Differences between BioMart and Ensembl site

Question

[jpuntomarcos]

Hi,

I have observed different transcripts correspondence between BioMart and the Ensemble site. If we observe the transcripts table at Ensembl site for A2ML1 gene, the ENST00000299698.7 is only related to NM_144670.4 transcript:

However, if we retrieve BioMart data, ENST00000299698.7 is related to two transcripts: NM_001282424 and NM_144670.

Could anyone explain this difference?

Thanks a lot in advance.

[GenoMax]

Looks like you linked GRCh37 site for Ensembl. Are you using the same genome build in BioMart?

[jpuntomarcos]

Yes, both are GRCh37.p13. This is the link to the Biomart query (you have to click Results), but I don't know how long the link will work.

Answer 1

[Ben Moore]

Hi jpuntomarcos,

The transcript table you have observed will only show you a single RefSeq transcript that is mapped per Ensembl transcript. You can view the full list by clicking on the 'General Identifiers' link on the left hand side of the page: http://grch37.ensembl.org/Homo_sapiens/Transcript/Similarity?db=core;g=ENSG00000166535;r=12:8975068-9029381;t=ENST00000299698

[jpuntomarcos]

Thanks! I would suggest adding a small explanation/note, probably in the RefSeq column tooltip.