[ensembl-dev] same CDS, different exons; was Re: VEP: reporting HGVS identifiers with RefSeq accessions

Amonida Zadissa amonida at sanger.ac.uk
Wed Feb 15 13:43:57 GMT 2012


Looking closer at the ENST00000382673 transcript, it seems the
underlying evidence (NM_001006117.2) was wrongly aligned, mainly
because of the high repetative nature of the region. RMBY1D and RMBY1E
genes have very similar structure.

This is an Ensembl annotated transcript and we will remove it in
release e67. It is unfortunately too late to do this in e66 because
e66 will be release in the coming weeks.

Hopefully this explains the situation.


On Wed, Feb 15, 2012 at 12:28:09PM +0000, Matthew Astley wrote:
> On Tue, Feb 14, 2012 at 10:39:09PM -0800, Reece Hart wrote:
> > In the [previous] I excerpted 3 prominent cases.
> [...]
> > 3) NM_001006120.2 overlaps ENST00000382673 and has an identical
> > translation *but has a different exon structure*. This is the case I
> > alluded to in my previous email that might cause a coding variant to
> > appear as non-coding or vice versa.
> I was curious about 3), so asked the Havana annotator next to me.  I'm
> not sure how relevant the ensuing conversation is to VEP, sorry.
> Here's a link to the region in Ensembl, enabling some tracks and
> showing two of the four duplicated genes in the region
>   http://v.gd/add5rs
> The other two are around 23.7 Mb
> ENST00000382673 is a transcript which spans the two copies, taking its
> last exon from the second copy.  Mark thinks this is probably an
> incorrect gene prediction.
> He also pointed out the sequence gap at 23.90Mb - it suggests the
> region is tricky to sequence.
> The supporting sequences
>   http://www.ncbi.nlm.nih.gov/nuccore/NM_001006121,NM_001006120,NM_005058,NM_001006118
> are very similar, except at the ends.
> I think the conclusion was that it can happen, that CDS is the same
> for a different exon structure, but in this case it's a bug.
> I hope this is helpful.  Please let us know if you have questions,
> -- 
> Matthew
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