ArticleNucleic acids research2010
A network of conserved co-occurring motifs for the regulation of alternative splicing.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Integrative transcriptomic analysis reveals alternative splicing complexity and transcriptomic diversity in porcine placentas across altitudes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Article
- At Least Two Genes Encode Many Variants of Irak3 in Rainbow Trout, but Neither the Full-Length Factor Nor Its Variants Interfere Directly With the TLR-Mediated Stimulation of Inflammation.Frontiers in immunology · 2019Article
- The combinatorial control of alternative splicing in C. elegans.PLoS genetics · 2017Article
- CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements.BMC bioinformatics · 2015Article
- A biophysical model for identifying splicing regulatory elements and their interactions.PloS one · 2013Article
- DECOD: fast and accurate discriminative DNA motif finding.Bioinformatics (Oxford, England) · 2011Article
- Mechanistic control of carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) splice isoforms by the heterogeneous nuclear ribonuclear proteins hnRNP L, hnRNP A1, and hnRNP M.The Journal of biological chemistry · 2011Article
- Nonsense mutation-associated Becker muscular dystrophy: interplay between exon definition and splicing regulatory elements within the DMD gene.Human mutation · 2011Article
- Article
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6 authors.
Funding
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Abstract
Cis-acting short sequence motifs play important roles in alternative splicing. It is now possible to identify such sequence motifs as conserved sequence patterns in genome sequence alignments. Here, we report the systematic search for motifs in the neighboring introns of alternatively spliced exons by using comparative analysis of mammalian genome alignments. We identified 11 conserved sequence motifs that might be involved in the regulation of alternative splicing. These motifs are not only significantly overrepresented near alternatively spliced exons, but they also co-occur with each other, thus, forming a network of cis-elements, likely to be the basis for context-dependent regulation. Based on this finding, we applied the motif co-occurrence to predict alternatively skipped exons. We verified exon skipping in 29 cases out of 118 predictions (25%) by EST and mRNA sequences in the databases. For the predictions not verified by the database sequences, we confirmed exon skipping in 10 additional cases by using both RT-PCR experiments and the publicly available RNA-Seq data. These results indicate that even more alternative splicing events will be found with the progress of large-scale and high-throughput analyses for various tissue samples and developmental stages.
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