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Nucleic Acids Research Advance Access originally published online on November 16, 2006
Nucleic Acids Research 2007 35(Database issue):D188-D192; doi:10.1093/nar/gkl762
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Nucleic Acids Research, 2007, Vol. 35, Database issue D188-D192
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

TassDB: a database of alternative tandem splice sites

Michael Hiller*, Swetlana Nikolajewa1, Klaus Huse2, Karol Szafranski2, Philip Rosenstiel3, Stefan Schuster1, Rolf Backofen and Matthias Platzer2

Institute of Computer Science, Chair for Bioinformatics, Albert-Ludwigs-University Freiburg Georges-Koehler-Allee 106, 79110 Freiburg, Germany 1 Department of Bioinformatics, Friedrich-Schiller-University Jena Ernst-Abbe-Platz 2, 07743 Jena, Germany 2 Genome Analysis, Leibniz Institute for Age Research—Fritz Lipmann Institute Beutenbergstrasse 11, 07745 Jena, Germany 3 Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel Schittenhelmstrasse, 12, 24105 Kiel, Germany

*To whom correspondence should be addressed. Tel: +49 761 203 8254; Fax: +49 761 203 7462; Email: hiller{at}informatik.uni-freiburg.de

Received July 14, 2006. Accepted September 26, 2006.

Subtle alternative splice events at tandem splice sites are frequent in eukaryotes and substantially increase the complexity of transcriptomes and proteomes. We have developed a relational database, TassDB (TAndem Splice Site DataBase), which stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. These splice events are of subtle nature since they mostly result in the insertion/deletion of a single amino acid or the substitution of one amino acid by two others. Currently, TassDB contains 114 554 tandem splice sites of eight species, 5209 of which have EST/mRNA evidence for alternative splicing. In addition, human SNPs that affect NAGNAG acceptors are annotated. The database provides 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 large datasets. This database should facilitate further experimental studies and large-scale bioinformatics analyses of tandem splice sites. The database is available at http://helios.informatik.uni-freiburg.de/TassDB/.


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