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

Authors: Okazaki, Y  Furuno, M  Kasukawa, T  Adachi, J  Bono, H  Kondo, S  Nikaido, I  Osato, N  Saito, R  Suzuki, H  Yamanaka, I  Kiyosawa, H  Yagi, K  Tomaru, Y  Hasegawa, Y  Nogami, A  Schönbach, C  Gojobori, T  Baldarelli, R  Hill, D P  Bult, C  Hume, D A  Quackenbush, J  Schriml, L M  Kanapin, A  Matsuda, H  Batalov, S  Beisel, K W  Blake, J A  Bradt, D  Brusic, V  Chothia, C  Corbani, L E  Cousins, S  Dalla, E  Dragani, T A  Fletcher, C F  Forrest, A  Frazer, K S  Gaasterland, T  Gariboldi, M  Gissi, C  Godzik, A  Gough, J  Grimmond, S  Gustincich, S  Hirokawa, N  Jackson, I J  Jarvis, E D  Kanai, A  Kawaji, H  Kawasawa, Y  Kedzierski, R M  King, B L  Konagaya, A  Kurochkin, I V  Lee, Y  Lenhard, B  Lyons, P A  Maglott, D R  Maltais, L  Marchionni, L  McKenzie, L  Miki, H  Nagashima, T  Numata, K  Okido, T  Pavan, W J  Pertea, G  Pesole, G  Petrovsky, N  Pillai, R  Pontius, J U  Qi, D  Ramachandran, S  Ravasi, T  Reed, J C  Reed, D J  Reid, J  Ring, B Z  Ringwald, M  Sandelin, A  Schneider, C  Semple, C A M  Setou, M  Shimada, K  Sultana, R  Takenaka, Y  Taylor, M S  Teasdale, R D  Tomita, M  Verardo, R  Wagner, L  Wahlestedt, C  Wang, Y  Watanabe, Y  Wells, C  Wilming, L G  Wynshaw-Boris, A  Yanagisawa, M  Yang, I  Yang, L  Yuan, Z  Zavolan, M  Zhu, Y  Zimmer, A  Carninci, P  Hayatsu, N  Hirozane-Kishikawa, T  Konno, H  Nakamura, M  Sakazume, N  Sato, K  Shiraki, T  Waki, K  Kawai, J  Aizawa, K  Arakawa, T  Fukuda, S  Hara, A  Hashizume, W  Imotani, K  Ishii, Y  Itoh, M  Kagawa, I  Miyazaki, A  Sakai, K  Sasaki, D  Shibata, K  Shinagawa, A  Yasunishi, A  Yoshino, M  Waterston, R  Lander, E S  Rogers, J  Birney, E  Hayashizaki, Y  FANTOM Consortium,   RIKEN Genome Exploration Research Group Phase I & II Team,  
Citation: Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
Pubmed: (View Article at PubMed) PMID:12466851
DOI: Full-text: DOI:10.1038/nature01266

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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