Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

Jun Ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Roberto A. Barrero, Kanako O. Koyanagi, Lihua Jin, Chie Motono, Hiroko Hata, Takao Isogai, Keiichi Nagai, Tetsuji Otsuki, Vladimir Kuryshev, Masafumi Shionyu, Kei Yura, Mitiko Go, Jean Thierry-Mieg, Danielle Thierry-Mieg, Stefan Wiemann, Nobuo Nomura, Sumio SuganoTakashi Gojobori, Tadashi Iman ishi

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32 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)3917-3928
Number of pages12
JournalNucleic acids research
Volume34
Issue number14
DOIs
Publication statusPublished - 2006 Sep 21

ASJC Scopus subject areas

  • Genetics

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    Takeda, J. I., Suzuki, Y., Nakao, M., Barrero, R. A., Koyanagi, K. O., Jin, L., Motono, C., Hata, H., Isogai, T., Nagai, K., Otsuki, T., Kuryshev, V., Shionyu, M., Yura, K., Go, M., Thierry-Mieg, J., Thierry-Mieg, D., Wiemann, S., Nomura, N., ... Iman ishi, T. (2006). Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs. Nucleic acids research, 34(14), 3917-3928. https://doi.org/10.1093/nar/gkl507