Convert refSeq ProteinIds in ENSP

Question

[Natan]

Hi Guys,

I downloaded the RefSeq protein-database. Now I want to map all RefSeq Protein ids (i.e.XP_011516301) to ensembl protein Ids (i.e.ENSP00000482598), where such an id is available. Does anyone know a convenient way to do it?

Thanks a lot! Natan

Answer 1

[GenoMax]

Accession numbers that begin with the prefix XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein) are model RefSeqs produced either by NCBI’s genome annotation pipeline or copied from computationally annotated submissions to the INSDC. These RefSeq records are derived from the genome sequence and have varying levels of transcript or protein homology support.

So it is likely that they may have no Ensembl counterpart ID's.

You can try with BioMart.

BTW: XP_011516301 is an obsolete ID at NCBI.