TassDB2 - A comprehensive database of subtle alternative splicing events

BMC Bioinformatics

Database

Thorsten Lenser¹  Rolf Backofen²  Rileen Sinha³  Stefan Schuster⁴  Michael Hiller⁵  Jochen Hampe⁶  Niels Jahn⁷  Ulrike Gausmann⁷  Matthias Platzer⁷  Klaus Huse⁷  Karol Szafranski⁷  Philip Rosenstiel⁸  Swetlana Friedel⁹ 

[1] Bio Systems Analysis Group, Friedrich Schiller University Jena, Ernst-Abbe-Platz 1-4, D-07743, Jena, Germany;Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany;Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany;Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104, Freiburg, Germany;Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany;Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany;Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany;Department of Developmental Biology, Stanford University, 94305, Stanford, CA, USA;Department of General Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstrasse, 12, 24105, Kiel, Germany;Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany;Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse, 12, 24105, Kiel, Germany;Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Systems Biology/Bioinformatics, Beutenbergstrasse. 11a, 07745, Jena, Germany;

关键词: Alternative Splice;    Splice Site;    Splice Event;    UCSC Genome Browser;    Intron Phase;   

DOI  :  10.1186/1471-2105-11-216

 received in 2009-11-05, accepted in 2010-04-29,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundSubtle 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.DescriptionWe 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.ConclusionTassDB2, 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.

【 授权许可】

Unknown   
© Sinha et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.