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A network of conserved co-occurring motifs for the regulation of alternative splicing

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Item Type:Article
Title:A network of conserved co-occurring motifs for the regulation of alternative splicing
Creators Name:Suyama, M., Harrington, E.D., Vinokourova, S., von Knebel Doeberitz, M., Ohara, O. and Bork, P.
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.
Keywords:Alternative Splicing, Base Sequence, Conserved Sequence, Exons, Genomics, Introns, Molecular Sequence Data, Ribonucleic Acid Regulatory Sequences, Sequence Alignment, Animals
Source:Nucleic Acids Research
Publisher:Oxford University Press
Page Range:7916-7926
Date:1 December 2010
Official Publication:https://doi.org/10.1093/nar/gkq705
PubMed:View item in PubMed

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