[ensembl-dev] stop codons missing in CDS definitions wheat Ensembl v22

Arnaud Kerhornou arnaud at ebi.ac.uk
Thu Jul 17 11:10:58 BST 2014

Dear Ksenia,

Thanks for reporting this problem.
You're right, and we'll aim to fix them in the coming release which is 
coming in August. It is actually also a problem on barley, and we'll fix 
them as well.

We notified MIPS who generated the gene sets, and they fixed this issue 
in the gene pipeline, so it should not happen again.

All the best,

On 17/07/2014 00:31, Ksenia Krasileva wrote:
> Dear Ensembl team,
> This is regarding T. aestivum annotation Ensembl v22.
> It looks like the stop codons are not part of CDS as defined by 
> Sequence Ontology but are placed instead in 3'UTRs.
> This affects some feature extractions and variant prediction with VEP 
> (no 'stop_loss' category).
> Thank you in advance.
> Best wishes,
> Ksenia
> -- 
> Ksenia Krasileva, PhD
> Post Doctoral Scholar
> USDA NIFA Fellowship
> The Dubcovsky Lab
> Department of Plant Sciences
> University of California, Davis
> 124 Robbins Hall
> Davis, CA 95616
> krasileva at ucdavis.edu <mailto:krasileva at ucdavis.edu>
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