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

[Ewan Birney]

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
confirm.


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
>>>
>>> _______________________________________________
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>>
>>
>>
>
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