The Rice Annotation Project Database (RAP-DB): 2008 update

T. Tanaka; B.A. Antonio; S. Kikuchi; T. Matsumoto; Y. Nagamura; H. Numa; H. Sakai; J. Wu; T. Itoh; T. Sasaki; R. Aono; Y. Fujii; T. Habara; E. Harada; M. Kanno; Y. Kawahara; H. Kawashima; H. Kubooka; A. Matsuya; H. Nakaoka; N. Saichi; R. Sanbonmatsu; Y. Sato; Y. Shinso; M. Suzuki; J.-i. Takeda; M. Tanino; F. Todokoro; K. Yamaguchi; N. Yamamoto; C. Yamasaki; T. Imanishi; T. Okido; M. Tada; K. Ikeo; Y. Tateno; T. Gojobori; Y-C Lin; F-J Wei; Y-i Hsing; Q. Zhao; H. Bin; M.R. Kramer; R.W. McCombie; D. Lonsdale; C.C. O’Donovan; E.J. Whitfield; R. Apweiler; K.O. Koyanagi; J.P. Khurana; S. Raghuvanshi; N.K. Singh; A.K. Tyagi; G. Haberer; M. Fujisawa; S. Hosokawa; Y. Ito; H. Ikawa; M. Shibata; M. Yamamoto; R.M. Bruskiewich; D.R. Hoen; T.E. Bureau; N. Namiki; H. Ohyanagi; Y. Sakai; S. Nobushima; K. Sakata; R.A. Barrero; A. Souvorov; B. Smith-White; T. Tatusova; S. An; G. An; S. OOta; G. Fuks; J. Messing; K.R. Christie; D. Lieberherr; H-R Kim; A. Zuccolo; R.A. Wing; K. Nobuta; P.J. Green; C. Lu; B.C. Meyers; C. Chaparro; B. Piegu; O. Panaud; M. Echeverria

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

T. Tanaka, B.A. Antonio, S. Kikuchi, T. Matsumoto, Y. Nagamura, H. Numa, H. Sakai, J. Wu, T. Itoh, T. Sasaki, …

Nucleic Acids Research, Vol.36(Supp 1), pp.D1028-D1033

2008

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

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Abstract

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. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

Details

Title: The Rice Annotation Project Database (RAP-DB): 2008 update
Authors/Creators: T. Tanaka (Author/Creator) - University of Tsukuba
B.A. Antonio (Author/Creator) - University of Tsukuba
S. Kikuchi (Author/Creator) - University of Tsukuba
T. Matsumoto (Author/Creator) - University of Tsukuba
Y. Nagamura (Author/Creator) - University of Tsukuba
H. Numa (Author/Creator) - University of Tsukuba
H. Sakai (Author/Creator) - University of Tsukuba
J. Wu (Author/Creator) - University of Tsukuba
T. Itoh (Author/Creator) - National Institute of Advanced Industrial Science and Technology
T. Sasaki (Author/Creator) - University of Tsukuba
R. Aono (Author/Creator)
Y. Fujii (Author/Creator) - Okayama University
T. Habara (Author/Creator)
E. Harada (Author/Creator)
M. Kanno (Author/Creator)
Y. Kawahara (Author/Creator) - Tokyo Metropolitan University
H. Kawashima (Author/Creator)
H. Kubooka (Author/Creator)
A. Matsuya (Author/Creator)
H. Nakaoka (Author/Creator)
N. Saichi (Author/Creator)
R. Sanbonmatsu (Author/Creator)
Y. Sato (Author/Creator) - Nagoya University
Y. Shinso (Author/Creator)
M. Suzuki (Author/Creator)
J.-i. Takeda (Author/Creator)
M. Tanino (Author/Creator)
F. Todokoro (Author/Creator)
K. Yamaguchi (Author/Creator)
N. Yamamoto (Author/Creator)
C. Yamasaki (Author/Creator)
T. Imanishi (Author/Creator) - National Institute of Advanced Industrial Science and Technology
T. Okido (Author/Creator)
M. Tada (Author/Creator)
K. Ikeo (Author/Creator)
Y. Tateno (Author/Creator)
T. Gojobori (Author/Creator)
Y-C Lin (Author/Creator) - Academia Sinica
F-J Wei (Author/Creator) - Academia Sinica
Y-i Hsing (Author/Creator) - Academia Sinica
Q. Zhao (Author/Creator)
H. Bin (Author/Creator)
M.R. Kramer (Author/Creator) - Cold Spring Harbor Laboratory
R.W. McCombie (Author/Creator) - Cold Spring Harbor Laboratory
D. Lonsdale (Author/Creator) - Wellcome Trust
C.C. O’Donovan (Author/Creator)
E.J. Whitfield (Author/Creator) - Wellcome Trust
R. Apweiler (Author/Creator) - Wellcome Trust
K.O. Koyanagi (Author/Creator) - Hokkaido University
J.P. Khurana (Author/Creator) - University of Delhi
S. Raghuvanshi (Author/Creator) - University of Delhi
N.K. Singh (Author/Creator) - Indian Council of Agricultural Research
A.K. Tyagi (Author/Creator) - University of Delhi
G. Haberer (Author/Creator)
M. Fujisawa (Author/Creator)
S. Hosokawa (Author/Creator)
Y. Ito (Author/Creator)
H. Ikawa (Author/Creator)
M. Shibata (Author/Creator)
M. Yamamoto (Author/Creator)
R.M. Bruskiewich (Author/Creator) - International Rice Research Institute
D.R. Hoen (Author/Creator) - McGill University
T.E. Bureau (Author/Creator) - McGill University
N. Namiki (Author/Creator) - Mitsubishi Group (Japan)
H. Ohyanagi (Author/Creator) - Mitsubishi Group (Japan)
Y. Sakai (Author/Creator) - Mitsubishi Group (Japan)
S. Nobushima (Author/Creator) - Mitsubishi Group (Japan)
K. Sakata (Author/Creator) - Mitsubishi Group (Japan)
R.A. Barrero (Author/Creator) - Murdoch University
Y. Sato (Author/Creator) - Nagoya University
A. Souvorov (Author/Creator) - National Institutes of Health
B. Smith-White (Author/Creator) - National Institutes of Health
T. Tatusova (Author/Creator) - National Institutes of Health
S. An (Author/Creator) - Pohang University of Science and Technology
G. An (Author/Creator) - Pohang University of Science and Technology
S. OOta (Author/Creator)
G. Fuks (Author/Creator) - Rutgers, The State University of New Jersey
J. Messing (Author/Creator)
K.R. Christie (Author/Creator) - Stanford University
D. Lieberherr (Author/Creator) - SIB Swiss Institute of Bioinformatics
H-R Kim (Author/Creator) - University of Arizona
A. Zuccolo (Author/Creator) - University of Arizona
R.A. Wing (Author/Creator)
K. Nobuta (Author/Creator) - University of Delaware
P.J. Green (Author/Creator) - University of Delaware
C. Lu (Author/Creator) - University of Delaware
B.C. Meyers (Author/Creator) - University of Delaware
C. Chaparro (Author/Creator) - Université de Perpignan
B. Piegu (Author/Creator) - Université de Perpignan
O. Panaud (Author/Creator) - Université de Perpignan
M. Echeverria (Author/Creator) - Université de Perpignan
Publication Details: Nucleic Acids Research, Vol.36(Supp 1), pp.D1028-D1033
Publisher: Oxford University Press
Identifiers: 991005543066507891
Copyright: © The Author(s) 2007.
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article
Note: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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