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How to properly handle selenoproteins #710

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holtgrewe opened this issue Nov 10, 2023 · 3 comments
Open

How to properly handle selenoproteins #710

holtgrewe opened this issue Nov 10, 2023 · 3 comments
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@holtgrewe
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One example is gene SELENON with transcript NM_206926.2. Here, an alternative translation table must:

Note=UGA stop codon recoded as selenocysteine

Example line from the NCBI GFF3 file:

NC_000001.10    BestRefSeq      CDS     26126722        26126904        .       +       0       ID=cds-NP_996809.1;Parent=rna-NM_206926.2;Dbxref=CCDS:CCDS41283.1,GeneID:57190,Genbank:NP_996809.1,HGNC:HGNC:15999,MIM:606210;Name=NP_996809.1;Note=UGA stop codon recoded as selenocysteine%3B isoform 1 is encoded by transcript variant 1;gbkey=CDS;gene=SELENON;product=selenoprotein N isoform 1;protein_id=NP_996809.1;transl_except=(pos:26139280..26139282%2Caa:Sec)

biocommons.bioutils already contains the proper table. Is this implemented in UTA/hgvs anywhere? There are some matches of "seleno" in the UTA repository limited to misc/EnsemblUTA/*.

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github-actions bot commented Feb 9, 2024

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label Feb 9, 2024
@holtgrewe
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@github-actions github-actions bot removed the stale Issue is stale and subject to automatic closing label Feb 10, 2024
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This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 7 days.

@github-actions github-actions bot added the stale Issue is stale and subject to automatic closing label May 10, 2024
@jsstevenson jsstevenson added keep alive exempt issue from staleness checks and removed stale Issue is stale and subject to automatic closing labels May 17, 2024
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