Transcript variants conversion from Ensembl ENST to NM

Question

[Carmen]

Hi all,

I downloaded the 3'UTR folding dataset of human transcripts from Ensembl. However, the mRNA IDs do not contain the transcript variant (example: NM_001662). This causes problems when I have to combine datasets from different sources, as I won't be able to assign the proper 3'UTR information to the right transcript variant.

Do you know how to convert the Ensembl IDs to the right transcript variant and not just to the gene transcript?

If this is not possible, do you know about other datasets similar to the foldUtr3?

Thank you in advance!

Answer 1

[Ben_Ensembl]

Hi Carmen,

Since Ensembl and NCBI RefSeq have different annotation methodologies, not all Ensembl transcripts will have a 1-to-1 mapping with a RefSeq counterpart.

However, You can use BioMart to convert ENST into NMs. You can also use the xref endpoint available through the Ensembl REST API or the mapping file available on the FTP site.