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. 2002 Dec 5;420(6915):563-73.
doi: 10.1038/nature01266.

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

Y Okazaki  1 , M Furuno, T Kasukawa, J Adachi, H Bono, S Kondo, I Nikaido, N Osato, R Saito, H Suzuki, I Yamanaka, H Kiyosawa, K Yagi, Y Tomaru, Y Hasegawa, A Nogami, C Schönbach, T Gojobori, R Baldarelli, D P Hill, C Bult, D A Hume, J Quackenbush, L M Schriml, A Kanapin, H Matsuda, S Batalov, K W Beisel, J A Blake, D Bradt, V Brusic, C Chothia, L E Corbani, S Cousins, E Dalla, T A Dragani, C F Fletcher, A Forrest, K S Frazer, T Gaasterland, M Gariboldi, C Gissi, A Godzik, J Gough, S Grimmond, S Gustincich, N Hirokawa, I J Jackson, E D Jarvis, A Kanai, H Kawaji, Y Kawasawa, R M Kedzierski, B L King, A Konagaya, I V Kurochkin, Y Lee, B Lenhard, P A Lyons, D R Maglott, L Maltais, L Marchionni, L McKenzie, H Miki, T Nagashima, K Numata, T Okido, W J Pavan, G Pertea, G Pesole, N Petrovsky, R Pillai, J U Pontius, D Qi, S Ramachandran, T Ravasi, J C Reed, D J Reed, J Reid, B Z Ring, M Ringwald, A Sandelin, C Schneider, C A M Semple, M Setou, K Shimada, R Sultana, Y Takenaka, M S Taylor, R D Teasdale, M Tomita, R Verardo, L Wagner, C Wahlestedt, Y Wang, Y Watanabe, C Wells, L G Wilming, A Wynshaw-Boris, M Yanagisawa, I Yang, L Yang, Z Yuan, M Zavolan, Y Zhu, A Zimmer, P Carninci, N Hayatsu, T Hirozane-Kishikawa, H Konno, M Nakamura, N Sakazume, K Sato, T Shiraki, K Waki, J 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 S Lander, J Rogers, E Birney, Y Hayashizaki; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team
Affiliations

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

Y Okazaki et al. Nature. .

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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