Mercurial > repos > iuc > snpeff
view test-data/pBR322.gff3 @ 30:c7275bd8b4d6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 280d5247becaa9a70db9c5c4a2f1fc50d302838a
| author | iuc |
|---|---|
| date | Mon, 18 Nov 2024 22:15:34 +0000 |
| parents | cfcf33df7fc0 |
| children |
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##gff-version 3 ##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