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

  1. Hiromi Kochiwa1,3,
  2. Ryosuke Suzuki1,3,
  3. Takanori Washio3,
  4. Rintaro Saito4,
  5. The RIKEN Genome Exploration Research Group Phase, II Team4,5,
  6. Hidemasa Bono4,
  7. Piero Carninci4,
  8. Yasushi Okazaki4,
  9. Rika Miki4,
  10. Yoshihide Hayashizaki4, and
  11. Masaru Tomita2,3,6
  1. 1Graduate School of Media and Governance, 2Department of Environmental Information, and 3Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan; 4Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

Abstract

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 ofMus 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 athttp://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.

Footnotes

  • ↵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.

  • E-MAIL mt{at}sfc.keio.ac.jp; FAX 81 (466) 47-5099.

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.220302. Article published online before print in July 2002.

    • Received October 26, 2001.
    • Accepted May 17, 2002.
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  1. Published in Advance July 19, 2002, doi: 10.1101/gr.220302 Genome Res. 12: 1286-1293 Cold Spring Harbor Laboratory Press

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