Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Nature

Authors	Y Okazaki M Furuno T Kasukawa J Adachi H Bono S Kondo I Nikaido N Osato R Saito Suzuki I Yamanaka H Kiyosawa K Yagi Y Tomaru Y Hasegawa A Nogami C Schönbach T Gojobori R Baldarelli D Hill C Bult D Hume Quackenbush L Schriml A Kanapin H Matsuda S Batalov K Beisel J Blake D Bradt Brusic C Chothia L Corbani S Cousins E Dalla T Dragani C Fletcher A Forrest K Frazer T Gaasterland M Gariboldi C Gissi A Godzik J Gough S Grimmond S Gustincich N Hirokawa I Jackson E Jarvis A Kanai H Kawaji Y Kawasawa R Kedzierski B King A Konagaya I Kurochkin Lee B Lenhard P Lyons D Maglott L Maltais Marchionni L McKenzie H Miki T Nagashima K Numata T Okido W Pavan Pertea Pesole N Petrovsky R Pillai J Pontius D Qi S Ramachandran T Ravasi J Reed D Reed Reid B Ring M Ringwald Sandelin C Schneider C Semple M Setou Shimada R Sultana Y Takenaka M Taylor R Teasdale M Tomita R Verardo L Wagner C Wahlestedt Wang Watanabe C Wells L Wilming A Wynshaw-Boris M Yanagisawa I Yang Yang Z Yuan M Zavolan Zhu Zimmer Carninci N Hayatsu Hirozane-Kishikawa H Konno M Nakamura N Sakazume Sato Shiraki K Waki Kawai K Aizawa T Arakawa S Fukuda A Hara W Hashizume K Imotani Y Ishii M Itoh I Kagawa A Miyazaki K Sakai D Sasaki K Shibata A Shinagawa A Yasunishi M Yoshino R Waterston E Lander Rogers Birney Hayashizaki FANTOM Consortium RIKEN Genome Exploration Research Group Phase I & II Team
Keywords	Animals Humans Mice Genes Genomics Expressed Sequence Tags Protein Structure, Tertiary Transcription, Genetic Membrane Proteins Physical Chromosome Mapping Proteome DNA, Complementary RNA, Messenger Transcription Initiation Site Cloning, Molecular Databases, Genetic Amino Acid Motifs Alternative Splicing Chromosomes, Mammalian RNA, Untranslated RNA, Antisense
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.
Year of Publication	2002
Journal	Nature
Volume	420
Issue	6915
Pages	563-73
Date Published	2002 Dec 5
ISSN	0028-0836
DOI	10.1038/nature01266
PubMed ID	12466851
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