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

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...

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Main Authors:	Takeda, Jun-ichi, Suzuki, Yutaka, Nakao, Mitsuteru, Barrero, Roberto A., Koyanagi, Kanako O., Jin, Lihua, Motono, Chie, Hata, Hiroko, Isogai, Takao, Nagai, Keiichi, Otsuki, Tetsuji, Kuryshev, Vladimir, Shionyu, Masafumi, Yura, Kei, Go, Mitiko, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Wiemann, Stefan, Nomura, Nobuo, Sugano, Sumio, Gojobori, Takashi, Imanishi, Tadashi
Format:	Online
Language:	English
Published:	Oxford University Press 2006
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557807/

id	pubmed-1557807
recordtype	oai_dc
spelling	pubmed-15578072006-09-06 Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs Takeda, Jun-ichi Suzuki, Yutaka Nakao, Mitsuteru Barrero, Roberto A. Koyanagi, Kanako O. Jin, Lihua Motono, Chie Hata, Hiroko Isogai, Takao Nagai, Keiichi Otsuki, Tetsuji Kuryshev, Vladimir Shionyu, Masafumi Yura, Kei Go, Mitiko Thierry-Mieg, Jean Thierry-Mieg, Danielle Wiemann, Stefan Nomura, Nobuo Sugano, Sumio Gojobori, Takashi Imanishi, Tadashi Genomics 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. Oxford University Press 2006 2006-08-12 /pmc/articles/PMC1557807/ /pubmed/16914452 http://dx.doi.org/10.1093/nar/gkl507 Text en © 2006 The Author(s).
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Takeda, Jun-ichi Suzuki, Yutaka Nakao, Mitsuteru Barrero, Roberto A. Koyanagi, Kanako O. Jin, Lihua Motono, Chie Hata, Hiroko Isogai, Takao Nagai, Keiichi Otsuki, Tetsuji Kuryshev, Vladimir Shionyu, Masafumi Yura, Kei Go, Mitiko Thierry-Mieg, Jean Thierry-Mieg, Danielle Wiemann, Stefan Nomura, Nobuo Sugano, Sumio Gojobori, Takashi Imanishi, Tadashi
spellingShingle	Takeda, Jun-ichi Suzuki, Yutaka Nakao, Mitsuteru Barrero, Roberto A. Koyanagi, Kanako O. Jin, Lihua Motono, Chie Hata, Hiroko Isogai, Takao Nagai, Keiichi Otsuki, Tetsuji Kuryshev, Vladimir Shionyu, Masafumi Yura, Kei Go, Mitiko Thierry-Mieg, Jean Thierry-Mieg, Danielle Wiemann, Stefan Nomura, Nobuo Sugano, Sumio Gojobori, Takashi Imanishi, Tadashi Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs
author_facet	Takeda, Jun-ichi Suzuki, Yutaka Nakao, Mitsuteru Barrero, Roberto A. Koyanagi, Kanako O. Jin, Lihua Motono, Chie Hata, Hiroko Isogai, Takao Nagai, Keiichi Otsuki, Tetsuji Kuryshev, Vladimir Shionyu, Masafumi Yura, Kei Go, Mitiko Thierry-Mieg, Jean Thierry-Mieg, Danielle Wiemann, Stefan Nomura, Nobuo Sugano, Sumio Gojobori, Takashi Imanishi, Tadashi
author_sort	Takeda, Jun-ichi
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
title_short	Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs
title_full	Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs
title_fullStr	Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs
title_full_unstemmed	Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs
title_sort	large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cdnas
description	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.
publisher	Oxford University Press
publishDate	2006
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557807/
_version_	1611387130121027584

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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