diff --git a/generate_transcript_data/gff_parser.py b/generate_transcript_data/gff_parser.py index e76d235..958e0fa 100644 --- a/generate_transcript_data/gff_parser.py +++ b/generate_transcript_data/gff_parser.py @@ -322,6 +322,11 @@ def _get_transcript_accession(feature, version_key) -> Optional[str]: else: # print(f"warning: Couldn't get out {version_key} from {feature.type=} {feature.attr=}") transcript_accession = transcript_id + else: + # In RefSeq there are no transcript_ids for MT genes/mRNAs + # The proteins have "YP_" prefix (no corresp. NM_ transcript, so we will create fake ones + if feature.type == "mRNA": + transcript_accession = "fake-" + feature.attr.get("ID") return transcript_accession @staticmethod diff --git a/tests/test_data/refseq_grch38.p14_mt.gff b/tests/test_data/refseq_grch38.p14_mt.gff new file mode 100644 index 0000000..3a9269b --- /dev/null +++ b/tests/test_data/refseq_grch38.p14_mt.gff @@ -0,0 +1,128 @@ +##sequence-region NC_012920.1 1 16569 +NC_012920.1 RefSeq region 1 16569 . + . ID=NC_012920.1:1..16569;Dbxref=taxon:9606;Is_circular=true;Name=MT;country=United Kingdom: Great Britain;gbkey=Src;genome=mitochondrion;isolation-source=caucasian;mol_type=genomic DNA;note=this is the rCRS;tissue-type=placenta +NC_012920.1 RefSeq gene 577 647 . + . ID=gene-TRNF;Dbxref=GeneID:4558,HGNC:HGNC:7481,MIM:590070;Name=TRNF;gbkey=Gene;gene=TRNF;gene_biotype=tRNA +NC_012920.1 RefSeq tRNA 577 647 . + . ID=rna-TRNF;Parent=gene-TRNF;Dbxref=GeneID:4558,HGNC:HGNC:7481,MIM:590070;Note=NAR: 1455;anticodon=(pos:611..613);codons=1;gbkey=tRNA;gene=TRNF;product=tRNA-Phe +NC_012920.1 RefSeq exon 577 647 . + . ID=exon-TRNF-1;Parent=rna-TRNF;Dbxref=GeneID:4558,HGNC:HGNC:7481,MIM:590070;Note=NAR: 1455;anticodon=(pos:611..613);codons=1;gbkey=tRNA;gene=TRNF;product=tRNA-Phe +NC_012920.1 RefSeq gene 648 1601 . + . ID=gene-RNR1;Dbxref=GeneID:4549,HGNC:HGNC:7470,MIM:561000;Name=RNR1;gbkey=Gene;gene=RNR1;gene_biotype=rRNA;gene_synonym=MTRNR1 +NC_012920.1 RefSeq rRNA 648 1601 . + . ID=rna-RNR1;Parent=gene-RNR1;Dbxref=GeneID:4549,HGNC:HGNC:7470,MIM:561000;Note=12S rRNA%3B 12S ribosomal RNA;gbkey=rRNA;gene=RNR1;product=s-rRNA +NC_012920.1 RefSeq exon 648 1601 . + . ID=exon-RNR1-1;Parent=rna-RNR1;Dbxref=GeneID:4549,HGNC:HGNC:7470,MIM:561000;Note=12S rRNA%3B 12S ribosomal RNA;gbkey=rRNA;gene=RNR1;product=s-rRNA +NC_012920.1 RefSeq gene 1602 1670 . + . ID=gene-TRNV;Dbxref=GeneID:4577,HGNC:HGNC:7500,MIM:590105;Name=TRNV;gbkey=Gene;gene=TRNV;gene_biotype=tRNA;gene_synonym=MTTV +NC_012920.1 RefSeq tRNA 1602 1670 . + . ID=rna-TRNV;Parent=gene-TRNV;Dbxref=GeneID:4577,HGNC:HGNC:7500,MIM:590105;Note=NAR: 2053;anticodon=(pos:1633..1635);codons=50;gbkey=tRNA;gene=TRNV;product=tRNA-Val +NC_012920.1 RefSeq exon 1602 1670 . + . ID=exon-TRNV-1;Parent=rna-TRNV;Dbxref=GeneID:4577,HGNC:HGNC:7500,MIM:590105;Note=NAR: 2053;anticodon=(pos:1633..1635);codons=50;gbkey=tRNA;gene=TRNV;product=tRNA-Val +NC_012920.1 RefSeq gene 1671 3229 . + . ID=gene-RNR2;Dbxref=GeneID:4550,HGNC:HGNC:7471,MIM:561010;Name=RNR2;gbkey=Gene;gene=RNR2;gene_biotype=rRNA;gene_synonym=MTRNR2 +NC_012920.1 RefSeq rRNA 1671 3229 . + . ID=rna-RNR2;Parent=gene-RNR2;Dbxref=GeneID:4550,HGNC:HGNC:7471,MIM:561010;Note=16S ribosomal RNA%3B 16S rRNA;gbkey=rRNA;gene=RNR2;product=l-rRNA +NC_012920.1 RefSeq exon 1671 3229 . + . ID=exon-RNR2-1;Parent=rna-RNR2;Dbxref=GeneID:4550,HGNC:HGNC:7471,MIM:561010;Note=16S ribosomal RNA%3B 16S rRNA;gbkey=rRNA;gene=RNR2;product=l-rRNA +NC_012920.1 RefSeq sequence_feature 3107 3107 . + . ID=id-NC_012920.1:3107..3107;Note=preserves historical genome annotation numbering;gbkey=misc_feature +NC_012920.1 RefSeq gene 3230 3304 . + . ID=gene-TRNL1;Dbxref=GeneID:4567,HGNC:HGNC:7490,MIM:590050;Name=TRNL1;gbkey=Gene;gene=TRNL1;gene_biotype=tRNA;gene_synonym=MTTL1 +NC_012920.1 RefSeq tRNA 3230 3304 . + . ID=rna-TRNL1;Parent=gene-TRNL1;Dbxref=GeneID:4567,HGNC:HGNC:7490,MIM:590050;Note=NAR: 1054;anticodon=(pos:3265..3267);codons=2%2C3;gbkey=tRNA;gene=TRNL1;product=tRNA-Leu +NC_012920.1 RefSeq exon 3230 3304 . + . ID=exon-TRNL1-1;Parent=rna-TRNL1;Dbxref=GeneID:4567,HGNC:HGNC:7490,MIM:590050;Note=NAR: 1054;anticodon=(pos:3265..3267);codons=2%2C3;gbkey=tRNA;gene=TRNL1;product=tRNA-Leu +NC_012920.1 RefSeq gene 3307 4262 . + . ID=gene-ND1;Dbxref=GeneID:4535,HGNC:HGNC:7455,MIM:516000;Name=ND1;gbkey=Gene;gene=ND1;gene_biotype=protein_coding;gene_synonym=MTND1 +NC_012920.1 RefSeq mRNA 3307 4262 . + . ID=rna-ND1;Parent=gene-ND1;Dbxref=GeneID:4535,HGNC:HGNC:7455,MIM:516000;gbkey=mRNA;gene=ND1 +NC_012920.1 RefSeq exon 3307 4262 . + . ID=exon-ND1-1;Parent=rna-ND1;Dbxref=GeneID:4535,HGNC:HGNC:7455,MIM:516000;gbkey=mRNA;gene=ND1 +NC_012920.1 RefSeq CDS 3307 4262 . + 0 ID=cds-YP_003024026.1;Parent=rna-ND1;Dbxref=GenBank:YP_003024026.1,GeneID:4535,HGNC:HGNC:7455,MIM:516000;Name=YP_003024026.1;Note=TAA stop codon is completed by the addition of 3' A residues to the mRNA;gbkey=CDS;gene=ND1;product=NADH dehydrogenase subunit 1;protein_id=YP_003024026.1;transl_except=(pos:4261..4262%2Caa:TERM);transl_table=2 +NC_012920.1 RefSeq gene 4263 4331 . + . ID=gene-TRNI;Dbxref=GeneID:4565,HGNC:HGNC:7488,MIM:590045;Name=TRNI;gbkey=Gene;gene=TRNI;gene_biotype=tRNA;gene_synonym=MTTI +NC_012920.1 RefSeq tRNA 4263 4331 . + . ID=rna-TRNI;Parent=gene-TRNI;Dbxref=GeneID:4565,HGNC:HGNC:7488,MIM:590045;Note=NAR: 0997;anticodon=(pos:4292..4294);codons=33;gbkey=tRNA;gene=TRNI;product=tRNA-Ile +NC_012920.1 RefSeq exon 4263 4331 . + . ID=exon-TRNI-1;Parent=rna-TRNI;Dbxref=GeneID:4565,HGNC:HGNC:7488,MIM:590045;Note=NAR: 0997;anticodon=(pos:4292..4294);codons=33;gbkey=tRNA;gene=TRNI;product=tRNA-Ile +NC_012920.1 RefSeq gene 4329 4400 . - . ID=gene-TRNQ;Dbxref=GeneID:4572,HGNC:HGNC:7495,MIM:590030;Name=TRNQ;gbkey=Gene;gene=TRNQ;gene_biotype=tRNA;gene_synonym=MTTQ +NC_012920.1 RefSeq tRNA 4329 4400 . - . ID=rna-TRNQ;Parent=gene-TRNQ;Dbxref=GeneID:4572,HGNC:HGNC:7495,MIM:590030;Note=NAR: 0597;anticodon=(pos:complement(4365..4367));codons=26;gbkey=tRNA;gene=TRNQ;product=tRNA-Gln +NC_012920.1 RefSeq exon 4329 4400 . - . ID=exon-TRNQ-1;Parent=rna-TRNQ;Dbxref=GeneID:4572,HGNC:HGNC:7495,MIM:590030;Note=NAR: 0597;anticodon=(pos:complement(4365..4367));codons=26;gbkey=tRNA;gene=TRNQ;product=tRNA-Gln +NC_012920.1 RefSeq gene 4402 4469 . + . ID=gene-TRNM;Dbxref=GeneID:4569,HGNC:HGNC:7492,MIM:590065;Name=TRNM;gbkey=Gene;gene=TRNM;gene_biotype=tRNA;gene_synonym=MTTM +NC_012920.1 RefSeq tRNA 4402 4469 . + . ID=rna-TRNM;Parent=gene-TRNM;Dbxref=GeneID:4569,HGNC:HGNC:7492,MIM:590065;Note=NAR: 1297;anticodon=(pos:4432..4434);codons=35;gbkey=tRNA;gene=TRNM;product=tRNA-Met +NC_012920.1 RefSeq exon 4402 4469 . + . ID=exon-TRNM-1;Parent=rna-TRNM;Dbxref=GeneID:4569,HGNC:HGNC:7492,MIM:590065;Note=NAR: 1297;anticodon=(pos:4432..4434);codons=35;gbkey=tRNA;gene=TRNM;product=tRNA-Met +NC_012920.1 RefSeq gene 4470 5511 . + . ID=gene-ND2;Dbxref=GeneID:4536,HGNC:HGNC:7456,MIM:516001;Name=ND2;gbkey=Gene;gene=ND2;gene_biotype=protein_coding;gene_synonym=MTND2 +NC_012920.1 RefSeq mRNA 4470 5511 . + . ID=rna-ND2;Parent=gene-ND2;Dbxref=GeneID:4536,HGNC:HGNC:7456,MIM:516001;gbkey=mRNA;gene=ND2 +NC_012920.1 RefSeq exon 4470 5511 . + . ID=exon-ND2-1;Parent=rna-ND2;Dbxref=GeneID:4536,HGNC:HGNC:7456,MIM:516001;gbkey=mRNA;gene=ND2 +NC_012920.1 RefSeq CDS 4470 5511 . + 0 ID=cds-YP_003024027.1;Parent=rna-ND2;Dbxref=GenBank:YP_003024027.1,GeneID:4536,HGNC:HGNC:7456,MIM:516001;Name=YP_003024027.1;Note=TAA stop codon is completed by the addition of 3' A residues to the mRNA;gbkey=CDS;gene=ND2;product=NADH dehydrogenase subunit 2;protein_id=YP_003024027.1;transl_except=(pos:5511..5511%2Caa:TERM);transl_table=2 +NC_012920.1 RefSeq gene 5512 5579 . + . ID=gene-TRNW;Dbxref=GeneID:4578,HGNC:HGNC:7501,MIM:590095;Name=TRNW;gbkey=Gene;gene=TRNW;gene_biotype=tRNA;gene_synonym=MTTW +NC_012920.1 RefSeq tRNA 5512 5579 . + . ID=rna-TRNW;Parent=gene-TRNW;Dbxref=GeneID:4578,HGNC:HGNC:7501,MIM:590095;Note=NAR: 1897;anticodon=(pos:5544..5546);codons=14;gbkey=tRNA;gene=TRNW;product=tRNA-Trp +NC_012920.1 RefSeq exon 5512 5579 . + . ID=exon-TRNW-1;Parent=rna-TRNW;Dbxref=GeneID:4578,HGNC:HGNC:7501,MIM:590095;Note=NAR: 1897;anticodon=(pos:5544..5546);codons=14;gbkey=tRNA;gene=TRNW;product=tRNA-Trp +NC_012920.1 RefSeq gene 5587 5655 . - . ID=gene-TRNA;Dbxref=GeneID:4553,HGNC:HGNC:7475,MIM:590000;Name=TRNA;gbkey=Gene;gene=TRNA;gene_biotype=tRNA;gene_synonym=MTTA +NC_012920.1 RefSeq tRNA 5587 5655 . - . ID=rna-TRNA;Parent=gene-TRNA;Dbxref=GeneID:4553,HGNC:HGNC:7475,MIM:590000;Note=NAR: 0097;anticodon=(pos:complement(5623..5625));codons=54;gbkey=tRNA;gene=TRNA;product=tRNA-Ala +NC_012920.1 RefSeq exon 5587 5655 . - . ID=exon-TRNA-1;Parent=rna-TRNA;Dbxref=GeneID:4553,HGNC:HGNC:7475,MIM:590000;Note=NAR: 0097;anticodon=(pos:complement(5623..5625));codons=54;gbkey=tRNA;gene=TRNA;product=tRNA-Ala +NC_012920.1 RefSeq gene 5657 5729 . - . ID=gene-TRNN;Dbxref=GeneID:4570,HGNC:HGNC:7493,MIM:590010;Name=TRNN;gbkey=Gene;gene=TRNN;gene_biotype=tRNA;gene_synonym=MTTN +NC_012920.1 RefSeq tRNA 5657 5729 . - . ID=rna-TRNN;Parent=gene-TRNN;Dbxref=GeneID:4570,HGNC:HGNC:7493,MIM:590010;Note=NAR: 0297;anticodon=(pos:complement(5694..5696));codons=41;gbkey=tRNA;gene=TRNN;product=tRNA-Asn +NC_012920.1 RefSeq exon 5657 5729 . - . ID=exon-TRNN-1;Parent=rna-TRNN;Dbxref=GeneID:4570,HGNC:HGNC:7493,MIM:590010;Note=NAR: 0297;anticodon=(pos:complement(5694..5696));codons=41;gbkey=tRNA;gene=TRNN;product=tRNA-Asn +NC_012920.1 RefSeq gene 5761 5826 . - . ID=gene-TRNC;Dbxref=GeneID:4511,HGNC:HGNC:7477,MIM:590020;Name=TRNC;gbkey=Gene;gene=TRNC;gene_biotype=tRNA;gene_synonym=MTTC +NC_012920.1 RefSeq tRNA 5761 5826 . - . ID=rna-TRNC;Parent=gene-TRNC;Dbxref=GeneID:4511,HGNC:HGNC:7477,MIM:590020;Note=NAR: 0497;anticodon=(pos:complement(5796..5798));codons=13;gbkey=tRNA;gene=TRNC;product=tRNA-Cys +NC_012920.1 RefSeq exon 5761 5826 . - . ID=exon-TRNC-1;Parent=rna-TRNC;Dbxref=GeneID:4511,HGNC:HGNC:7477,MIM:590020;Note=NAR: 0497;anticodon=(pos:complement(5796..5798));codons=13;gbkey=tRNA;gene=TRNC;product=tRNA-Cys +NC_012920.1 RefSeq gene 5826 5891 . - . ID=gene-TRNY;Dbxref=GeneID:4579,HGNC:HGNC:7502,MIM:590100;Name=TRNY;gbkey=Gene;gene=TRNY;gene_biotype=tRNA;gene_synonym=MTTY +NC_012920.1 RefSeq tRNA 5826 5891 . - . ID=rna-TRNY;Parent=gene-TRNY;Dbxref=GeneID:4579,HGNC:HGNC:7502,MIM:590100;Note=NAR: 1997;anticodon=(pos:complement(5860..5862));codons=9;gbkey=tRNA;gene=TRNY;product=tRNA-Tyr +NC_012920.1 RefSeq exon 5826 5891 . - . ID=exon-TRNY-1;Parent=rna-TRNY;Dbxref=GeneID:4579,HGNC:HGNC:7502,MIM:590100;Note=NAR: 1997;anticodon=(pos:complement(5860..5862));codons=9;gbkey=tRNA;gene=TRNY;product=tRNA-Tyr +NC_012920.1 RefSeq gene 5904 7445 . + . ID=gene-COX1;Dbxref=GeneID:4512,HGNC:HGNC:7419,MIM:516030;Name=COX1;gbkey=Gene;gene=COX1;gene_biotype=protein_coding;gene_synonym=COI,MTCO1 +NC_012920.1 RefSeq mRNA 5904 7445 . + . ID=rna-COX1;Parent=gene-COX1;Dbxref=GeneID:4512,HGNC:HGNC:7419,MIM:516030;gbkey=mRNA;gene=COX1 +NC_012920.1 RefSeq exon 5904 7445 . + . ID=exon-COX1-1;Parent=rna-COX1;Dbxref=GeneID:4512,HGNC:HGNC:7419,MIM:516030;gbkey=mRNA;gene=COX1 +NC_012920.1 RefSeq CDS 5904 7445 . + 0 ID=cds-YP_003024028.1;Parent=rna-COX1;Dbxref=GenBank:YP_003024028.1,GeneID:4512,HGNC:HGNC:7419,MIM:516030;Name=YP_003024028.1;Note=cytochrome c oxidase I;gbkey=CDS;gene=COX1;product=cytochrome c oxidase subunit I;protein_id=YP_003024028.1;transl_table=2 +NC_012920.1 RefSeq gene 7446 7514 . - . ID=gene-TRNS1;Dbxref=GeneID:4574,HGNC:HGNC:7497,MIM:590080;Name=TRNS1;gbkey=Gene;gene=TRNS1;gene_biotype=tRNA;gene_synonym=MTTS1 +NC_012920.1 RefSeq tRNA 7446 7514 . - . ID=rna-TRNS1;Parent=gene-TRNS1;Dbxref=GeneID:4574,HGNC:HGNC:7497,MIM:590080;Note=NAR: 1697;anticodon=(pos:complement(7482..7484));codons=4%2C5%2C6%2C7;gbkey=tRNA;gene=TRNS1;product=tRNA-Ser +NC_012920.1 RefSeq exon 7446 7514 . - . ID=exon-TRNS1-1;Parent=rna-TRNS1;Dbxref=GeneID:4574,HGNC:HGNC:7497,MIM:590080;Note=NAR: 1697;anticodon=(pos:complement(7482..7484));codons=4%2C5%2C6%2C7;gbkey=tRNA;gene=TRNS1;product=tRNA-Ser +NC_012920.1 RefSeq gene 7518 7585 . + . ID=gene-TRND;Dbxref=GeneID:4555,HGNC:HGNC:7478,MIM:590015;Name=TRND;gbkey=Gene;gene=TRND;gene_biotype=tRNA;gene_synonym=MTTD +NC_012920.1 RefSeq tRNA 7518 7585 . + . ID=rna-TRND;Parent=gene-TRND;Dbxref=GeneID:4555,HGNC:HGNC:7478,MIM:590015;Note=NAR: 0397;anticodon=(pos:7548..7550);codons=57;gbkey=tRNA;gene=TRND;product=tRNA-Asp +NC_012920.1 RefSeq exon 7518 7585 . + . ID=exon-TRND-1;Parent=rna-TRND;Dbxref=GeneID:4555,HGNC:HGNC:7478,MIM:590015;Note=NAR: 0397;anticodon=(pos:7548..7550);codons=57;gbkey=tRNA;gene=TRND;product=tRNA-Asp +NC_012920.1 RefSeq gene 7586 8269 . + . ID=gene-COX2;Dbxref=GeneID:4513,HGNC:HGNC:7421,MIM:516040;Name=COX2;gbkey=Gene;gene=COX2;gene_biotype=protein_coding;gene_synonym=COII,MTCO2 +NC_012920.1 RefSeq mRNA 7586 8269 . + . ID=rna-COX2;Parent=gene-COX2;Dbxref=GeneID:4513,HGNC:HGNC:7421,MIM:516040;gbkey=mRNA;gene=COX2 +NC_012920.1 RefSeq exon 7586 8269 . + . ID=exon-COX2-1;Parent=rna-COX2;Dbxref=GeneID:4513,HGNC:HGNC:7421,MIM:516040;gbkey=mRNA;gene=COX2 +NC_012920.1 RefSeq CDS 7586 8269 . + 0 ID=cds-YP_003024029.1;Parent=rna-COX2;Dbxref=GenBank:YP_003024029.1,GeneID:4513,HGNC:HGNC:7421,MIM:516040;Name=YP_003024029.1;Note=cytochrome c oxidase II;gbkey=CDS;gene=COX2;product=cytochrome c oxidase subunit II;protein_id=YP_003024029.1;transl_table=2 +NC_012920.1 RefSeq gene 8295 8364 . + . ID=gene-TRNK;Dbxref=GeneID:4566,HGNC:HGNC:7489,MIM:590060;Name=TRNK;gbkey=Gene;gene=TRNK;gene_biotype=tRNA;gene_synonym=MTTK +NC_012920.1 RefSeq tRNA 8295 8364 . + . ID=rna-TRNK;Parent=gene-TRNK;Dbxref=GeneID:4566,HGNC:HGNC:7489,MIM:590060;Note=NAR: 1197;anticodon=(pos:8323..8325);codons=42;gbkey=tRNA;gene=TRNK;product=tRNA-Lys +NC_012920.1 RefSeq exon 8295 8364 . + . ID=exon-TRNK-1;Parent=rna-TRNK;Dbxref=GeneID:4566,HGNC:HGNC:7489,MIM:590060;Note=NAR: 1197;anticodon=(pos:8323..8325);codons=42;gbkey=tRNA;gene=TRNK;product=tRNA-Lys +NC_012920.1 RefSeq gene 8366 8572 . + . ID=gene-ATP8;Dbxref=GeneID:4509,HGNC:HGNC:7415,MIM:516070;Name=ATP8;gbkey=Gene;gene=ATP8;gene_biotype=protein_coding;gene_synonym=ATPase8,MTATP8 +NC_012920.1 RefSeq mRNA 8366 8572 . + . ID=rna-ATP8;Parent=gene-ATP8;Dbxref=GeneID:4509,HGNC:HGNC:7415,MIM:516070;gbkey=mRNA;gene=ATP8 +NC_012920.1 RefSeq exon 8366 8572 . + . ID=exon-ATP8-1;Parent=rna-ATP8;Dbxref=GeneID:4509,HGNC:HGNC:7415,MIM:516070;gbkey=mRNA;gene=ATP8 +NC_012920.1 RefSeq CDS 8366 8572 . + 0 ID=cds-YP_003024030.1;Parent=rna-ATP8;Dbxref=GenBank:YP_003024030.1,GeneID:4509,HGNC:HGNC:7415,MIM:516070;Name=YP_003024030.1;Note=ATP synthase 8%3B ATPase subunit 8;gbkey=CDS;gene=ATP8;product=ATP synthase F0 subunit 8;protein_id=YP_003024030.1;transl_table=2 +NC_012920.1 RefSeq gene 8527 9207 . + . ID=gene-ATP6;Dbxref=GeneID:4508,HGNC:HGNC:7414,MIM:516060;Name=ATP6;gbkey=Gene;gene=ATP6;gene_biotype=protein_coding;gene_synonym=ATPase6,MTATP6 +NC_012920.1 RefSeq mRNA 8527 9207 . + . ID=rna-ATP6;Parent=gene-ATP6;Dbxref=GeneID:4508,HGNC:HGNC:7414,MIM:516060;gbkey=mRNA;gene=ATP6 +NC_012920.1 RefSeq exon 8527 9207 . + . ID=exon-ATP6-1;Parent=rna-ATP6;Dbxref=GeneID:4508,HGNC:HGNC:7414,MIM:516060;gbkey=mRNA;gene=ATP6 +NC_012920.1 RefSeq CDS 8527 9207 . + 0 ID=cds-YP_003024031.1;Parent=rna-ATP6;Dbxref=GenBank:YP_003024031.1,GeneID:4508,HGNC:HGNC:7414,MIM:516060;Name=YP_003024031.1;Note=ATP synthase 6%3B ATPase subunit 6;gbkey=CDS;gene=ATP6;product=ATP synthase F0 subunit 6;protein_id=YP_003024031.1;transl_table=2 +NC_012920.1 RefSeq gene 9207 9990 . + . ID=gene-COX3;Dbxref=GeneID:4514,HGNC:HGNC:7422,MIM:516050;Name=COX3;gbkey=Gene;gene=COX3;gene_biotype=protein_coding;gene_synonym=COIII,MTCO3 +NC_012920.1 RefSeq mRNA 9207 9990 . + . ID=rna-COX3;Parent=gene-COX3;Dbxref=GeneID:4514,HGNC:HGNC:7422,MIM:516050;gbkey=mRNA;gene=COX3 +NC_012920.1 RefSeq exon 9207 9990 . + . ID=exon-COX3-1;Parent=rna-COX3;Dbxref=GeneID:4514,HGNC:HGNC:7422,MIM:516050;gbkey=mRNA;gene=COX3 +NC_012920.1 RefSeq CDS 9207 9990 . + 0 ID=cds-YP_003024032.1;Parent=rna-COX3;Dbxref=GenBank:YP_003024032.1,GeneID:4514,HGNC:HGNC:7422,MIM:516050;Name=YP_003024032.1;Note=TAA stop codon is completed by the addition of 3' A residues to the mRNA;gbkey=CDS;gene=COX3;product=cytochrome c oxidase subunit III;protein_id=YP_003024032.1;transl_except=(pos:9990..9990%2Caa:TERM);transl_table=2 +NC_012920.1 RefSeq gene 9991 10058 . + . ID=gene-TRNG;Dbxref=GeneID:4563,HGNC:HGNC:7486,MIM:590035;Name=TRNG;gbkey=Gene;gene=TRNG;gene_biotype=tRNA;gene_synonym=MTTG +NC_012920.1 RefSeq tRNA 9991 10058 . + . ID=rna-TRNG;Parent=gene-TRNG;Dbxref=GeneID:4563,HGNC:HGNC:7486,MIM:590035;Note=NAR: 0797;anticodon=(pos:10021..10023);codons=62;gbkey=tRNA;gene=TRNG;product=tRNA-Gly +NC_012920.1 RefSeq exon 9991 10058 . + . ID=exon-TRNG-1;Parent=rna-TRNG;Dbxref=GeneID:4563,HGNC:HGNC:7486,MIM:590035;Note=NAR: 0797;anticodon=(pos:10021..10023);codons=62;gbkey=tRNA;gene=TRNG;product=tRNA-Gly +NC_012920.1 RefSeq gene 10059 10404 . + . ID=gene-ND3;Dbxref=GeneID:4537,HGNC:HGNC:7458,MIM:516002;Name=ND3;gbkey=Gene;gene=ND3;gene_biotype=protein_coding;gene_synonym=MTND3 +NC_012920.1 RefSeq mRNA 10059 10404 . + . ID=rna-ND3;Parent=gene-ND3;Dbxref=GeneID:4537,HGNC:HGNC:7458,MIM:516002;gbkey=mRNA;gene=ND3 +NC_012920.1 RefSeq exon 10059 10404 . + . ID=exon-ND3-1;Parent=rna-ND3;Dbxref=GeneID:4537,HGNC:HGNC:7458,MIM:516002;gbkey=mRNA;gene=ND3 +NC_012920.1 RefSeq CDS 10059 10404 . + 0 ID=cds-YP_003024033.1;Parent=rna-ND3;Dbxref=GenBank:YP_003024033.1,GeneID:4537,HGNC:HGNC:7458,MIM:516002;Name=YP_003024033.1;Note=TAA stop codon is completed by the addition of 3' A residues to the mRNA;gbkey=CDS;gene=ND3;product=NADH dehydrogenase subunit 3;protein_id=YP_003024033.1;transl_except=(pos:10404..10404%2Caa:TERM);transl_table=2 +NC_012920.1 RefSeq gene 10405 10469 . + . ID=gene-TRNR;Dbxref=GeneID:4573,HGNC:HGNC:7496,MIM:590005;Name=TRNR;gbkey=Gene;gene=TRNR;gene_biotype=tRNA;gene_synonym=MTTR +NC_012920.1 RefSeq tRNA 10405 10469 . + . ID=rna-TRNR;Parent=gene-TRNR;Dbxref=GeneID:4573,HGNC:HGNC:7496,MIM:590005;Note=NAR: 0197;anticodon=(pos:10435..10437);codons=30;gbkey=tRNA;gene=TRNR;product=tRNA-Arg +NC_012920.1 RefSeq exon 10405 10469 . + . ID=exon-TRNR-1;Parent=rna-TRNR;Dbxref=GeneID:4573,HGNC:HGNC:7496,MIM:590005;Note=NAR: 0197;anticodon=(pos:10435..10437);codons=30;gbkey=tRNA;gene=TRNR;product=tRNA-Arg +NC_012920.1 RefSeq gene 10470 10766 . + . ID=gene-ND4L;Dbxref=GeneID:4539,HGNC:HGNC:7460,MIM:516004;Name=ND4L;gbkey=Gene;gene=ND4L;gene_biotype=protein_coding;gene_synonym=MTND4L +NC_012920.1 RefSeq mRNA 10470 10766 . + . ID=rna-ND4L;Parent=gene-ND4L;Dbxref=GeneID:4539,HGNC:HGNC:7460,MIM:516004;gbkey=mRNA;gene=ND4L +NC_012920.1 RefSeq exon 10470 10766 . + . ID=exon-ND4L-1;Parent=rna-ND4L;Dbxref=GeneID:4539,HGNC:HGNC:7460,MIM:516004;gbkey=mRNA;gene=ND4L +NC_012920.1 RefSeq CDS 10470 10766 . + 0 ID=cds-YP_003024034.1;Parent=rna-ND4L;Dbxref=GenBank:YP_003024034.1,GeneID:4539,HGNC:HGNC:7460,MIM:516004;Name=YP_003024034.1;gbkey=CDS;gene=ND4L;product=NADH dehydrogenase subunit 4L;protein_id=YP_003024034.1;transl_table=2 +NC_012920.1 RefSeq gene 10760 12137 . + . ID=gene-ND4;Dbxref=GeneID:4538,HGNC:HGNC:7459,MIM:516003;Name=ND4;gbkey=Gene;gene=ND4;gene_biotype=protein_coding;gene_synonym=MTND4 +NC_012920.1 RefSeq mRNA 10760 12137 . + . ID=rna-ND4;Parent=gene-ND4;Dbxref=GeneID:4538,HGNC:HGNC:7459,MIM:516003;gbkey=mRNA;gene=ND4 +NC_012920.1 RefSeq exon 10760 12137 . + . ID=exon-ND4-1;Parent=rna-ND4;Dbxref=GeneID:4538,HGNC:HGNC:7459,MIM:516003;gbkey=mRNA;gene=ND4 +NC_012920.1 RefSeq CDS 10760 12137 . + 0 ID=cds-YP_003024035.1;Parent=rna-ND4;Dbxref=GenBank:YP_003024035.1,GeneID:4538,HGNC:HGNC:7459,MIM:516003;Name=YP_003024035.1;Note=TAA stop codon is completed by the addition of 3' A residues to the mRNA;gbkey=CDS;gene=ND4;product=NADH dehydrogenase subunit 4;protein_id=YP_003024035.1;transl_except=(pos:12137..12137%2Caa:TERM);transl_table=2 +NC_012920.1 RefSeq gene 12138 12206 . + . ID=gene-TRNH;Dbxref=GeneID:4564,HGNC:HGNC:7487,MIM:590040;Name=TRNH;gbkey=Gene;gene=TRNH;gene_biotype=tRNA;gene_synonym=MTTH +NC_012920.1 RefSeq tRNA 12138 12206 . + . ID=rna-TRNH;Parent=gene-TRNH;Dbxref=GeneID:4564,HGNC:HGNC:7487,MIM:590040;Note=NAR: 0897;anticodon=(pos:12168..12170);codons=25;gbkey=tRNA;gene=TRNH;product=tRNA-His +NC_012920.1 RefSeq exon 12138 12206 . + . ID=exon-TRNH-1;Parent=rna-TRNH;Dbxref=GeneID:4564,HGNC:HGNC:7487,MIM:590040;Note=NAR: 0897;anticodon=(pos:12168..12170);codons=25;gbkey=tRNA;gene=TRNH;product=tRNA-His +NC_012920.1 RefSeq gene 12207 12265 . + . ID=gene-TRNS2;Dbxref=GeneID:4575,HGNC:HGNC:7498,MIM:590085;Name=TRNS2;gbkey=Gene;gene=TRNS2;gene_biotype=tRNA;gene_synonym=MTTS2 +NC_012920.1 RefSeq tRNA 12207 12265 . + . ID=rna-TRNS2;Parent=gene-TRNS2;Dbxref=GeneID:4575,HGNC:HGNC:7498,MIM:590085;Note=NAR: 1656;anticodon=(pos:12226..12228);codons=44%2C45;gbkey=tRNA;gene=TRNS2;product=tRNA-Ser +NC_012920.1 RefSeq exon 12207 12265 . + . ID=exon-TRNS2-1;Parent=rna-TRNS2;Dbxref=GeneID:4575,HGNC:HGNC:7498,MIM:590085;Note=NAR: 1656;anticodon=(pos:12226..12228);codons=44%2C45;gbkey=tRNA;gene=TRNS2;product=tRNA-Ser +NC_012920.1 RefSeq gene 12266 12336 . + . ID=gene-TRNL2;Dbxref=GeneID:4568,HGNC:HGNC:7491,MIM:590055;Name=TRNL2;gbkey=Gene;gene=TRNL2;gene_biotype=tRNA;gene_synonym=MTTL2 +NC_012920.1 RefSeq tRNA 12266 12336 . + . ID=rna-TRNL2;Parent=gene-TRNL2;Dbxref=GeneID:4568,HGNC:HGNC:7491,MIM:590055;Note=NAR: 1097;anticodon=(pos:12298..12300);codons=16%2C17%2C18%2C19;gbkey=tRNA;gene=TRNL2;product=tRNA-Leu +NC_012920.1 RefSeq exon 12266 12336 . + . ID=exon-TRNL2-1;Parent=rna-TRNL2;Dbxref=GeneID:4568,HGNC:HGNC:7491,MIM:590055;Note=NAR: 1097;anticodon=(pos:12298..12300);codons=16%2C17%2C18%2C19;gbkey=tRNA;gene=TRNL2;product=tRNA-Leu +NC_012920.1 RefSeq gene 12337 14148 . + . ID=gene-ND5;Dbxref=GeneID:4540,HGNC:HGNC:7461,MIM:516005;Name=ND5;gbkey=Gene;gene=ND5;gene_biotype=protein_coding;gene_synonym=MTND5 +NC_012920.1 RefSeq mRNA 12337 14148 . + . ID=rna-ND5;Parent=gene-ND5;Dbxref=GeneID:4540,HGNC:HGNC:7461,MIM:516005;gbkey=mRNA;gene=ND5 +NC_012920.1 RefSeq exon 12337 14148 . + . ID=exon-ND5-1;Parent=rna-ND5;Dbxref=GeneID:4540,HGNC:HGNC:7461,MIM:516005;gbkey=mRNA;gene=ND5 +NC_012920.1 RefSeq CDS 12337 14148 . + 0 ID=cds-YP_003024036.1;Parent=rna-ND5;Dbxref=GenBank:YP_003024036.1,GeneID:4540,HGNC:HGNC:7461,MIM:516005;Name=YP_003024036.1;gbkey=CDS;gene=ND5;product=NADH dehydrogenase subunit 5;protein_id=YP_003024036.1;transl_table=2 +NC_012920.1 RefSeq gene 14149 14673 . - . ID=gene-ND6;Dbxref=GeneID:4541,HGNC:HGNC:7462,MIM:516006;Name=ND6;gbkey=Gene;gene=ND6;gene_biotype=protein_coding;gene_synonym=MTND6 +NC_012920.1 RefSeq mRNA 14149 14673 . - . ID=rna-ND6;Parent=gene-ND6;Dbxref=GeneID:4541,HGNC:HGNC:7462,MIM:516006;gbkey=mRNA;gene=ND6 +NC_012920.1 RefSeq exon 14149 14673 . - . ID=exon-ND6-1;Parent=rna-ND6;Dbxref=GeneID:4541,HGNC:HGNC:7462,MIM:516006;gbkey=mRNA;gene=ND6 +NC_012920.1 RefSeq CDS 14149 14673 . - 0 ID=cds-YP_003024037.1;Parent=rna-ND6;Dbxref=GenBank:YP_003024037.1,GeneID:4541,HGNC:HGNC:7462,MIM:516006;Name=YP_003024037.1;gbkey=CDS;gene=ND6;product=NADH dehydrogenase subunit 6;protein_id=YP_003024037.1;transl_table=2 +NC_012920.1 RefSeq gene 14674 14742 . - . ID=gene-TRNE;Dbxref=GeneID:4556,HGNC:HGNC:7479,MIM:590025;Name=TRNE;gbkey=Gene;gene=TRNE;gene_biotype=tRNA;gene_synonym=MTTE +NC_012920.1 RefSeq tRNA 14674 14742 . - . ID=rna-TRNE;Parent=gene-TRNE;Dbxref=GeneID:4556,HGNC:HGNC:7479,MIM:590025;Note=NAR: 0697;anticodon=(pos:complement(14710..14712));codons=58;gbkey=tRNA;gene=TRNE;product=tRNA-Glu +NC_012920.1 RefSeq exon 14674 14742 . - . ID=exon-TRNE-1;Parent=rna-TRNE;Dbxref=GeneID:4556,HGNC:HGNC:7479,MIM:590025;Note=NAR: 0697;anticodon=(pos:complement(14710..14712));codons=58;gbkey=tRNA;gene=TRNE;product=tRNA-Glu +NC_012920.1 RefSeq gene 14747 15887 . + . ID=gene-CYTB;Dbxref=GeneID:4519,HGNC:HGNC:7427,MIM:516020;Name=CYTB;gbkey=Gene;gene=CYTB;gene_biotype=protein_coding;gene_synonym=MTCYB +NC_012920.1 RefSeq mRNA 14747 15887 . + . ID=rna-CYTB;Parent=gene-CYTB;Dbxref=GeneID:4519,HGNC:HGNC:7427,MIM:516020;gbkey=mRNA;gene=CYTB +NC_012920.1 RefSeq exon 14747 15887 . + . ID=exon-CYTB-1;Parent=rna-CYTB;Dbxref=GeneID:4519,HGNC:HGNC:7427,MIM:516020;gbkey=mRNA;gene=CYTB +NC_012920.1 RefSeq CDS 14747 15887 . + 0 ID=cds-YP_003024038.1;Parent=rna-CYTB;Dbxref=GenBank:YP_003024038.1,GeneID:4519,HGNC:HGNC:7427,MIM:516020;Name=YP_003024038.1;Note=TAA stop codon is completed by the addition of 3' A residues to the mRNA;gbkey=CDS;gene=CYTB;product=cytochrome b;protein_id=YP_003024038.1;transl_except=(pos:15887..15887%2Caa:TERM);transl_table=2 +NC_012920.1 RefSeq gene 15888 15953 . + . ID=gene-TRNT;Dbxref=GeneID:4576,HGNC:HGNC:7499,MIM:590090;Name=TRNT;gbkey=Gene;gene=TRNT;gene_biotype=tRNA;gene_synonym=MTTT +NC_012920.1 RefSeq tRNA 15888 15953 . + . ID=rna-TRNT;Parent=gene-TRNT;Dbxref=GeneID:4576,HGNC:HGNC:7499,MIM:590090;Note=NAR: 1797;anticodon=(pos:15919..15921);codons=38;gbkey=tRNA;gene=TRNT;product=tRNA-Thr +NC_012920.1 RefSeq exon 15888 15953 . + . ID=exon-TRNT-1;Parent=rna-TRNT;Dbxref=GeneID:4576,HGNC:HGNC:7499,MIM:590090;Note=NAR: 1797;anticodon=(pos:15919..15921);codons=38;gbkey=tRNA;gene=TRNT;product=tRNA-Thr +NC_012920.1 RefSeq gene 15956 16023 . - . ID=gene-TRNP;Dbxref=GeneID:4571,HGNC:HGNC:7494,MIM:590075;Name=TRNP;gbkey=Gene;gene=TRNP;gene_biotype=tRNA;gene_synonym=MTTP +NC_012920.1 RefSeq tRNA 15956 16023 . - . ID=rna-TRNP;Parent=gene-TRNP;Dbxref=GeneID:4571,HGNC:HGNC:7494,MIM:590075;Note=NAR: 1597;anticodon=(pos:complement(15990..15992));codons=22;gbkey=tRNA;gene=TRNP;product=tRNA-Pro +NC_012920.1 RefSeq exon 15956 16023 . - . ID=exon-TRNP-1;Parent=rna-TRNP;Dbxref=GeneID:4571,HGNC:HGNC:7494,MIM:590075;Note=NAR: 1597;anticodon=(pos:complement(15990..15992));codons=22;gbkey=tRNA;gene=TRNP;product=tRNA-Pro +NC_012920.1 RefSeq D_loop 16024 17145 . - . ID=id-NC_012920.1:1..16569;gbkey=D-loop