Subtle discrepancies of SF2/ASF ESE sequence motif among human tissues: A computational approach
The intron removal during the pre-mRNA splicing in higher eukaryotes requires the accurate identification of the two splice sites at the ends of the exons, or exon definition. However, the consensus sequences at the splice sites provide insufficient information to distinguish true splice sites from the large number of the false ones that populate the primary transcripts. Additional information is provided by cis-acting regulatory sequences that serve to enhance or repress splicing, and that may be exonic or intronic in nature: the splicing enhancers and the splicing silencers, respectively. In this study, we tested by computational and statistical approaches if the exonic splicing enhancer motif binding to the SF2/ASF SR protein is conserved among several groups of human genes. The results showed that the SF2/ASF ESE consensus was conserved between genes within the same chromosome, within different chromosomes and between different levels of muscular cells differentiation. However, this motif displays subtle variations within the consensus sequence between genes expressed in different tissues. These results can emphasize the presence of different translational isoforms of the SFRS1 gene encoding for the SF2/ASF, or different post-translational protein maturations in different tissues. This tissular discrepancy can also account for the alternative splicing of several genes between tissues.
Journal: Computational Biology and Chemistry - Volume 34, Issue 3, June 2010, Pages 203–209