[ensembl-dev] Mapping between Ensembl transcripts and Refseq, specifically for ENSG00000167131

Magali mr6 at ebi.ac.uk
Tue Mar 5 10:19:50 GMT 2013

Hi Reece,

This is correct, we now try to use the refseq transcripts from the
otherfeatures database to infer direct mapping based on overlap with the
ensembl transcript.
Failing that, we use the exonerate alignments as before, but the first
method is given priority.
This will be available for human as of release 71, and we are planning
to do the same for mouse in release 72.

Hope that helps,

On 04/03/13 23:15, Reece Hart wrote:
> On Mon, Mar 4, 2013 at 5:50 AM, Magali <mr6 at ebi.ac.uk
> <mailto:mr6 at ebi.ac.uk>> wrote:
>     As of release 71, we are also mapping refseq entries based on
>     coordinates overlap.
>     This means that for this particular case, NM_001258395.1 is also
>     mapped
>     to ENST00000410006.
> Do you mean that exact exon structures (i.e., exon start,end
> coordinates) will now be used to define equivalence of two
> transcripts? What does this portend for RefSeq transcripts pulled from
> otherfeatures?
> We currently precompute the list of exon-equivalent <ENST,NM>
> transcript pairs for the purpose of filtering VEP effects that we can
> report on RefSeq transcripts (in otherfeatures). It sounds like we'll
> be able to get this equivalence from Ensembl directly with 71. Right?
> Thanks,
> Reece
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