Question: Human Alternative Isoforms In Uniprot
3
gravatar for Pierre
6.3 years ago by
Pierre120
Spain
Pierre120 wrote:

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

splicing human isoform uniprot • 2.1k views
ADD COMMENTlink modified 6.3 years ago by Elisabeth Gasteiger1.6k • written 6.3 years ago by Pierre120
5
gravatar for Elisabeth Gasteiger
6.3 years ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

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

ADD COMMENTlink written 6.3 years ago by Elisabeth Gasteiger1.6k
4
gravatar for Pappu
6.3 years ago by
Pappu1.9k
Pappu1.9k wrote:

Check Ensembl Transcripts for this purpose.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Pappu1.9k
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