fingerprinted+BAC+with+end+reads
 18ctgA	example	right_end_read	19500	20000	.	-	.	Parent=BAC:b101.2
 19ctgA	example	left_end_read	1000	1500	.	+	.	Parent=BAC:b101.2
 20ctgA	example	motif	13801	14007	.	-	.	ID=Motif:m05;Note=helix+loop+helix
 21ctgA	example	coding	1050	9000	.	+	.	ID=mRNA:EDEN.1;Gene=EDEN
 22ctgA	example	CDS	1201	1500	.	+	0	Parent=mRNA:EDEN.1
 23ctgA	example	CDS	3000	3902	.	+	0	Parent=mRNA:EDEN.1
 24ctgA	example	CDS	5000	5500	.	+	0	Parent=mRNA:EDEN.1
 25ctgA	example	CDS	7000	7608	.	+	0	Parent=mRNA:EDEN.1
 26ctgA	example	processed_transcript	1050	9000	.	+	.	ID=mRNA:EDEN.1
 27ctgA	example	5'-UTR	1050	1200	.	+	.	Parent=mRNA:EDEN.1
 28ctgA	example	3'-UTR	7609	9000	.	+	.	Parent=mRNA:EDEN.1
 29ctgA	est	match	5410	7503	.	-	.	ID=EST:agt830.3;Target=agt830.3+1+595
 30ctgA	est	HSP	7000	7503	.	-	.	Parent=EST:agt830.3;Target=agt830.3+1+504
 31ctgA	est	HSP	5410	5500	.	-	.	Parent=EST:agt830.3;Target=agt830.3+505+595
 32ctgA	example	motif	46012	48851	.	+	.	ID=Motif:m09;Note=kinase
 33ctgA	example	match	6885	8999	.	-	.	ID=Match:seg03
 34ctgA	example	HSP	8306	8999	.	-	.	Parent=Match:seg03
 35ctgA	example	HSP	8055	8080	.	-	.	Parent=Match:seg03
 36ctgA	example	HSP	7410	7737	.	-	.	Parent=Match:seg03
 37ctgA	example	HSP	6885	7241	.	-	.	Parent=Match:seg03
 38ctgA	example	my_feature	13280	16394	.	+	.	ID=My_feature:f08
 39ctgA	example	match	29771	32937	.	+	.	ID=Match:seg10
 40ctgA	example	HSP	29771	29942	.	+	.	Parent=Match:seg10
 41ctgA	example	HSP	30042	30340	.	+	.	Parent=Match:seg10
 42ctgA	example	HSP	30810	31307	.	+	.	Parent=Match:seg10
 43ctgA	example	HSP	31761	31984	.	+	.	Parent=Match:seg10
 44ctgA	example	HSP	32374	32937	.	+	.	Parent=Match:seg10
 45ctgA	example	match	36616	37227	.	-	.	ID=Match:seg09
 46ctgA	example	HSP	37208	37227	.	-	.	Parent=Match:seg09
 47ctgA	example	HSP	36616	37057	.	-	.	Parent=Match:seg09
 48ctgA	example	motif	11911	15561	.	+	.	ID=Motif:m11;Note=kinase
 49ctgA	est	match	1050	3202	.	+	.	ID=EST:agt830.5;Target=agt830.5+1+654
 50ctgA	est	HSP	1050	1500	.	+	.	Parent=EST:agt830.5;Target=agt830.5+1+451
 51ctgA	est	HSP	3000	3202	.	+	.	Parent=EST:agt830.5;Target=agt830.5+452+654
 52ctgA	example	motif	15396	16159	.	+	.	ID=Motif:m03;Note=zinc+finger
 53ctgA	est	match	1150	7200	.	+	.	ID=EST:agt767.5;Target=agt767.5+1+1153
 54ctgA	est	HSP	1150	1500	.	+	.	Parent=EST:agt767.5;Target=agt767.5+1+351
 55ctgA	est	HSP	5000	5500	.	+	.	Parent=EST:agt767.5;Target=agt767.5+352+852
 56ctgA	est	HSP	7000	7200	.	+	.	Parent=EST:agt767.5;Target=agt767.5+853+1153
 57ctgA	est	match	1050	7300	.	+	.	ID=EST:agt221.5;Target=agt221.5+1+1253
 58ctgA	est	HSP	1050	1500	.	+	.	Parent=EST:agt221.5;Target=agt221.5+1+451
 59ctgA	est	HSP	5000	5500	.	+	.	Parent=EST:agt221.5;Target=agt221.5+452+952
 60ctgA	est	HSP	7000	7300	.	+	.	Parent=EST:agt221.5;Target=agt221.5+953+1253
 61ctgA	example	my_feature	19157	22915	.	-	.	ID=My_feature:f13
 62ctgA	est	match	8000	9000	.	-	.	ID=EST:agt767.3;Target=agt767.3+1+1001
 63ctgA	est	HSP	8000	9000	.	-	.	Parent=EST:agt767.3;Target=agt767.3+1+1001
 64ctgA	example	motif	28342	28447	.	-	.	ID=Motif:m10;Note=DEAD+box
 65ctgA	example	motif	17667	17690	.	+	.	ID=Motif:m13;Note=DEAD+box
 66ctgA	example	trace	44401	45925	.	+	.	ID=name:trace;trace=volvox_trace.scf
 67ctgA	example	match	26122	34466	.	+	.	ID=Match:seg02
 68ctgA	example	HSP	26122	26126	.	+	.	Parent=Match:seg02
 69ctgA	example	HSP	26497	26869	.	+	.	Parent=Match:seg02
 70ctgA	example	HSP	27201	27325	.	+	.	Parent=Match:seg02
 71ctgA	example	HSP	27372	27433	.	+	.	Parent=Match:seg02
 72ctgA	example	HSP	27565	27565	.	+	.	Parent=Match:seg02
 73ctgA	example	HSP	27813	28091	.	+	.	Parent=Match:seg02
 74ctgA	example	HSP	28093	28201	.	+	.	Parent=Match:seg02
 75ctgA	example	HSP	28329	28377	.	+	.	Parent=Match:seg02
 76ctgA	example	HSP	28829	29194	.	+	.	Parent=Match:seg02
 77ctgA	example	HSP	29517	29702	.	+	.	Parent=Match:seg02
 78ctgA	example	HSP	29713	30061	.	+	.	Parent=Match:seg02
 79ctgA	example	HSP	30329	30774	.	+	.	Parent=Match:seg02
 80ctgA	example	HSP	30808	31306	.	+	.	Parent=Match:seg02
 81ctgA	example	HSP	31516	31729	.	+	.	Parent=Match:seg02
 82ctgA	example	HSP	31753	32154	.	+	.	Parent=Match:seg02
 83ctgA	example	HSP	32595	32696	.	+	.	Parent=Match:seg02
 84ctgA	example	HSP	32892	32901	.	+	.	Parent=Match:seg02
 85ctgA	example	HSP	33127	33388	.	+	.	Parent=Match:seg02
 86ctgA	example	HSP	33439	33443	.	+	.	Parent=Match:seg02
 87ctgA	example	HSP	33759	34209	.	+	.	Parent=Match:seg02
 88ctgA	example	HSP	34401	34466	.	+	.	Parent=Match:seg02
 89ctgA	example	contig	1	50000	.	.	.	ID=Contig:ctgA
 90ctgA	example	match	41137	47829	.	-	.	ID=Match:seg14
 91ctgA	example	HSP	47449	47829	.	-	.	Parent=Match:seg14
 92ctgA	example	HSP	46816	46992	.	-	.	Parent=Match:seg14
 93ctgA	example	HSP	46092	46318	.	-	.	Parent=Match:seg14
 94ctgA	example	HSP	45790	46022	.	-	.	Parent=Match:seg14
 95ctgA	example	HSP	45231	45488	.	-	.	Parent=Match:seg14
 96ctgA	example	HSP	44763	45030	.	-	.	Parent=Match:seg14
 97ctgA	example	HSP	44065	44556	.	-	.	Parent=Match:seg14
 98ctgA	example	HSP	43395	43811	.	-	.	Parent=Match:seg14
 99ctgA	example	HSP	42890	43270	.	-	.	Parent=Match:seg14
100ctgA	example	HSP	42057	42474	.	-	.	Parent=Match:seg14
101ctgA	example	HSP	41754	41948	.	-	.	Parent=Match:seg14
102ctgA	example	HSP	41137	41318	.	-	.	Parent=Match:seg14
103ctgA	example	match	12531	15870	.	+	.	ID=Match:seg12
104ctgA	example	HSP	12531	12895	.	+	.	Parent=Match:seg12
105ctgA	example	HSP	13122	13449	.	+	.	Parent=Match:seg12
106ctgA	example	HSP	13452	13745	.	+	.	Parent=Match:seg12
107ctgA	example	HSP	13908	13965	.	+	.	Parent=Match:seg12
108ctgA	example	HSP	13998	14488	.	+	.	Parent=Match:seg12
109ctgA	example	HSP	14564	14899	.	+	.	Parent=Match:seg12
110ctgA	example	HSP	15185	15276	.	+	.	Parent=Match:seg12
111ctgA	example	HSP	15639	15736	.	+	.	Parent=Match:seg12
112ctgA	example	HSP	15745	15870	.	+	.	Parent=Match:seg12
113ctgA	est	match	7500	8000	.	-	.	ID=EST:agt221.3;Target=agt221.3+1+501
114ctgA	est	HSP	7500	8000	.	-	.	Parent=EST:agt221.3;Target=agt221.3+1+501
115ctgA	example	coding	1300	9000	.	+	.	ID=mRNA:EDEN.3;Gene=EDEN
116ctgA	example	CDS	3301	3902	.	+	0	Parent=mRNA:EDEN.3
117ctgA	example	CDS	5000	5500	.	+	1	Parent=mRNA:EDEN.3
118ctgA	example	CDS	7000	7600	.	+	1	Parent=mRNA:EDEN.3
119ctgA	example	processed_transcript	1300	9000	.	+	.	ID=mRNA:EDEN.3
120ctgA	example	5'-UTR	1300	1500	.	+	.	Parent=mRNA:EDEN.3
121ctgA	example	5'-UTR	3000	3300	.	+	.	Parent=mRNA:EDEN.3
122ctgA	example	3'-UTR	7601	9000	.	+	.	Parent=mRNA:EDEN.3
123ctgA	example	match	26503	35904	.	-	.	ID=Match:seg05
124ctgA	example	HSP	35642	35904	.	-	.	Parent=Match:seg05
125ctgA	example	HSP	35333	35507	.	-	.	Parent=Match:seg05
126ctgA	example	HSP	34605	34983	.	-	.	Parent=Match:seg05
127ctgA	example	HSP	34244	34313	.	-	.	Parent=Match:seg05
128ctgA	example	HSP	33438	33868	.	-	.	Parent=Match:seg05
129ctgA	example	HSP	33053	33325	.	-	.	Parent=Match:seg05
130ctgA	example	HSP	32208	32680	.	-	.	Parent=Match:seg05
131ctgA	example	HSP	32010	32057	.	-	.	Parent=Match:seg05
132ctgA	example	HSP	31421	31817	.	-	.	Parent=Match:seg05
133ctgA	example	HSP	31232	31236	.	-	.	Parent=Match:seg05
134ctgA	example	HSP	30465	30798	.	-	.	Parent=Match:seg05
135ctgA	example	HSP	30108	30216	.	-	.	Parent=Match:seg05
136ctgA	example	HSP	29513	29647	.	-	.	Parent=Match:seg05
137ctgA	example	HSP	28777	29058	.	-	.	Parent=Match:seg05
138ctgA	example	HSP	28225	28316	.	-	.	Parent=Match:seg05
139ctgA	example	HSP	27887	28076	.	-	.	Parent=Match:seg05
140ctgA	example	HSP	27448	27860	.	-	.	Parent=Match:seg05
141ctgA	example	HSP	27172	27185	.	-	.	Parent=Match:seg05
142ctgA	example	HSP	26503	26799	.	-	.	Parent=Match:seg05
143ctgA	example	match	49406	50000	.	+	.	ID=Match:seg13
144ctgA	example	HSP	49406	49476	.	+	.	Parent=Match:seg13
145ctgA	example	HSP	49762	50000	.	+	.	Parent=Match:seg13
146ctgA	example	gene	1050	9000	.	+	.	ID=Gene:EDEN;Note=protein+kinase
147ctgA	example	motif	33325	35791	.	+	.	ID=Motif:m04;Note=Ig-like
148ctgA	example	match	31785	32359	.	+	.	ID=Match:seg01
149ctgA	example	HSP	31785	31939	.	+	.	Parent=Match:seg01
150ctgA	example	HSP	32329	32359	.	+	.	Parent=Match:seg01