International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)

Table of Contents * Genes, Physical Mapping and Sequencing * Gene Identification * Bioinformatics * Common Resources * RIKEN Session * Functional Genomics * Complex Traits * Mutagenesis * Developmental Genetics and Differentiation * Verne Chapman Memorial Lecture I and II

C19. Sequence analysis of alternative splicing patterns in the mouse cDNA clones.

Hiromi Kochiwa^1,2, Ryosuke Suzuki^1,2, Takanori Washio^1,3, Akira Shinagawa⁴, Masayoshi Itoh⁴, Kazuhiro Shibata⁴, Carninci Piero⁴, Hideaki Konno⁴, Jun Kawai⁴, Yoshifumi Fukunishi⁴, Yoshihide Hayashizaki⁴ and Masaru Tomita^1,2.
¹Lab. for Bioinfo.,²Dept. of Env. Info., ³Grad. Sch. of Media and Governance, Keio Univ., ⁴Laboratory for Genome Exploration Research Group, RIKEN Gemomic Sciences Center (GSC), RIKEN Yokohama Institute.

While a large number of studies on alternative splicing of specific genes have been reported in the literature, the general mechanism that regulates alternative splicing has not yet been clearly understood. In this study, we systematically aligned each pair of the 21,000 cDNA sequences of M. musculus, searched for putative alternative splicing patterns, and constructed a list of potential alternative splicing sites. Two cDNAs are suspected to be alternatively spliced originating from the common gene, if they share most of the region with a high degree of sequence homology but parts of the sequences are very distinctive or deleted in either cDNA.

The list contains the following information, 1) expressed tissue 2) splicing position, and 3) alternative splicing type. Using this dataset, we also analyzed the length of alternatively spliced sequences, as well as the consensus nucleotide patterns around the splice sites