[ensembl-dev] Ensembl ids and RefSeq ids

[Gustavo Franca]

Hi ib,

I have chosen RefSeq mRNA and RefSeq protein ID in Attributes -> External
References, but still, I didn't get RefSeq version. For example, via
BioMart, I've got:

ENSG00000259662    ENST00000539570     NP_976307     NM_203373

Note that there are no RefSeq versions. Instead, I would like to get:

ENSG00000259662    ENST00000539570    NP_976307.2   NM_203373.2

Do you know how to get data this way?
Regards,
Gustavo


On Thu, Aug 23, 2012 at 6:18 PM, i b <ibseq12 at gmail.com> wrote:

> hi gustavo,
> I have done a similar thing on biomart and was ok...did you choose
> refseq on the list on biomart while doing the conversion.if im not
> wrong shoudl be under attributes/external...
>
> let me know i might be able to do it and see if it works
>
> regards,
> ib
>
> On Thu, Aug 23, 2012 at 9:52 PM, Gustavo Franca <gsfranca at gmail.com>
> wrote:
> > Hello,
> >
> > I would like to retrieve a table with all human genes, containing Ensembl
> > Gene IDs, Ensembl Transcript IDs, Ensembl Protein IDs and their
> respective
> > RefSeq mRNA IDs and RefSeq peptide IDs. As an example, see the last table
> > (External references) shown in KIR2DL5A page:
> >
> http://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000215764;r=GL000209.1:7891-96246
> >
> > I realized that it is possible to get ID conversions via BioMart,
> however,
> > the BioMart output does not provide me the version of the RefSeq entry as
> > shown in the above example. (e.g: ENST00000344867    NP_055034.2
> > NM_014219.2). So, I would like to retrieve Ensembl transcripts and their
> > corresponding RefSeq versions.
> > Anyone could help me out on this?
> >
> > Thank you very much,
> > Gustavo
> >
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>
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