International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)

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

Hiromi Kochiwa1,2, Ryosuke Suzuki1,2, Takanori Washio1,3, Akira Shinagawa4, Masayoshi Itoh4, Kazuhiro Shibata4, Carninci Piero4, Hideaki Konno4, Jun Kawai4, Yoshifumi Fukunishi4, Yoshihide Hayashizaki4 and Masaru Tomita1,2.
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

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