Computational prediction of splicing regulatory elements shared by Tetrapoda organisms

A total of 2,546 Tetrapoda enhancers and silencers were clustered into 15 putative core motifs based on their Markov properties. Most of these elements have been identified previously, but 118 putative silencers and 260 enhancers (~15%) were novel. Examination of previously published experimental data for the presence of predicted elements showed that their mutations in 21/23 (91.3%) cases altered the splicing pattern as expected. Predicted intronic motifs flanking 3' and 5' splice sites had higher evolutionary conservation than other sequences within intronic flanks and the intronic enhancers were markedly differed between 3' and 5' intronic flanks.Difference in intronic enhancers supporting 5' and 3' splice sites suggests an independent splicing commitment for neighboring exons. Increased evolutionary conservation for ISEs/ISSs within intronic flanks and effect of modulation of predicted elements on splicing suggest functional significance of found elements in splicing regulation. Most of the elements identified were shown to have direct implications in human splicing and therefore could be useful for building computational splicing models in biomedical research.Eukaryotic genes contain intervening sequences or introns that need to be removed from precursor messenger RNA (pre-mRNA) in a complex process termed splicing. During pre-mRNA splicing, relatively short exonic sequences are recognized by spliceosome, a large RNA-protein complex. During splicing, introns are removed and exons are joined together to form mature RNA. In addition to splice site (SS) signals at the exonic 5' and 3' ends, accurate discrimination of exons and introns requires additional auxiliary elements [1-3]. These conserved but degenerate motifs have been termed exonic (ESEs) and intronic (ISEs) splicing enhancers and exonic (ESSs) and intronic (ISSs) splicing silencers that activate or repress splicing, respectively. These elements are thought to bind splicing regulatory factors, including t