Release 4.2
Published March 1, 2005
Headlines
More than 10'000 additional sequences encoded on splice variants in Swiss-Prot
Swiss-Prot is a non-redundant protein knowledgebase where the protein sequences from the same organism originating from the same gene are merged into one entry. When alternative products are produced by alternative splicing, the number of isoforms and their properties are indicated in the comment lines under the "Alternative products" topic, and the "Alternative splicing" keyword is added to the entry. The sequences of the alternative forms, if known, are described in the feature table under the key name "VARSPLIC". E.g. PRKN2_HUMAN (O60260).More frequently than not, it is the longest isoform that is shown in a Swiss-Prot entry. The additional isoforms can be reconstructed from the annotation. We assign an unique identifier for each isoform (IsoId), and unique feature identifiers (FTId) to each "VARSPLIC" feature described in the feature table. Each IsoId comes with a list of FTIds which serve as "instructions" to be applied in order to reconstruct the isoform's sequence.
The number of these additional Swiss-Prot recreated splice variants has recently reached the 10'000 mark.
More than a half are human isoforms. More than 80% are from mammals.
A fasta-formatted file containing all splice variants annotated in Swiss-Prot and TrEMBL can be downloaded for use with similarity search programs. Most sequence analysis and proteomic tools on ExPASy, e.g. BLAST or Aldente, have been adapted to take into account, in addition to all Swiss-Prot and TrEMBL entries, all other annotated splice isoforms.
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