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

[Emily Perry]

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/ <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 <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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