TassDB2 - A comprehensive database of subtle alternative splicing events.
BACKGROUND
Subtle alternative splicing events involving tandem splice sites separated by a short (2-12 nucleotides) distance are frequent and evolutionarily widespread in eukaryotes, and a major contributor to the complexity of transcriptomes and proteomes. However, these events have been either omitted altogether in databases on alternative splicing, or only the cases of experimentally confirmed alternative splicing have been reported. Thus, a database which covers all confirmed cases of subtle alternative splicing as well as the numerous putative tandem splice sites (which might be confirmed once more transcript data becomes available), and allows to search for tandem splice sites with specific features and download the results, is a valuable resource for targeted experimental studies and large-scale bioinformatics analyses of tandem splice sites. Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species.


METHODS
We have substantially revised and extended TassDB. The currently available version 2 contains extensive information about tandem splice sites separated by 2-12 nt for the human and mouse transcriptomes including data on the conservation of the tandem motifs in five vertebrates. TassDB2 offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download result datasets. For example, users can search for cases of alternative splicing where the proportion of EST/mRNA evidence supporting the minor isoform exceeds a specific threshold, or where the difference in splice site scores is specified by the user. The predicted impact of each event on the protein is also reported, along with information about being a putative target for the nonsense-mediated decay (NMD) pathway. Links are provided to the UCSC genome browser and other external resources.


CONCLUSIONS
TassDB2, available via http://www.tassdb.info, provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.
Sinha
Rileen
R
Albert-Ludwigs-University Freiburg, Germany.
Lenser
Thorsten
T
Jahn
Niels
N
Gausmann
Ulrike
U
Friedel
Swetlana
S
Szafranski
Karol
K
Huse
Klaus
K
Rosenstiel
Philip
P
Hampe
Jochen
J
Schuster
Stefan
S
Hiller
Michael
M
Backofen
Rolf
R
Platzer
Matthias
M
D017398:Alternative Splicing; D000818:Animals; D016208:Databases, Factual; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D022821:RNA Splice Sites; D012326:RNA Splicing; D012984:Software
D022821:RNA Splice Sites