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Updated: Jun 13, 2026
08:35
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
TassDB2 - A comprehensive database of subtle alternative splicing events.
Rileen Sinha1, Thorsten Lenser, Niels Jahn
1Albert-Ludwigs-University Freiburg, Germany.
BMC Bioinformatics
|May 1, 2010
Summary
TassDB2 is a comprehensive database for short distance tandem splice sites, aiding researchers in analyzing alternative splicing events. It includes putative and confirmed events, offering valuable data for experimental and bioinformatics studies.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Subtle alternative splicing events involving tandem splice sites (2-12 nucleotides apart) are common in eukaryotes and contribute to transcriptome and proteome complexity.
- Existing databases often omit these subtle events or only include experimentally confirmed cases, limiting their utility for comprehensive analysis.
- Tandem splice sites are crucial for understanding gene regulation and protein diversity.
Purpose of the Study:
- To create a comprehensive and searchable database of subtle alternative splicing events involving tandem splice sites.
- To provide a valuable resource for targeted experimental studies and large-scale bioinformatics analyses of tandem splice sites.
- To extend the coverage of tandem splice site data beyond experimentally confirmed events to include putative sites.
Main Methods:
- Substantial revision and extension of the initial TassDB (version 1).
- Inclusion of tandem splice sites separated by 2-12 nucleotides for human and mouse transcriptomes.
- Data on conservation of tandem motifs in five vertebrates.
- Development of a user-friendly interface for searching specific genes or features and downloading results.
- Inclusion of predicted protein impact and potential for nonsense-mediated decay (NMD) pathway targeting.
- Integration with external resources like the UCSC genome browser.
Main Results:
- TassDB version 2 now contains extensive information on tandem splice sites (2-12 nt) in human and mouse.
- The database includes data on the conservation of these motifs across five vertebrate species.
- Users can search based on criteria such as the proportion of evidence for minor isoforms or splice site score differences.
- Predicted protein impacts and NMD pathway targeting information are provided for each event.
Conclusions:
- TassDB2 offers a comprehensive resource for researchers studying short distance tandem splice sites.
- The database facilitates both targeted experimental investigations and large-scale bioinformatics analyses.
- TassDB2 is accessible online at http://www.tassdb.info, serving as a valuable tool for the scientific community.
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