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

Emily Perry emily at ebi.ac.uk
Wed Mar 10 15:58:00 GMT 2021


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> 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>
>> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org>
>> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
> 
>> 
> 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 <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org>
> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
> _______________________________________________
> 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/

—

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 




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20210310/5c3b938f/attachment-0001.html>


More information about the Dev mailing list