Properly tag selenoproteins

[holtgrewe]

NCBI denotes recoding of UGA to selenocysteine by a Note=UGA stop codon recoded as selenocysteine.

This could be interpreted and a new tag. Overall, we should look for matches of the following in the Note tag:

UGA stop codon recoded as selenocysteine
UGA stop codons recoded as selenocysteine

Example lines

# "codon"
NC_000001.10    BestRefSeq      CDS     54375604        54375672        .       +       0       ID=cds-NP_998758.1;Parent=rna-NM_213593.5;Dbxref=CCDS:CCDS53320.1,GeneID:1733,Genbank:NP_998758.1,HGNC:HGNC:2883,MIM:147892;Name=NP_998758.1;Note=UGA stop codon recoded as selenocysteine%3B isoform b is encoded by transcript variant 2;gbkey=CDS;gene=DIO1;product=type I iodothyronine deiodinase isoform b;protein_id=NP_998758.1;transl_except=(pos:54370377..54370379%2Caa:Sec)

# "codons"
NC_000005.9     BestRefSeq      CDS     42804758        42804875        .       -       1       ID=cds-NP_005401.3;Parent=rna-NM_005410.4;Dbxref=CCDS:CCDS43311.1,GeneID:6414,Genbank:NP_005401.3,HGNC:HGNC:10751,MIM:601484;Name=NP_005401.3;Note=UGA stop codons recoded as selenocysteine%3B isoform 1 precursor is encoded by transcript variant 1;gbkey=CDS;gene=SELENOP;product=selenoprotein P isoform 1 precursor;protein_id=NP_005401.3;tag=RefSeq Select;transl_except=(pos:complement(42808279..42808281)%2Caa:Sec),(pos:complement(42801068..42801070)%2Caa:Sec),(pos:complement(42801014..42801016)%2Caa:Sec),(pos:complement(42800978..42800980)%2Caa:Sec),(pos:complement(42800933..42800935)%2Caa:Sec),(pos:complement(42800912..42800914)%2Caa:Sec),(pos:complement(42800867..42800869)%2Caa:Sec),(pos:complement(42800861..42800863)%2Caa:Sec),(pos:complement(42800840..42800842)%2Caa:Sec),(pos:complement(42800834..42800836)%2Caa:Sec)

Also see here:

• How to properly handle selenoproteins biocommons/hgvs#710

[davmlaw]

I've started collecting the "Note" fields as "note"

The HGVS change will probably take a few years, they need to add a column to UTA SQL schema, change their scripts to capture this from RefSeq, change the data provider API to include this, then have the HGVS client handle it.

But at least our data will have it for when HGVS can use it

[holtgrewe]

Excellen, thanks!