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Published online before print July 19, 2002, 10.1101/gr.220302
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Vol. 12, Issue 8, 1286-1293, August 2002

RESOURCES
Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data

Hiromi Kochiwa,1,3 Ryosuke Suzuki,1,3 Takanori Washio,3 Rintaro Saito,4 The RIKEN Genome Exploration Research Group Phase II Team,4,5 Hidemasa Bono,4 Piero Carninci,4 Yasushi Okazaki,4 Rika Miki,4 Yoshihide Hayashizaki,4 and Masaru Tomita2,3,6

1 Graduate School of Media and Governance, 2 Department of Environmental Information, and 3 Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan; 4 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

Although many studies on alternative splicing of specific genes have been reported in the literature, the general mechanism that regulates alternative splicing has not been clearly understood. In this study, we systematically aligned each pair of the 21,076 cDNA sequences of Mus musculus, searched for putative alternative splicing patterns, and constructed a list of potential alternative splicing sites. Two cDNAs are suspected to be alternatively spliced and originating from a common gene if they share most of their 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) tissue, (2) developmental stage, (3) sequences around splice sites, (4) the length of each gapped region, and (5) other comments. The list is available at http://www.bioinfo.sfc.keio.ac.jp/intron. Our results have predicted a number of unreported alternatively spliced genes, some of which are expressed only in a specific tissue or at a specific developmental stage.

5 The RIKEN Genome Exploration Research Group Phase II Team: Jun Kawai, Akira Shinagawa, Kazuhiro Shibata, Masayasu Yoshino, Masayoshi Itoh, Yoshiyuki Ishii, Takahiro Arakawa, Ayako Hara, Yoshifumi Fukunishi, Hideaki Konno, Jun Adachi, Shiro Fukuda, Katsunori Aizawa, Izawa Masaki, Katsuo Nishi, Hidenori Kiyosawa, Shinji Kondo, Itaru Yamanaka, and Tetsuya Saito.

6 Corresponding author.

12:1286-1293 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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