[ensembl-dev] translation question GTG --> Methionine?

[Julie Sullivan]

Thank you! That answers my question!

I would really like to be able to access that tag (non-ATG start)
programmatically. Are there plans for putting it with the other transcript
flags in the GTF file?

On Wed, 10 Mar 2021 at 10:09, Emily Perry <emily at ebi.ac.uk> wrote:

> Hi Julie
>
> We have some information about non-ATG start codons in our blog post from
> release 102:
> https://www.ensembl.info/2020/11/30/ensembl-102-has-been-released/
>
> Quite simply, there is not a rule. This is a situation of exceptional
> biology which we are only able to annotate correctly because of our expert
> manual gene annotators analysing the data in detail.
>
> All the best
>
> Emily
>
> On 10 Mar 2021, at 09:08, Julie Sullivan <julie.sullivan at gmail.com> wrote:
>
>
> https://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000288649;r=20:33667144-33668235;t=ENST00000678634
> The first codon is GTG. I would not have expected that to be Methionine.
>
> I looked in the text files, and there are 123 of these transcripts where
> the start codon is NOT ATG but the aa is M, in Homo sapiens.
>
> {'error': 0,
>  'methionine': 91434,
>  'GTG': 22,
>  'ATA': 10,
>  'CTG': 67,
>  'ACG': 8,
>  'TTG': 9,
>  'ATT': 5,
>  'AAC': 1,
>  'AAG': 1}
>
>
> Why is that?
>
> Specifically I would like a rule I can use, as my HGVSp strings are
> different from VEP for this reason.
>
> Thanks!
> Julie
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> —
>
> Dr Emily Perry (Pritchard)
> Ensembl Outreach Project Leader
> (she/her)
>
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> UK
>
>
>
>
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