ArticleBMC bioinformatics2007
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- No Association between the Plasmodium vivaxAntimicrobial agents and chemotherapy · 2023Article
- Mutations in RZF1, a zinc-finger protein, reduce magnesium uptake in roots and translocation to shoots in rice.Plant physiology · 2023Article
- Delayed Protein Changes During Seed Germination.Frontiers in plant science · 2021Article
- Phytochrome Coordinates with a hnRNP to Regulate Alternative Splicing via an Exonic Splicing Silencer.Plant physiology · 2020Article
- Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross.Nature communications · 2019Article
- Evolution of Alternative Splicing in Eudicots.Frontiers in plant science · 2019Article
- Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize.The Plant cell · 2018Article
- Exploring the relationship between intron retention and chromatin accessibility in plants.BMC genomics · 2018Article
- Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize.Plant physiology · 2016Article
- Article
- Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA Processing.The Plant cell · 2015Article
- CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements.BMC bioinformatics · 2015Article
- Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana.Molecular ecology · 2015Article
- Identifying splicing regulatory elements with de Bruijn graphs.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation.The Plant cell · 2014Article
- Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens.Plant physiology · 2014Article
- Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens.Genome biology · 2014Article
- Article
- Complexity of the alternative splicing landscape in plants.The Plant cell · 2013Review
- Splicing and alternative splicing in rice and humans.BMB reports · 2013Review
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Authors and funding
3 authors.
Funding
Abstract
backgroundAlgorithmic approaches to splice site prediction have relied mainly on the consensus patterns found at the boundaries between protein coding and non-coding regions. However exonic splicing enhancers have been shown to enhance the utilization of nearby splice sites.
resultsWe have developed a new computational technique to identify significantly conserved motifs involved in splice site regulation. First, 84 putative exonic splicing enhancer hexamers are identified in Arabidopsis thaliana. Then a Gibbs sampling program called ELPH was used to locate conserved motifs represented by these hexamers in exonic regions near splice sites in confirmed genes. Oligomers containing 35 of these motifs have been shown experimentally to induce significant inclusion of A. thaliana exons. Second, integration of our regulatory motifs into two different splice site recognition programs significantly improved the ability of the software to correctly predict splice sites in a large database of confirmed genes. We have released GeneSplicerESE, the improved splice site recognition code, as open source software.
conclusionOur results show that the use of the ESE motifs consistently improves splice site prediction accuracy.
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