ArticleBMC bioinformatics2010
TassDB2 - A comprehensive database of subtle alternative splicing events.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs.Nucleic acids research · 2024Article
- Identification of a Novel Canonical Splice Site VariantFrontiers in genetics · 2022Article
- An extended catalogue of tandem alternative splice sites in human tissue transcriptomes.PLoS computational biology · 2021Article
- Combination of novel and public RNA-seq datasets to generate an mRNA expression atlas for the domestic chicken.BMC genomics · 2018Article
- Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Coupling and coordination in gene expression processes with pre-mRNA splicing.International journal of molecular sciences · 2015Review
- Article
- Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation.Nucleic acids research · 2014Article
- Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons.Nucleic acids research · 2014Article
- Fungal alternative splicing is associated with multicellular complexity and virulence: a genome-wide multi-species study.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing.Statistics in biosciences · 2013Article
- Function of alternative splicing.Gene · 2013Review
- Alternative splicing for diseases, cancers, drugs, and databases.TheScientificWorldJournal · 2013Review
- APPRIS: annotation of principal and alternative splice isoforms.Nucleic acids research · 2013Article
- Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence.BMC bioinformatics · 2012Article
- Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome.RNA (New York, N.Y.) · 2012Article
- SpliceDisease database: linking RNA splicing and disease.Nucleic acids research · 2012Article
- Increased complexity of Tmem16a/Anoctamin 1 transcript alternative splicing.BMC molecular biology · 2011Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. 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.
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.
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Registered trials
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