Finding Gff File For All Uniprot Protein Isoform Domain Annotations

Question

[user]

where can I download a UniProtKB GFF file containing all the domain annotations for a particular proteome, e.g. mouse?

I found that if I look at this page: http://www.uniprot.org/uniprot/?query=taxonomy%3a10090&format=*

I can download a GFF but it does not contain the annotation for all protein isoforms. It only includes the major / canonical isoform for each protein. Where can I get the complete set? Thanks.

Answer 1

[Andrzej Zielezinski]

1. Use the link you gave to download the list of all UniProtKB accession numbers.
2. Click the Retrieve tab on the UniProtKB homepage, upload the downloaded file and click the Retrieve button.
3. Download domain annotations as a GFF file.

[Michi]

Doing this query (http://www.uniprot.org/uniprot/?query=taxonomy:9606&format=gff) I only get the canonical Isoforms - and no data for the alternative isoforms