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

J-I Takeda; Y. Suzuki; M. Nakao; R.A. Barrero; K.O. Koyanagi; L. Jin; C. Motono; H. Hata; T. Isogai; K. Nagai; T. Otsuki; V. Kuryshev; M. Shionyu; K. Yura; M. Go; J. Thierry-Mieg; D. Thierry-Mieg; S. Wiemann; N. Nomura; S. Sugano; T. Gojobori; T. Imanishi

doi:10.1093/nar/gkl507

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

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

J-I Takeda, Y. Suzuki, M. Nakao, R.A. Barrero, K.O. Koyanagi, L. Jin, C. Motono, H. Hata, T. Isogai, K. Nagai, …

Nucleic Acids Research, Vol.34(14), pp.3917-3928

2006

DOI: https://doi.org/10.1093/nar/gkl507

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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.

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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
Authors/Creators: J-I Takeda (Author/Creator)
Y. Suzuki (Author/Creator)
M. Nakao (Author/Creator)
R.A. Barrero (Author/Creator)
K.O. Koyanagi (Author/Creator)
L. Jin (Author/Creator)
C. Motono (Author/Creator)
H. Hata (Author/Creator)
T. Isogai (Author/Creator)
K. Nagai (Author/Creator)
T. Otsuki (Author/Creator)
V. Kuryshev (Author/Creator)
M. Shionyu (Author/Creator)
K. Yura (Author/Creator)
M. Go (Author/Creator)
J. Thierry-Mieg (Author/Creator)
D. Thierry-Mieg (Author/Creator)
S. Wiemann (Author/Creator)
N. Nomura (Author/Creator)
S. Sugano (Author/Creator)
T. Gojobori (Author/Creator)
T. Imanishi (Author/Creator)
Publication Details: Nucleic Acids Research, Vol.34(14), pp.3917-3928
Publisher: Oxford University Press
Identifiers: 991005543823907891
Copyright: © 2006 The Author(s)
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article
Note: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Collaboration types: Industry collaboration; Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.469 Alternative Splicing
Web Of Science research areas: Biochemistry & Molecular Biology
ESI research areas: Biology & Biochemistry