[ensembl-dev] RefSeq <-> Ensembl Transcript ID?

Ewan Birney birney at ebi.ac.uk
Thu Oct 7 15:15:02 BST 2010

It is done at the transcript level (not the gene level) though I can't
remember (and it might have changed) whether the Xref stores it
at the protein or cDNA level.

In Ensembl there is a 1 to 1 link between proteins and transcripts,
so mapping "at the protein level" (in terms of how it is stored)
is the same as the cDNA level.

I am pretty sure we now do quite alot of the Xref mapping at the
cDNA level to help resolve very close paralogs - Ian and Glenn to

On 7 Oct 2010, at 15:01, Cei Abreu-Goodger wrote:

> Thanks Bert and Sergei,
> Yeah, I was kind of hoping that there would be a direct relationship  
> between transcripts. But if the connection is done at the protein  
> level, I'll have to drop down to gene IDs.
> Does anyone in Ensembl know if there's a plan to perform mapping at  
> the transcript level to UCSC or NCBI?
> Cheers,
> Cei
> On 07/10/2010 14:57, Bert Overduin wrote:
>> Hello Cei,
>> I think the NCBI RefSeq IDs are on the level of the translation,  
>> not the
>> transcript. So, you have to get the DBEntries for the translation  
>> of your
>> transcript or alternatively get the DBLinks for your transcript.
>> Cheers,
>> Bert
>> On Thu, Oct 7, 2010 at 2:40 PM, Cei Abreu-Goodger<cei at ebi.ac.uk>   
>> wrote:
>>> Hello,
>>> Is it possible to obtain the relationship between Ensembl  
>>> Transcript IDs
>>> and NCBI's RefSeq transcript ids (NM_########)? I've been  
>>> searching in the
>>> DBEntries assigned to the transcripts, but can't seem to find this.
>>> Thanks!
>>> Cei
>>> _______________________________________________
>>> Dev mailing list
>>> Dev at ensembl.org
>>> http://lists.ensembl.org/mailman/listinfo/dev
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

More information about the Dev mailing list