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Open Access Database

TassDB2 - A comprehensive database of subtle alternative splicing events

Rileen Sinha12, Thorsten Lenser3, Niels Jahn2, Ulrike Gausmann2, Swetlana Friedel4, Karol Szafranski2, Klaus Huse2, Philip Rosenstiel5, Jochen Hampe6, Stefan Schuster7, Michael Hiller8, Rolf Backofen1109 and Matthias Platzer2*

Author Affiliations

1 Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany

2 Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany

3 Bio Systems Analysis Group, Friedrich Schiller University Jena, Ernst-Abbe-Platz 1-4, D-07743 Jena, Germany

4 Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Systems Biology/Bioinformatics, Beutenbergstrasse. 11a, 07745 Jena, Germany

5 Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse, 12, 24105 Kiel, Germany

6 Department of General Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstrasse, 12, 24105 Kiel, Germany

7 Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany

8 Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA

9 Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany

10 Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany

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BMC Bioinformatics 2010, 11:216  doi:10.1186/1471-2105-11-216

Published: 29 April 2010

Abstract

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.

Description

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.

Conclusion

TassDB2, available via http://www.tassdb.info webcite, provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.