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

[Hervé Pagès]

Hi Julie, Emily,

It's worth noting that the TTG and CTG start codons are totally expected 
and officially part of the Standard Code:

   https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG1

Also the GTG start codon is expected for transcripts found on the 
Mitochondrial chromosome and is officially part of the Vertebrate 
Mitochondrial Code:

   https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG2

So what breaks the rule in the case of transcript ENST00000678634.1 is 
that the GTG start codon is found on chromosome 20.

H.


On 3/10/21 7:58 AM, Emily Perry wrote:
> Hi Julie
> 
> The information is stored in the transcript_attrib table under 
> attribution_id 380:
> http://www.ensembl.org/info/docs/api/core/core_schema.html#transcript_attrib 
> <http://www.ensembl.org/info/docs/api/core/core_schema.html#transcript_attrib>
> 
> You can fetch it from the Perl API using $transcript->get_all_Attributes
> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Transcript.html#a59f9ff2079a28ba80bc8b62a5e636327 
> <http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Transcript.html#a59f9ff2079a28ba80bc8b62a5e636327>
> 
> All the best
> 
> Emily
> 
>> On 10 Mar 2021, at 14:37, Julie Sullivan <julie.sullivan at gmail.com 
>> <mailto:julie.sullivan at gmail.com>> wrote:
>>
>> 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 
>> <mailto: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/
>>     <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 <mailto: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
>>>     _______________________________________________
>>>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
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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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>>
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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
> 
> 
> 
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
> 

-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github at gmail.com