The rice annotation project database (RAP-DB): 2008 update

Tsuyoshi Tanaka; Baltazar A. Antonio; Shoshi Kikuchi; Takashi Matsumoto; Yoshiaki Nagamura; Hisataka Numa; Hiroaki Sakai; Jianzhong Wu; Takeshi Itoh; Takuji Sasaki; Ryo Aono; Yasuyuki Fujii; Takuya Habara; Erimi Harada; Masako Kanno; Yoshihiro Kawahara; Hiroaki Kawashima; Hiromi Kubooka; Akihiro Matsuya; Hajime Nakaoka; Naomi Saichi; Ryoko Sanbonmatsu; Yoshiharu Sato; Yuji Shinso; Mami Suzuki; Jun-Ichi Takeda; Motohiko Tanino; Fusano Todokoro; Kaori Yamaguchi; Naoyuki Yamamoto; Chisato Yamasaki; Tadashi Imanishi; Toshihisa Okido; Masahito Tada; Kazuho Ikeo; Yoshio Tateno; Takashi Gojobori; Yao-Cheng Lin; Fu-Jin Wei; Yue-Ie Hsing; Qiang Zhao; Bin Han; Melissa R. Kramer; Richard W. McCombie; David Lonsdale; Claire C. O'Donovan; Eleanor J. Whitfield; Rolf Apweiler; Kanako O. Koyanagi; Jitendra P. Khurana; Saurabh Raghuvanshi; Nagendra K. Singh; Akhilesh K. Tyagi; Georg Haberer; Masaki Fujisawa; Satomi Hosokawa; Yukiyo Ito; Hiroshi Ikawa; Michie Shibata; Mayu Yamamoto; Richard M. Bruskiewich; Douglas R. Hoen; Thomas E. Bureau; Nobukazu Namiki; Hajime Ohyanagi; Yasumichi Sakai; Satoshi Nobushima; Katsumi Sakata; Roberto A. Barrero; Yutaka Sato; Alexandre Souvorov; Brian Smith-White; Tatiana Tatusova; Suyoung An; Gynheung An; Satoshi OOta; Galina Fuks; Joachim Messing; Karen R. Christie; Damien Lieberherr; HyeRan Kim; Andrea Zuccolo; Rod A. Wing; Kan Nobuta; Pamela J. Green; Cheng Lu; Blake C. Meyers; Cristian Chaparro; Benoit Piegu; Olivier Panaud; Manuel Echeverria; Rice Annotation Project

doi:10.1093/nar/gkm978

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The rice annotation project database (RAP-DB): 2008 update

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The rice annotation project database (RAP-DB): 2008 update

Tsuyoshi Tanaka, Baltazar A. Antonio, Shoshi Kikuchi, Takashi Matsumoto, Yoshiaki Nagamura, Hisataka Numa, Hiroaki Sakai, Jianzhong Wu, Takeshi Itoh, Takuji Sasaki, …

Nucleic acids research, Vol.36(suppl-1), pp.D1028-D1033

01/01/2008

DOI: https://doi.org/10.1093/nar/gkm978

PMCID: PMC2238920

PMID: 18089549

Abstract

Biochemistry & Molecular Biology

Life Sciences & Biomedicine

Science & Technology

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information.TheRAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

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Title: The rice annotation project database (RAP-DB): 2008 update
Creators - without role: Tsuyoshi Tanaka - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Baltazar A. Antonio - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Shoshi Kikuchi - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Takashi Matsumoto - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Yoshiaki Nagamura - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Hisataka Numa - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Hiroaki Sakai - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Jianzhong Wu - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Takeshi Itoh - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Takuji Sasaki - Natl Inst Agrobiol Sci, Tsukuba 3058602, Japan
Ryo Aono - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Yasuyuki Fujii - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Takuya Habara - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Erimi Harada - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Masako Kanno - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Yoshihiro Kawahara - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Hiroaki Kawashima - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Hiromi Kubooka - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Akihiro Matsuya - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Hajime Nakaoka - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Naomi Saichi - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Ryoko Sanbonmatsu - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Yoshiharu Sato - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Yuji Shinso - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Mami Suzuki - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Jun-Ichi Takeda - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Motohiko Tanino - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Fusano Todokoro - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Kaori Yamaguchi - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Naoyuki Yamamoto - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Chisato Yamasaki - Japan Biol Informat Consortium, Tokyo 1350064, Japan
Tadashi Imanishi - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Nagoya, Aichi, Japan
Toshihisa Okido - Bank of Japan
Masahito Tada - Bank of Japan
Kazuho Ikeo - Bank of Japan
Yoshio Tateno - Bank of Japan
Takashi Gojobori - Bank of Japan
Yao-Cheng Lin - Acad Sinica, Inst Bot, Taipei 11529, Taiwan
Fu-Jin Wei - Acad Sinica, Inst Bot, Taipei 11529, Taiwan
Yue-Ie Hsing
Qiang Zhao - Chinese Acad Sci, Shanghai Inst Biol Sci, Shanghai 200233, Peoples R China
Bin Han - Chinese Acad Sci, Shanghai Inst Biol Sci, Shanghai 200233, Peoples R China
Melissa R. Kramer - Cold Spring Harbor Lab, Cold Spring Harbor, NY 11723 USA
Richard W. McCombie - Cold Spring Harbor Lab, Cold Spring Harbor, NY 11723 USA
David Lonsdale - European Bioinformat Inst, Cambridge CB10 1SD, England
Claire C. O'Donovan - European Bioinformat Inst, Cambridge CB10 1SD, England
Eleanor J. Whitfield - European Bioinformat Inst, Cambridge CB10 1SD, England
Rolf Apweiler - European Bioinformat Inst, Cambridge CB10 1SD, England
Kanako O. Koyanagi - Hokkaido University
Jitendra P. Khurana - University of Delhi
Saurabh Raghuvanshi - University of Delhi
Nagendra K. Singh - Plant
Akhilesh K. Tyagi - University of Delhi
Georg Haberer - GSF Natl Res Ctr Environm & Hlth, MIPS, Inst Bioinformat, D-85764 Neuherberg, Germany
Masaki Fujisawa - Inst Soc Technoinnovat Agr Forestry & Fisheries, Tsukuba 3050854, Japan
Satomi Hosokawa - Inst Soc Technoinnovat Agr Forestry & Fisheries, Tsukuba 3050854, Japan
Yukiyo Ito - Inst Soc Technoinnovat Agr Forestry & Fisheries, Tsukuba 3050854, Japan
Hiroshi Ikawa - Inst Soc Technoinnovat Agr Forestry & Fisheries, Tsukuba 3050854, Japan
Michie Shibata - Inst Soc Technoinnovat Agr Forestry & Fisheries, Tsukuba 3050854, Japan
Mayu Yamamoto - Inst Soc Technoinnovat Agr Forestry & Fisheries, Tsukuba 3050854, Japan
Richard M. Bruskiewich - Rice Research Institute
Douglas R. Hoen - McGill University
Thomas E. Bureau - McGill University
Nobukazu Namiki - Mitsubishi Space Software
Hajime Ohyanagi - Mitsubishi Space Software
Yasumichi Sakai - Mitsubishi Space Software
Satoshi Nobushima - Mitsubishi Space Software
Katsumi Sakata - Mitsubishi Space Software
Roberto A. Barrero - Bank of Japan
Yutaka Sato - Nagoya University
Alexandre Souvorov - NIH, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA
Brian Smith-White - NIH, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA
Tatiana Tatusova - NIH, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA
Suyoung An - Pohang Univ Sci & Technol, Pohang 790784, South Korea
Gynheung An - Pohang Univ Sci & Technol, Pohang 790784, South Korea
Satoshi OOta - RIKEN
Galina Fuks - Rutgers State Univ, Waksman Inst Microbiol, Piscataway, NJ 08854 USA
Joachim Messing - Rutgers, The State University of New Jersey
Karen R. Christie - Stanford University
Damien Lieberherr - Swiss Inst Bioinformat, Swiss Port Grp, CH-1206 Geneva, Switzerland
HyeRan Kim - University of Arizona
Andrea Zuccolo - University of Arizona
Rod A. Wing - University of Arizona
Kan Nobuta - University of Delaware
Pamela J. Green - University of Delaware
Cheng Lu - University of Delaware
Blake C. Meyers - University of Delaware
Cristian Chaparro - University of Perpignan
Benoit Piegu - University of Perpignan
Olivier Panaud - University of Perpignan
Manuel Echeverria - University of Perpignan
Rice Annotation Project
Publication Details: Nucleic acids research, Vol.36(suppl-1), pp.D1028-D1033
Publisher: Oxford Univ Press
Number of pages: 6
Identifiers: 9943826508331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article