Domain coordinates from InterPro to Ensembl transcripts

Question

[svet.sidorov]

Hello!

Is it possible to obtain InterPro coordinates of a protein domain in human alternative protein-coding transcripts from Ensembl?

For example, for TFAP2A gene, Ensembl has 9 alternative protein-coding transcripts, and for each of them I can see domains and their coordinates in different databases integrated into InterPro (Pfam, PRINTS, etc.; see, for example, the "Domains" section for ENST00000379608). But these domains don't have coordinates from InterPro itself.

On the other hand, I can see coordinates of a domain in different proteins in InterPro (example), but there is no data on alternative transcripts.

I saw a similar question, but I would need to use Ensembl.

Any advice is very much appreciated!

Answer 1

[Emily]

Yes. You can find them in the transcript tab in Ensembl.

Alternatively, if you want to see a table with all the coordinates for all transcripts, you can use BioMart. Filter by your gene of interest, then get the domains and transcript or protein IDs as Attributes. If you've not used BioMart before, there's a help video to get you started.

[svet.sidorov]

Dear Emily,

Thank you so much for your quick reply! But I meant a bit different thing: I can see in InterPro that AP-2 C-terminal domain in TFAP2A has coordinates 211..263,264..279,280..294 (see the bars for IPR013854 here), but I cannot see these coordinates for any of TFAP2A transcripts in Ensembl.

[Emily]

We don't have the InterPro summary of the domains, only the domains from the different prediction methods.

[svet.sidorov]

Thank you so much Emily! That is exactly what I wanted.