ArticleNucleic acids research2006
Identification of alternative 5'/3' splice sites based on the mechanism of splice site competition.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 31 citations in OpenAlex.
- A NovelPlants (Basel, Switzerland) · 2026Article
- Alternative splicing: from tumorigenesis to neoantigen-mediated cancer immunotherapy.Biomarker research · 2025Review
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- Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee,G3 (Bethesda, Md.) · 2019Article
- 50/50 Expressional Odds of Retention Signifies the Distinction between Retained Introns and Constitutively Spliced Introns inFrontiers in plant science · 2017Article
- Functional analysis of alternative splicing of theHorticulture research · 2016Article
- Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2014Article
- Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements.Frontiers in plant science · 2012Article
- Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.BMC genomics · 2008Article
- Bioinformatics in China: a personal perspective.PLoS computational biology · 2008Review
- The emergence of alternative 3' and 5' splice site exons from constitutive exons.PLoS computational biology · 2007Article
- Does distance matter? Variations in alternative 3' splicing regulation.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing plays an important role in regulating gene expression. Currently, most efficient methods use expressed sequence tags or microarray analysis for large-scale detection of alternative splicing. However, it is difficult to detect all alternative splice events with them because of their inherent limitations. Previous computational methods for alternative splicing prediction could only predict particular kinds of alternative splice events. Thus, it would be highly desirable to predict alternative 5'/3' splice sites with various splicing levels using genomic sequences alone. Here, we introduce the competition mechanism of splice sites selection into alternative splice site prediction. This approach allows us to predict not only rarely used but also frequently used alternative splice sites. On a dataset extracted from the AltSplice database, our method correctly classified approximately 70% of the splice sites into alternative and constitutive, as well as approximately 80% of the locations of real competitors for alternative splice sites. It outperforms a method which only considers features extracted from the splice sites themselves. Furthermore, this approach can also predict the changes in activation level arising from mutations in flanking cryptic splice sites of a given splice site. Our approach might be useful for studying alternative splicing in both computational and molecular biology.
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