Human Alternative Isoforms In Uniprot

Question

[Pierre]

Hi,

I have been working with a couple of human alternative isoforms listed in uniprot database. Now I would like to expand the study and check hundreds of transcripts.

Complete proteome file available at Uniprot provides protein sequences for each isoform but does not include any information how each isoform differs from the canonical isoform.

Does Uniprot provide this information for all available isoforms in some workable format (e.g., some flat file)?

I am interested in identifying distinct types of alternative splicing (e.g., skipped/missing exon, mutually exclusive exons etc.) for such transcripts.

I would like to stick to Uniprot for this analysis.

Thanks

Answer 1

[Elisabeth Gasteiger]

The UniProt complete proteome file is in fasta format and indeed does not contain information on how the isoforms differ from the canonical sequences.

However, the flat file format of the canonical isoform entry does contain the information: e.g. http://www.uniprot.org/uniprot/P28223#section_alternative (html view) or http://www.uniprot.org/uniprot/P28223.txt (flat file):

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=P28223-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=P28223-2; Sequence=VSP_044593, VSP_044594;
CC         Note=No experimental confirmation available;
..
FT   VAR_SEQ       1     54       MDILCEENTSLSSTTNSLMQLNDDTRLYSNDFNSGEANTSD
FT                                AFNWTVDSENRTN -> MQFLKSAKQKPNYYHIMLVEDQEE
FT                                GTLHQFNYCERCSESQNNKCISCVNPEDKW (in
FT                                isoform 2).
FT                                /FTId=VSP_044593.
FT   VAR_SEQ      55    138       Missing (in isoform 2).
FT                                /FTId=VSP_044594.

See this page for documentation: http://www.uniprot.org/manual/alternative_products

Answer 2

[Pappu]

Check Ensembl Transcripts for this purpose.