Genome Informatics 14: 428--429 (2003) Identifying Potential Regulatory Sequences of

Abstract

Introduction Alternative splicing is an important mechanism that contributes to expanding protein diversity by generating multiple protein isoforms from a single gene. We have previously reported computational approach to infer alternative splicing patterns from Mus musculus full-length cDNA clones and microarray data [4]. Although we have predicted a large number of unreported splice variants, general mechanisms that regulate those alternative splicing were yet to be understood. In the present study, we constructed datasets of putative alternatively spliced genes by use of full-length cDNA clones and genomic DNA sequences. Our putative datasets were then evaluated by comparing information contents of constitutive splice-sites and those of alternative splice-sites. Using phylogenetic footprinting approach, we identified the potential regulatory sequences of alternative splicing. 2 Method and Results 2.1 Detection of Putative Alternative Splicing Patterns We detected putative splice