Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data

Hiromi Kochiwa, Ryosuke Suzuki, Takanori Washio, Rintaro Saito, 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 & 9 others Shinji Kondo, Itaru Yamanaka, Tetsuya Saito, Hidemasa Bono, Piero Carninci, Yasushi Okazaki, Rika Miki, Yoshihide Hayashizaki, Masaru Tomita

Research output: Contribution to journalArticle

12 Citations (Scopus)

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 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.

Original languageEnglish
Pages (from-to)1286-1293
Number of pages8
JournalGenome Research
Volume12
Issue number8
DOIs
Publication statusPublished - 2002 Aug 1

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Alternative Splicing
Oligonucleotide Array Sequence Analysis
Gene Library
Complementary DNA
Recombinant DNA
Sequence Homology
Introns
Genes

ASJC Scopus subject areas

  • Genetics

Cite this

Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. / Kochiwa, Hiromi; Suzuki, Ryosuke; Washio, Takanori; Saito, Rintaro; Kawai, Jun; Shinagawa, Akira; Shibata, Kazuhiro; Yoshino, Masayasu; Itoh, Masayoshi; Ishii, Yoshiyuki; Arakawa, Takahiro; Hara, Ayako; Fukunishi, Yoshifumi; Konno, Hideaki; Adachi, Jun; Fukuda, Shiro; Aizawa, Katsunori; Masaki, Izawa; Nishi, Katsuo; Kiyosawa, Hidenori; Kondo, Shinji; Yamanaka, Itaru; Saito, Tetsuya; Bono, Hidemasa; Carninci, Piero; Okazaki, Yasushi; Miki, Rika; Hayashizaki, Yoshihide; Tomita, Masaru.

In: Genome Research, Vol. 12, No. 8, 01.08.2002, p. 1286-1293.

Research output: Contribution to journalArticle

Kochiwa, H, Suzuki, R, Washio, T, Saito, R, Kawai, J, Shinagawa, A, Shibata, K, Yoshino, M, Itoh, M, Ishii, Y, Arakawa, T, Hara, A, Fukunishi, Y, Konno, H, Adachi, J, Fukuda, S, Aizawa, K, Masaki, I, Nishi, K, Kiyosawa, H, Kondo, S, Yamanaka, I, Saito, T, Bono, H, Carninci, P, Okazaki, Y, Miki, R, Hayashizaki, Y & Tomita, M 2002, 'Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data', Genome Research, vol. 12, no. 8, pp. 1286-1293. https://doi.org/10.1101/gr.220302
Kochiwa H, Suzuki R, Washio T, Saito R, Kawai J, Shinagawa A et al. Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Research. 2002 Aug 1;12(8):1286-1293. https://doi.org/10.1101/gr.220302
Kochiwa, Hiromi ; Suzuki, Ryosuke ; Washio, Takanori ; Saito, Rintaro ; Kawai, Jun ; Shinagawa, Akira ; Shibata, Kazuhiro ; Yoshino, Masayasu ; Itoh, Masayoshi ; Ishii, Yoshiyuki ; Arakawa, Takahiro ; Hara, Ayako ; Fukunishi, Yoshifumi ; Konno, Hideaki ; Adachi, Jun ; Fukuda, Shiro ; Aizawa, Katsunori ; Masaki, Izawa ; Nishi, Katsuo ; Kiyosawa, Hidenori ; Kondo, Shinji ; Yamanaka, Itaru ; Saito, Tetsuya ; Bono, Hidemasa ; Carninci, Piero ; Okazaki, Yasushi ; Miki, Rika ; Hayashizaki, Yoshihide ; Tomita, Masaru. / Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. In: Genome Research. 2002 ; Vol. 12, No. 8. pp. 1286-1293.
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