title: Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes.
abstract: Exonic splicing enhancers (ESEs) are pre-mRNA cis-acting elements required for splice-site recognition. We previously developed a web-based program called ESEfinder that scores any sequence for the presence of ESE motifs recognized by the human SR proteins SF2/ASF, SRp40, SRp55 and SC35 (http://rulai.cshl.edu/tools/ESE/). Using ESEfinder, we have undertaken a large-scale analysis of ESE motif distribution in human protein-coding genes. Significantly higher frequencies of ESE motifs were observed in constitutive internal protein-coding exons, compared with both their flanking intronic regions and with pseudo exons. Statistical analysis of ESE motif frequency distributions revealed a complex relationship between splice-site strength and increased or decreased frequencies of particular SR protein motifs. Comparison of constitutively and alternatively spliced exons demonstrated slightly weaker splice-site scores, as well as significantly fewer ESE motifs, in the alternatively spliced group. Our results underline the importance of ESE-mediated SR protein function in the process of exon definition, in the context of both constitutive splicing and regulated alternative splicing.
authors.affiliation: Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
authors.forename: Jinhua
authors.initials: J
authors.lastname: Wang
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Smith
authors.forename: Adrian R
authors.initials: AR
authors.lastname: Krainer
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing; D019295:Computational Biology; D005091:Exons; D006801:Humans; D011506:Proteins / Q000235:genetics; D012322:RNA Precursors / Q000737:chemistry*; D022821:RNA Splice Sites; D012326:RNA Splicing; D012333:RNA, Messenger / Q000737:chemistry*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D011506:Proteins; D012322:RNA Precursors; D022821:RNA Splice Sites; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D038621:Regulatory Sequences, Ribonucleic Acid