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view test-data/pBR322.gff3 @ 20:8f92c2b26e6d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
author iuc
date Fri, 25 Jan 2019 12:29:48 -0500
parents 479c4f2f4826
children cfcf33df7fc0
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##sequence-region J01749.1 1 4361
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=47470
J01749.1	Genbank	region	1	4361	.	+	.	ID=id-1;Dbxref=taxon:47470;Is_circular=true;gbkey=Src;mol_type=other DNA;tissue-lib=ATCC 31344%2C ATCC 37017
J01749.1	Genbank	region	1	1762	.	+	.	ID=id-J01749.1:1..1762;gbkey=Src
J01749.1	Genbank	binding_site	24	27	.	+	.	ID=id-J01749.1:24..27;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	promoter	27	33	.	-	.	ID=id-J01749.1:27..33;Note=promoter P1 (6);gbkey=promoter
J01749.1	Genbank	binding_site	39	42	.	+	.	ID=id-J01749.1:39..42;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	promoter	43	49	.	+	.	ID=id-J01749.1:43..49;Note=promoter P2 (6);gbkey=promoter
J01749.1	Genbank	binding_site	53	56	.	+	.	ID=id-J01749.1:53..56;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	binding_site	67	70	.	+	.	ID=id-J01749.1:67..70;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	binding_site	80	83	.	+	.	ID=id-J01749.1:80..83;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	gene	86	1276	.	+	.	ID=gene-tet;Name=tet;gbkey=Gene;gene=tet
J01749.1	Genbank	CDS	86	1276	.	+	0	ID=cds-AAB59735.1;Parent=gene-tet;Dbxref=NCBI_GP:AAB59735.1;Name=AAB59735.1;gbkey=CDS;gene=tet;product=tetracycline resistance protein;protein_id=AAB59735.1;transl_table=11
J01749.1	Genbank	binding_site	411	414	.	+	.	ID=id-tet;bound_moiety=echinomycin;gbkey=misc_binding;gene=tet
J01749.1	Genbank	binding_site	469	472	.	+	.	ID=id-tet-2;bound_moiety=echinomycin;gbkey=misc_binding;gene=tet
J01749.1	Genbank	sequence_difference	426	426	.	+	.	ID=id-tet-3;Note=conflict;gbkey=misc_difference;gene=tet;replace=
J01749.1	Genbank	sequence_feature	146	147	.	+	.	ID=id-tet-4;Note=Endo.Sce I cleavage site coordinated with site at base 142 (10);gbkey=misc_feature;gene=tet
J01749.1	Genbank	region	526	528	.	+	.	ID=id-tet-5;gbkey=old_sequence;gene=tet
J01749.1	Genbank	sequence_feature	141	142	.	-	.	ID=id-J01749.1:141..142;Note=Endo.Sce I cleavage site coordinated with site at base 146 (10);gbkey=misc_feature
J01749.1	Genbank	direct_repeat	1515	1519	.	-	.	ID=id-J01749.1:1515..1519;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct
J01749.1	Genbank	sequence_feature	1636	1762	.	+	.	ID=id-J01749.1:1636..1762;Note=from pSC101 (bp 1860-1986);gbkey=misc_feature
J01749.1	Genbank	direct_repeat	1788	1792	.	-	.	ID=id-J01749.1:1788..1792;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct
J01749.1	Genbank	sequence_difference	1891	1892	.	+	.	ID=id-J01749.1:1891..1892;Note=conflict;gbkey=misc_difference;replace=att
J01749.1	Genbank	region	1892	1893	.	+	.	ID=id-J01749.1:1892..1893;gbkey=old_sequence
J01749.1	Genbank	region	1905	1910	.	+	.	ID=id-J01749.1:1905..1910;gbkey=RBS
J01749.1	Genbank	region	1905	1909	.	+	.	ID=id-J01749.1:1905..1909;Note=Shine-Dalgarno sequence;gbkey=RBS
J01749.1	Genbank	sequence_difference	1913	1914	.	+	.	ID=id-J01749.1:1913..1914;Note=conflict;gbkey=misc_difference;replace=caa
J01749.1	Genbank	region	1914	1915	.	+	.	ID=id-J01749.1:1914..1915;gbkey=old_sequence
J01749.1	Genbank	CDS	1915	2106	.	+	0	ID=cds-AAB59736.1;Dbxref=NCBI_GP:AAB59736.1;Name=AAB59736.1;gbkey=CDS;product=ROP protein;protein_id=AAB59736.1;transl_table=11
J01749.1	Genbank	sequence_feature	2011	2167	.	+	.	ID=id-J01749.1:2011..2167;Note=H-strand Y effector site;gbkey=misc_feature
J01749.1	Genbank	direct_repeat	2245	2249	.	-	.	ID=id-J01749.1:2245..2249;Note=gamma-delta insertion target sequence;gbkey=repeat_region;rpt_type=direct
J01749.1	Genbank	sequence_feature	2351	2414	.	-	.	ID=id-J01749.1:2351..2414;Note=L-strand Y effector site;gbkey=misc_feature
J01749.1	Genbank	binding_site	2439	2447	.	+	.	ID=id-J01749.1:2439..2447;bound_moiety=dnaA;gbkey=misc_binding
J01749.1	Genbank	origin_of_replication	2535	2535	.	+	.	ID=id-J01749.1:2535..2535;gbkey=rep_origin
J01749.1	Genbank	region	2729	2730	.	+	.	ID=id-J01749.1:2729..2730;Note=revision according to (17);gbkey=old_sequence;replace=at
J01749.1	Genbank	region	2729	2729	.	+	.	ID=id-J01749.1:2729..2729;gbkey=old_sequence
J01749.1	Genbank	region	2730	2730	.	+	.	ID=id-J01749.1:2730..2730;Note=revision according to (16);gbkey=old_sequence;replace=t
J01749.1	Genbank	mobile_genetic_element	3148	4361	.	+	.	ID=id-J01749.1:3148..4361;gbkey=mobile_element;mobile_element_type=transposon:Tn3
J01749.1	Genbank	inverted_repeat	3148	3185	.	+	.	ID=id-J01749.1:3148..3185;Note=corresponds to one of the 38bp repeats found in Tn3 (bp 1-38 and complement (4920-4957));gbkey=repeat_region;rpt_type=inverted
J01749.1	Genbank	gene	3293	4153	.	-	.	ID=gene-bla;Name=bla;gbkey=Gene;gene=bla
J01749.1	Genbank	CDS	3293	4153	.	-	0	ID=cds-AAB59737.1;Parent=gene-bla;Dbxref=NCBI_GP:AAB59737.1;Name=AAB59737.1;Note=E-286;gbkey=CDS;gene=bla;product=beta-lactamase;protein_id=AAB59737.1;transl_table=11
J01749.1	Genbank	region	4161	4165	.	-	.	ID=id-J01749.1:4161..4165;Note=Shine-Dalgarno sequence;gbkey=RBS
J01749.1	Genbank	promoter	4188	4194	.	-	.	ID=id-J01749.1:4188..4194;Note=promoter P3 (6);gbkey=promoter
J01749.1	Genbank	binding_site	4268	4271	.	-	.	ID=id-J01749.1:4268..4271;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	binding_site	4280	4283	.	-	.	ID=id-J01749.1:4280..4283;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	binding_site	4285	4288	.	-	.	ID=id-J01749.1:4285..4288;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	binding_site	4296	4299	.	-	.	ID=id-J01749.1:4296..4299;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	binding_site	4311	4314	.	-	.	ID=id-J01749.1:4311..4314;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	binding_site	4317	4320	.	-	.	ID=id-J01749.1:4317..4320;bound_moiety=echinomycin;gbkey=misc_binding
J01749.1	Genbank	binding_site	4331	4334	.	-	.	ID=id-J01749.1:4331..4334;bound_moiety=echinomycin;gbkey=misc_binding