title: Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.
abstract: We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56,419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37,670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants.
authors.affiliation: Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio-IT Research, Building Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Takeda
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Mitsuteru
authors.initials: M
authors.lastname: Nakao
authors.forename: Roberto A
authors.initials: RA
authors.lastname: Barrero
authors.forename: Kanako O
authors.initials: KO
authors.lastname: Koyanagi
authors.forename: Lihua
authors.initials: L
authors.lastname: Jin
authors.forename: Chie
authors.initials: C
authors.lastname: Motono
authors.forename: Hiroko
authors.initials: H
authors.lastname: Hata
authors.forename: Takao
authors.initials: T
authors.lastname: Isogai
authors.forename: Keiichi
authors.initials: K
authors.lastname: Nagai
authors.forename: Tetsuji
authors.initials: T
authors.lastname: Otsuki
authors.forename: Vladimir
authors.initials: V
authors.lastname: Kuryshev
authors.forename: Masafumi
authors.initials: M
authors.lastname: Shionyu
authors.forename: Kei
authors.initials: K
authors.lastname: Yura
authors.forename: Mitiko
authors.initials: M
authors.lastname: Go
authors.forename: Jean
authors.initials: J
authors.lastname: Thierry-Mieg
authors.forename: Danielle
authors.initials: D
authors.lastname: Thierry-Mieg
authors.forename: Stefan
authors.initials: S
authors.lastname: Wiemann
authors.forename: Nobuo
authors.initials: N
authors.lastname: Nomura
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Tadashi
authors.initials: T
authors.lastname: Imanishi
mesh_terms: D017398:Alternative Splicing; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000737:chemistry*; D005091:Exons; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D011506:Proteins / Q000737:chemistry / Q000235:genetics* / Q000502:physiology; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D018076:DNA, Complementary; D011506:Proteins; D012333:RNA, Messenger