[ensembl-dev] Ensembl ids and RefSeq ids

[i b]

Hi Gustavo,
if you know which accession number you want in this "format" you can
just find it on Pubmed. The number after the accession number, e.g. in
NM_203373.2, the number 2, does not change the identity of the
protein/transcript. I have seen this only on pubmed, thus I don't
think you will find it since NM_203373.2 is the same as NM_203373 as
RefSeq.
You can easily see this if on Pubmed, under nucleotide, you digit
NM_203373 or NM_203373.2....the link is the same
(http://www.ncbi.nlm.nih.gov/nuccore/NM_203373 and
http://www.ncbi.nlm.nih.gov/nuccore/NM_203373.2)

hope it helps,
ib

On Thu, Aug 23, 2012 at 10:34 PM, Gustavo Franca <gsfranca at gmail.com> wrote:
> 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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