Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
Katsunaga Sakai(RIKEN Center for Integrative Medical Sciences), I. Nikaido(RIKEN Center for Integrative Medical Sciences), Mari Nakamura(RIKEN Center for Integrative Medical Sciences), R. Saito(Yamagata University), Ikuko Kagawa(RIKEN Center for Integrative Medical Sciences), M. Yoshino(RIKEN Center for Integrative Medical Sciences), Y. Hayashizaki(University of Tsukuba), Yoshiyuki Ishii(RIKEN Center for Integrative Medical Sciences), A. Nogami(RIKEN Center for Integrative Medical Sciences), Ken Yagi(RIKEN Center for Integrative Medical Sciences), Shinji Kondo(RIKEN Center for Integrative Medical Sciences), Takahiro Arakawa(RIKEN Center for Integrative Medical Sciences), Naoki Osato(RIKEN Center for Integrative Medical Sciences), Daisuke Sasaki(RIKEN Center for Integrative Medical Sciences), Ayako Hara(RIKEN Center for Integrative Medical Sciences), Ai Miyazaki(RIKEN Center for Integrative Medical Sciences), Wataru Hashizume(RIKEN Center for Integrative Medical Sciences), Kazunori Waki(RIKEN Center for Integrative Medical Sciences), J. Kawai(RIKEN), Hidemasa Bono(RIKEN Center for Integrative Medical Sciences), Hiroyuki Konno(RIKEN Center for Integrative Medical Sciences), T. Kasukawa(NTT (Japan)), Koichi Imotani(RIKEN Center for Integrative Medical Sciences), Y. Tomaru(University of Tsukuba), Norihito Hayatsu(RIKEN Center for Integrative Medical Sciences), Harukazu Suzuki(RIKEN Center for Integrative Medical Sciences), Yuki Hasegawa(RIKEN Center for Integrative Medical Sciences), Akira Shinagawa(RIKEN Center for Integrative Medical Sciences), H. Kiyosawa(RIKEN Center for Integrative Medical Sciences), Naoko Sakazume(RIKEN Center for Integrative Medical Sciences), Itaru Yamanaka(RIKEN Center for Integrative Medical Sciences), Shiro Fukuda(RIKEN Center for Integrative Medical Sciences), Masaaki Furuno(RIKEN Center for Integrative Medical Sciences), Jun Adachi(RIKEN Center for Integrative Medical Sciences), Akira Yasunishi(RIKEN Center for Integrative Medical Sciences), Tomoko Hirozane-Kishikawa(RIKEN Center for Integrative Medical Sciences), Katsunori Aizawa(RIKEN Center for Integrative Medical Sciences), Y. Okazaki(RIKEN Center for Integrative Medical Sciences), Toshiyuki Shiraki(RIKEN Center for Integrative Medical Sciences), J. Kawai(RIKEN), Kazuhiro Shibata(RIKEN), Masayoshi Itoh(RIKEN), Y. Okazaki(RIKEN Center for Integrative Medical Sciences), Piero Carninci(RIKEN), Y. Hayashizaki(University of Tsukuba), T. Kasukawa (NTT (Japan)), H. Kawaji(NTT (Japan)), H. Kiyosawa(RIKEN Center for Integrative Medical Sciences), Yuki Hasegawa(RIKEN Center for Integrative Medical Sciences), I. Nikaido(RIKEN Center for Integrative Medical Sciences), A. Nogami (RIKEN Center for Integrative Medical Sciences), Y. Hayashizaki(University of Tsukuba), R. Saito(Yamagata University), Masaru Tomita(Yamagata University), Koji Numata(Yamagata University), Akio Kanai(Yamagata University), K Sato(University of Tsukuba), Y. Tomaru(University of Tsukuba), Yoshihide Hayashizaki(University of Tsukuba), Christian Schönbach(RIKEN Center for Integrative Medical Sciences), Akihiko Konagaya(RIKEN Center for Integrative Medical Sciences), Takeshi Nagashima(RIKEN Center for Integrative Medical Sciences), Igor V. Kurochkin(RIKEN Center for Integrative Medical Sciences), Toshihisa Okido(National Institute of Genetics), Takashi Gojobori(National Institute of Genetics), Judith A. Blake(Jackson Laboratory), Benjamin L. King(Jackson Laboratory), Martin Ringwald(Jackson Laboratory), Carol J. Bult(Jackson Laboratory), David P. Hill(Jackson Laboratory), Louise M. McKenzie(Jackson Laboratory), Qi Dong(Jackson Laboratory), Sridhar Ramachandran(Jackson Laboratory), Dirck Bradt(Jackson Laboratory), Lois J. Maltais(Jackson Laboratory), K. S. Frazer(University of Oregon), Richard M. Baldarelli(Jackson Laboratory), Deborah J. Reed(Jackson Laboratory), Lori E Corbani(Jackson Laboratory), Sharon Cousins(Jackson Laboratory), Linsen Yang(Jackson Laboratory), Y. Zhu(Jackson Laboratory), Zheng Yuan(The University of Queensland), David Hume(The University of Queensland), Rohan D. Teasdale(The University of Queensland), Sean M. Grimmond(The University of Queensland), Alistair R. R. Forrest(The University of Queensland), Christine A. Wells(The University of Queensland), Timothy Ravasi(The University of Queensland), Geo Pertea(Human Genome Sciences (United States)), Yan Wang(Human Genome Sciences (United States)), Răzvan Sultana(Human Genome Sciences (United States)), John Quackenbush(Human Genome Sciences (United States)), Yong Suk Lee(Human Genome Sciences (United States)), Ines Yang(Human Genome Sciences (United States)), Lukas Wagner(National Center for Biotechnology Information), Donna Maglott(National Center for Biotechnology Information), Joan Pontius(National Center for Biotechnology Information), Lynn M. Schriml(National Center for Biotechnology Information), Alexander Kanapin(European Bioinformatics Institute), Ewan Birney(European Bioinformatics Institute), Hideo Matsuda(The University of Osaka), Yasuhiro Takenaka(The University of Osaka), H. Kawaji (NTT (Japan)), C. F. Fletcher(Scripps Research Institute), Serge Batalov(Genomics Institute of the Novartis Research Foundation), Kirk W. Beisel(Boys Town National Research Hospital), Rekha Sukamar Pillai(Institute for Infocomm Research), Vladimir Brusić(Institute for Infocomm Research), C. Chothia(MRC Laboratory of Molecular Biology), Julian Gough(MRC Laboratory of Molecular Biology), Emiliano Dalla(AREA Science Park), C. Schneider(AREA Science Park), Roberto Verardo(AREA Science Park), James F. Reid(AREA Science Park), Luigi Marchionni(AREA Science Park), Tommaso A. Dragani(Fondazione IRCCS Istituto Nazionale dei Tumori), Manuela Gariboldi(Fondazione IRCCS Istituto Nazionale dei Tumori), C. F. Fletcher(Scripps Research Institute), K. S. Frazer(University of Oregon), Terry Gaasterland(Rockefeller University), Mihaela Zavolan(Rockefeller University), Graziano Pesole(University of Milan), Carmela Gissi(University of Milan), James Reed(Sanford Burnham Prebys Medical Discovery Institute), Adam Godzik(Sanford Burnham Prebys Medical Discovery Institute), Stefano Gustincich(Harvard University), Nobutaka Hirokawa(The University of Tokyo), Mitsutoshi Setou(The University of Tokyo), Hiromi Miki(The University of Tokyo), Colin A. Semple(Institute of Genetics and Cancer), Martin S. Taylor(Institute of Genetics and Cancer), Ian J. Jackson(Institute of Genetics and Cancer), Erich D. Jarvis(Duke University), Yuka Imamura Kawasawa(Howard Hughes Medical Institute), Rafal M. Kedzierski(Howard Hughes Medical Institute), Masashi Yanagisawa(Howard Hughes Medical Institute), Albin Sandelin(Karolinska Institutet), Boris Lenhard(Karolinska Institutet), Claes Wahlestedt(Karolinska Institutet), Paul Lyons(Juvenile Diabetes Research Foundation), William J. Pavan(National Human Genome Research Institute), Nikolai Petrovsky(Canberra Hospital), Brian Z. Ring(ID Genomics (United States)), K. Shimada (Hyogo Medical University), Y. Watanabe(Hyogo Medical University), K. Shimada (Hyogo Medical University), Y. Watanabe(Hyogo Medical University), Laurens Wilming(Wellcome Sanger Institute), Jane Rogers(Wellcome Sanger Institute), Anthony Wynshaw‐Boris(University of California San Diego), Andreas Zimmer(University of Bonn), R Waterston(Washington University in St. Louis), Eric S. Lander(Whitehead Institute for Biomedical Research)
Cited by 1,645Open Access
Abstract
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
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