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

Y. Okazaki; 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; Masashi 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

doi:10.1038/nature01266

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

Y. Okazaki, 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. HillC. 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, Masashi 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

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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.

Original language	English (US)
Pages (from-to)	563-573
Number of pages	11
Journal	Nature
Volume	420
Issue number	6915
DOIs	https://doi.org/10.1038/nature01266
State	Published - Dec 5 2002

ASJC Scopus subject areas

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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., ... Hayashizaki, Y. (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420(6915), 563-573. https://doi.org/10.1038/nature01266

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, DP, Bult, C, Hume, DA, Quackenbush, J, Schriml, LM, Kanapin, A, Matsuda, H, Batalov, S, Beisel, KW, Blake, JA, Bradt, D, Brusic, V, Chothia, C, Corbani, LE, Cousins, S, Dalla, E, Dragani, TA, Fletcher, CF, Forrest, A, Frazer, KS, Gaasterland, T, Gariboldi, M, Gissi, C, Godzik, A, Gough, J, Grimmond, S, Gustincich, S, Hirokawa, N, Jackson, IJ, Jarvis, ED, Kanai, A, Kawaji, H, Kawasawa, Y, Kedzierski, RM, King, BL, Konagaya, A, Kurochkin, IV, Lee, Y, Lenhard, B, Lyons, PA, Maglott, DR, Maltais, L, Marchionni, L, McKenzie, L, Miki, H, Nagashima, T, Numata, K, Okido, T, Pavan, WJ, Pertea, G, Pesole, G, Petrovsky, N, Pillai, R, Pontius, JU, Qi, D, Ramachandran, S, Ravasi, T, Reed, JC, Reed, DJ, Reid, J, Ring, BZ, Ringwald, M, Sandelin, A, Schneider, C, Semple, CAM, Setou, M, Shimada, K, Sultana, R, Takenaka, Y, Taylor, MS, Teasdale, RD, Tomita, M, Verardo, R, Wagner, L, Wahlestedt, C, Wang, Y, Watanabe, Y, Wells, C, Wilming, LG, 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, ES, Rogers, J, Birney, E & Hayashizaki, Y 2002, 'Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs', Nature, vol. 420, no. 6915, pp. 563-573. https://doi.org/10.1038/nature01266

@article{2809d51827b94384b027e8a54f90c17f,

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

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.",

author = "Y. Okazaki and M. Furuno and T. Kasukawa and J. Adachi and H. Bono and S. Kondo and I. Nikaido and N. Osato and R. Saito and H. Suzuki and I. Yamanaka and H. Kiyosawa and K. Yagi and Y. Tomaru and Y. Hasegawa and A. Nogami and C. Sch{\"o}nbach and T. Gojobori and R. Baldarelli and Hill, {D. P.} and C. Bult and Hume, {D. A.} and J. Quackenbush and Schriml, {L. M.} and A. Kanapin and H. Matsuda and S. Batalov and Beisel, {K. W.} and Blake, {J. A.} and D. Bradt and V. Brusic and C. Chothia and Corbani, {L. E.} and S. Cousins and E. Dalla and Dragani, {T. A.} and Fletcher, {C. F.} and A. Forrest and Frazer, {K. S.} and T. Gaasterland and M. Gariboldi and C. Gissi and A. Godzik and J. Gough and S. Grimmond and S. Gustincich and N. Hirokawa and Jackson, {I. J.} and Jarvis, {E. D.} and A. Kanai and H. Kawaji and Y. Kawasawa and Kedzierski, {R. M.} and King, {B. L.} and A. Konagaya and Kurochkin, {I. V.} and Y. Lee and B. Lenhard and Lyons, {P. A.} and Maglott, {D. R.} and L. Maltais and L. Marchionni and L. McKenzie and H. Miki and T. Nagashima and K. Numata and T. Okido and Pavan, {W. J.} and G. Pertea and G. Pesole and N. Petrovsky and R. Pillai and Pontius, {J. U.} and D. Qi and S. Ramachandran and T. Ravasi and Reed, {J. C.} and Reed, {D. J.} and J. Reid and Ring, {B. Z.} and M. Ringwald and A. Sandelin and C. Schneider and Semple, {C. A M} and M. Setou and K. Shimada and R. Sultana and Y. Takenaka and Taylor, {M. S.} and Teasdale, {R. D.} and M. Tomita and R. Verardo and L. Wagner and C. Wahlestedt and Y. Wang and Y. Watanabe and C. Wells and Wilming, {L. G.} and A. Wynshaw-Boris and Masashi Yanagisawa and I. Yang and L. Yang and Z. Yuan and M. Zavolan and Y. Zhu and A. Zimmer and P. Carninci and N. Hayatsu and T. Hirozane-Kishikawa and H. Konno and M. Nakamura and N. Sakazume and K. Sato and T. Shiraki and K. Waki and J. Kawai and K. Aizawa and T. Arakawa and S. Fukuda and A. Hara and W. Hashizume and K. Imotani and Y. Ishii and M. Itoh and I. Kagawa and A. Miyazaki and K. Sakai and D. Sasaki and K. Shibata and A. Shinagawa and A. Yasunishi and M. Yoshino and R. Waterston and Lander, {E. S.} and J. Rogers and E. Birney and Y. Hayashizaki",

note = "Funding Information: Acknowledgements We thank the following (listed in alphabetical order) for discussion, encouragement and technical assistance: K. Abe, T. Akimura, T. Hanagaki, K. Hayashida, K. Hiramoto, T. Hiraoka, M. Honda, F. Hori, T. Huber, M. Izawa, H. Kato, M. Kohda, Y. Kojima, S. Koya, K. Koyama, C. Kurihara, J. Mashima, T. Matsuyama, M. Murata, K. Nishi, K. Nomura, R. Numazaki, M. Ohno, H. Saitou, C. Sakai, H. Sano, Y. Shibata, A. J. G. Simpson, Y. Sogabe, M. Tagami, A. Tagawa, F. Takahashi, S. Takaku, Y. Takeda, T. Tanaka, A. Tomaru, W. W. Wasserman, A. Watahiki, C. Wicking, H. Yamanishi, T. Yao, K. Yoshida. We especially thank A. Wada, M. Muramatsu, T. Ogawa, A. Kira, and all the members of RIKEN Yokohama Research Promotion Division for supporting and encouraging the project. We also thank the Laboratory for Genome Exploration Research Group for secretarial and technical assistance. This work was mainly supported by a research grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of the Japanese Government to Y.H., and by a Research and Development for Applying Advanced Computational Science and Technology (ACT) grant from the Japan Science and Technology Corporation to Y.H. and J.K.",

year = "2002",

month = dec,

day = "5",

doi = "10.1038/nature01266",

language = "English (US)",

volume = "420",

pages = "563--573",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "6915",

}

TY - JOUR

T1 - Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

AU - Okazaki, Y.

AU - Furuno, M.

AU - Kasukawa, T.

AU - Adachi, J.

AU - Bono, H.

AU - Kondo, S.

AU - Nikaido, I.

AU - Osato, N.

AU - Saito, R.

AU - Suzuki, H.

AU - Yamanaka, I.

AU - Kiyosawa, H.

AU - Yagi, K.

AU - Tomaru, Y.

AU - Hasegawa, Y.

AU - Nogami, A.

AU - Schönbach, C.

AU - Gojobori, T.

AU - Baldarelli, R.

AU - Hill, D. P.

AU - Bult, C.

AU - Hume, D. A.

AU - Quackenbush, J.

AU - Schriml, L. M.

AU - Kanapin, A.

AU - Matsuda, H.

AU - Batalov, S.

AU - Beisel, K. W.

AU - Blake, J. A.

AU - Bradt, D.

AU - Brusic, V.

AU - Chothia, C.

AU - Corbani, L. E.

AU - Cousins, S.

AU - Dalla, E.

AU - Dragani, T. A.

AU - Fletcher, C. F.

AU - Forrest, A.

AU - Frazer, K. S.

AU - Gaasterland, T.

AU - Gariboldi, M.

AU - Gissi, C.

AU - Godzik, A.

AU - Gough, J.

AU - Grimmond, S.

AU - Gustincich, S.

AU - Hirokawa, N.

AU - Jackson, I. J.

AU - Jarvis, E. D.

AU - Kanai, A.

AU - Kawaji, H.

AU - Kawasawa, Y.

AU - Kedzierski, R. M.

AU - King, B. L.

AU - Konagaya, A.

AU - Kurochkin, I. V.

AU - Lee, Y.

AU - Lenhard, B.

AU - Lyons, P. A.

AU - Maglott, D. R.

AU - Maltais, L.

AU - Marchionni, L.

AU - McKenzie, L.

AU - Miki, H.

AU - Nagashima, T.

AU - Numata, K.

AU - Okido, T.

AU - Pavan, W. J.

AU - Pertea, G.

AU - Pesole, G.

AU - Petrovsky, N.

AU - Pillai, R.

AU - Pontius, J. U.

AU - Qi, D.

AU - Ramachandran, S.

AU - Ravasi, T.

AU - Reed, J. C.

AU - Reed, D. J.

AU - Reid, J.

AU - Ring, B. Z.

AU - Ringwald, M.

AU - Sandelin, A.

AU - Schneider, C.

AU - Semple, C. A M

AU - Setou, M.

AU - Shimada, K.

AU - Sultana, R.

AU - Takenaka, Y.

AU - Taylor, M. S.

AU - Teasdale, R. D.

AU - Tomita, M.

AU - Verardo, R.

AU - Wagner, L.

AU - Wahlestedt, C.

AU - Wang, Y.

AU - Watanabe, Y.

AU - Wells, C.

AU - Wilming, L. G.

AU - Wynshaw-Boris, A.

AU - Yanagisawa, Masashi

AU - Yang, I.

AU - Yang, L.

AU - Yuan, Z.

AU - Zavolan, M.

AU - Zhu, Y.

AU - Zimmer, A.

AU - Carninci, P.

AU - Hayatsu, N.

AU - Hirozane-Kishikawa, T.

AU - Konno, H.

AU - Nakamura, M.

AU - Sakazume, N.

AU - Sato, K.

AU - Shiraki, T.

AU - Waki, K.

AU - Kawai, J.

AU - Aizawa, K.

AU - Arakawa, T.

AU - Fukuda, S.

AU - Hara, A.

AU - Hashizume, W.

AU - Imotani, K.

AU - Ishii, Y.

AU - Itoh, M.

AU - Kagawa, I.

AU - Miyazaki, A.

AU - Sakai, K.

AU - Sasaki, D.

AU - Shibata, K.

AU - Shinagawa, A.

AU - Yasunishi, A.

AU - Yoshino, M.

AU - Waterston, R.

AU - Lander, E. S.

AU - Rogers, J.

AU - Birney, E.

AU - Hayashizaki, Y.

N1 - Funding Information: Acknowledgements We thank the following (listed in alphabetical order) for discussion, encouragement and technical assistance: K. Abe, T. Akimura, T. Hanagaki, K. Hayashida, K. Hiramoto, T. Hiraoka, M. Honda, F. Hori, T. Huber, M. Izawa, H. Kato, M. Kohda, Y. Kojima, S. Koya, K. Koyama, C. Kurihara, J. Mashima, T. Matsuyama, M. Murata, K. Nishi, K. Nomura, R. Numazaki, M. Ohno, H. Saitou, C. Sakai, H. Sano, Y. Shibata, A. J. G. Simpson, Y. Sogabe, M. Tagami, A. Tagawa, F. Takahashi, S. Takaku, Y. Takeda, T. Tanaka, A. Tomaru, W. W. Wasserman, A. Watahiki, C. Wicking, H. Yamanishi, T. Yao, K. Yoshida. We especially thank A. Wada, M. Muramatsu, T. Ogawa, A. Kira, and all the members of RIKEN Yokohama Research Promotion Division for supporting and encouraging the project. We also thank the Laboratory for Genome Exploration Research Group for secretarial and technical assistance. This work was mainly supported by a research grant for the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of the Japanese Government to Y.H., and by a Research and Development for Applying Advanced Computational Science and Technology (ACT) grant from the Japan Science and Technology Corporation to Y.H. and J.K.

PY - 2002/12/5

Y1 - 2002/12/5

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=0142104045&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0142104045&partnerID=8YFLogxK

U2 - 10.1038/nature01266

DO - 10.1038/nature01266

M3 - Article

C2 - 12466851

AN - SCOPUS:0142104045

SN - 0028-0836

VL - 420

SP - 563

EP - 573

JO - Nature

JF - Nature

IS - 6915

ER -

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

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