title: Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.
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.
authors.affiliation: Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Kochiwa
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Suzuki
authors.forename: Takanori
authors.initials: T
authors.lastname: Washio
authors.forename: Rintaro
authors.initials: R
authors.lastname: Saito
authors.forename: Hidemasa
authors.initials: H
authors.lastname: Bono
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Okazaki
authors.forename: Rika
authors.initials: R
authors.lastname: Miki
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000235:genetics*; D030541:Databases, Genetic / Q000706:statistics & numerical data; D005544:Forecasting / Q000379:methods; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D005786:Gene Expression Regulation / Q000235:genetics; D015723:Gene Library; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D018076:DNA, Complementary