Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice

被引：684

作者：

Kikuchi, S

Satoh, K

Nagata, T

Kawagashira, N

Doi, K

Kishimoto, N

Yazaki, J

Ishikawa, M

Yamada, H

Ooka, H

Hotta, I

Kojima, K

Namiki, T

Ohneda, E

Yahagi, W

Suzuki, K

Li, CJ

Ohtsuki, K

Shishiki, T

Otomo, Y

Murakami, K

Iida, Y

Sugano, S

Fujimura, T

Suzuki, Y

Tsunoda, Y

Kurosaki, T

Kodama, T

Masuda, H

Kobayashi, M

Xie, QH

Lu, M

Narikawa, R

Sugiyama, A

Mizuno, K

Yokomizo, S

Niikura, J

Ikeda, R

Ishibiki, J

Kawamata, M

Yoshimura, A

Miura, J

Kusumegi, T

Oka, M

Ryu, R

Ueda, M

Matsubara, K

Kawai, J

Carninci, P

Adachi, J

机构：

[1] Natl Inst Agrobiol Sci, Dept Mol Biol, Tsukuba, Ibaraki 3058602, Japan

[2] Hitachi Software Engn Co, Naka Ku, Yokohama, Kanagawa 2310015, Japan

[3] FAIS, Lab Genome Sequencing, Tsukuba, Ibaraki 3050062, Japan

[4] Univ Tokyo, Inst Med Sci, Dept Virol, Minato Ku, Tokyo 1088639, Japan

[5] Univ Tsukuba, Inst Agr & Forest Engn, Tsukuba, Ibaraki 3058577, Japan

[6] NAIST, Nara 6300101, Japan

[7] RIKEN, RIKEN Yokohama Inst, Inst Phys & Chem Res, Lab Genome Explorat Res Grp,Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[8] Genome Sci Lab, Wako, Saitama 3510198, Japan

[9] FAIS, Anal Grp, Tsukuba, Ibaraki 3050062, Japan

来源：

SCIENCE | 2003年 / 301卷 / 5631期

关键词：

D O I：

10.1126/science.1081288

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. Protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis. Sixty-four percent of our cDNAs are homologous to Arabidopsis proteins.

引用

页码：376 / 379

页数：4

共 13 条

[1] The InterPro database, an integrated documentation resource for protein families, domains and functional sites
Apweiler, R
Attwood, TK
Bairoch, A
Bateman, A
Birney, E
Biswas, M
Bucher, P
Cerutti, T
Corpet, F
Croning, MDR
Durbin, R
Falquet, L
Fleischmann, W
Gouzy, J
Hermjakob, H
Hulo, N
Jonassen, I
Kahn, D
Kanapin, A
Karavidopoulou, Y
Lopez, R
Marx, B
Mulder, NJ
Oinn, TM
Pagni, M
Servant, F
Sigrist, CJA
Zdobnov, EM
[J]. NUCLEIC ACIDS RESEARCH, 2001, 29 (01) : 37 - 40
[2] Sequence and analysis of rice chromosome 4
Feng, Q
Zhang, YJ
Hao, P
Wang, SY
Fu, G
Huang, YC
Li, Y
Zhu, JJ
Liu, YL
Hu, X
Jia, PX
Zhang, Y
Zhao, Q
Ying, K
Yu, SL
Tang, YS
Weng, QJ
Zhang, L
Lu, Y
Mu, J
Lu, YQ
Zhang, LS
Yu, Z
Fan, DL
Liu, XH
Lu, TT
Li, C
Wu, YR
Sun, TG
Lei, HY
Li, T
Hu, H
Guan, JP
Wu, M
Zhang, RQ
Zhou, B
Chen, ZH
Chen, L
Jin, ZQ
Wang, R
Yin, HF
Cai, Z
Ren, SX
Lv, G
Gu, WY
Zhu, GF
Tu, YF
Jia, J
Zhang, Y
Chen, J
[J]. NATURE, 2002, 420 (6913) : 316 - 320
[3] A draft sequence of the rice genome (Oryza sativa L. ssp japonica)
Goff, SA
Ricke, D
Lan, TH
Presting, G
Wang, RL
Dunn, M
Glazebrook, J
Sessions, A
Oeller, P
Varma, H
Hadley, D
Hutchinson, D
Martin, C
Katagiri, F
Lange, BM
Moughamer, T
Xia, Y
Budworth, P
Zhong, JP
Miguel, T
Paszkowski, U
Zhang, SP
Colbert, M
Sun, WL
Chen, LL
Cooper, B
Park, S
Wood, TC
Mao, L
Quail, P
Wing, R
Dean, R
Yu, YS
Zharkikh, A
Shen, R
Sahasrabudhe, S
Thomas, A
Cannings, R
Gutin, A
Pruss, D
Reid, J
Tavtigian, S
Mitchell, J
Eldredge, G
Scholl, T
Miller, RM
Bhatnagar, S
Adey, N
Rubano, T
Tusneem, N
[J]. SCIENCE, 2002, 296 (5565) : 92 - 100
[4] Plant cis-acting regulatory DNA elements (PLACE) database: 1999
Higo, K
Ugawa, Y
Iwamoto, M
Korenaga, T
[J]. NUCLEIC ACIDS RESEARCH, 1999, 27 (01) : 297 - 300
[5] A MODEL RECOGNITION APPROACH TO THE PREDICTION OF ALL-HELICAL MEMBRANE-PROTEIN STRUCTURE AND TOPOLOGY
JONES, DT
TAYLOR, WR
THORTON, JM
[J]. BIOCHEMISTRY, 1994, 33 (10) : 3038 - 3049
[6] NAGATA T, COMMUNICATION
[7] PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization
Nakai, K
Horton, P
[J]. TRENDS IN BIOCHEMICAL SCIENCES, 1999, 24 (01) : 34 - 35
[8] Arabidopsis transcription factors:: Genome-wide comparative analysis among eukaryotes
Riechmann, JL
Heard, J
Martin, G
Reuber, L
Jiang, CZ
Keddie, J
Adam, L
Pineda, O
Ratcliffe, OJ
Samaha, RR
Creelman, R
Pilgrim, M
Broun, P
Zhang, JZ
Ghandehari, D
Sherman, BK
Yu, CL
[J]. SCIENCE, 2000, 290 (5499) : 2105 - 2110
[9] The genome sequence and structure of rice chromosome 1
Sasaki, T
Matsumoto, T
Yamamoto, K
Sakata, K
Baba, T
Katayose, Y
Wu, JZ
Niimura, Y
Cheng, ZK
Nagamura, Y
Antonio, BA
Kanamori, H
Hosokawa, S
Masukawa, M
Arikawa, K
Chiden, Y
Hayashi, M
Okamoto, M
Ando, T
Aoki, H
Arita, K
Hamada, M
Harada, C
Hijishita, S
Honda, M
Ichikawa, Y
Idonuma, A
Iijima, M
Ikeno, M
Ito, S
Ito, T
Ito, Y
Ito, Y
Iwabuchi, A
Kamiya, K
Karasawa, W
Katagiri, S
Kikuta, A
Kobayashi, N
Kono, I
Machita, K
Maehara, T
Mizuno, H
Mizubayashi, T
Mukai, Y
Nagasaki, H
Nakashima, M
Nakama, Y
Nakamichi, Y
Nakamura, M
[J]. NATURE, 2002, 420 (6913) : 312 - 316
[10] Functional annotation of a full-length Arabidopsis cDNA collection
Seki, M
Narusaka, M
Kamiya, A
Ishida, J
Satou, M
Sakurai, T
Nakajima, M
Enju, A
Akiyama, K
Oono, Y
Muramatsu, M
Hayashizaki, Y
Kawai, J
Carninci, P
Itoh, M
Ishii, Y
Arakawa, T
Shibata, K
Shinagawa, A
Shinozaki, K
[J]. SCIENCE, 2002, 296 (5565) : 141 - 145

← 1 2 →