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Life Science Database Archive
RGP physicalmap

Database Description

General information of database

info Database name RGP physicalmap
info Alternative name Rice Genome Mapping and Sequencing Data from RGP, STAFF/NIAR, Japan
info DOI 
info Creator 
Creator Name:
Yosuke Umehara
Creator Affiliation:
National Institute of Agrobiological Sciences
Creator Name:
Nori Kurata
Creator Affiliation:
National Institute of Agrobiological Sciences
Creator Name:
Takuji Sasaki*
Creator Affiliation:
National Institute of Agrobiological Sciences
info Contact address 

2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
Takashi Matsumoto
E-mail : rgp_physicalmap_address
Yuichi Katayose
E-mail : rgp_physicalmap_address2

info Database classification Plant databases - Rice
info Database classification Sequence
Physical map
info Organism 
Taxonomy Name:
Oryza sativa
Taxonomy ID:
info Database description 

This site contains a physical map information of rice using yeast artificial chromosome (YAC) clones selected with the Rice Genome Research Program (RGP) DNA markers from 1994 through 1997 version. A rice YAC library of RGP was constructed from cultured cells of Oryza sativa L. cv. Nipponbare and contains 6934 clones with 350 kb average insert length.

info Features and manner of utilization of database 

You can see the data files of yeast artificial chromosome (YAC) clones by figures and tables, which clones were selected with DNA markers in the Rice Genome Research Program (RGP) for each chromosome. In the tables, YAC clones selected with RGP DNA markers for each chromosome are shown along with the markers and the genetic distances. In the figures, the YAC physical maps of each divided region on the chromosomes are shown.
Because this archive has been created based on the following data of the last update date, it may not match the data in the current situation.

info License CC BY-SA Detail
info Background and funding 
Name:
Phase 1 of Rice Genome Research Project (1991-1997)
info Reference(s) 
Article title:
Construction and characterization of a rice YAC library for physical mapping
Author name(s):
Yosuke Umehara, Akiko Inagaki, Hiroshi Tanoue, Yuji Yasukochi, Yoshiaki Nagamura, Shoko Saji, Yoshiaki Otsuki, Tatsuhito Fujimura, Nori Kurata, Yuzo Minobe
Journal:
Molecular Breeding (1995) 1(1): 79-89.
External Links:
 
Article title:
A 300 kilobase interval genetic map of rice including 883 expressed sequences
Author name(s):
N. Kurata, Y. Nagamura, K. Yamamoto, Y. Harushima, N. Sue, J. Wu, B.A. Antonio, A. Shomura, T. Shimizu, S-Y. Lin, T. Inoue, A. Fukuda, T. Shimano, Y. Kuboki, T. Toyama, Y. Miyamoto, T. Kirihara, K. Hayasaka, A. Miyao, L. Monna, H.S. Zhong, Y. Tamura, Z-X, Wang, T. Momma, Y. Umehara, M. Yano, T. Sasaki and Y. Minobe
Journal:
Nature Genetics (1994) 8: 365-372.
External Links:
 
Article title:
Physical Mapping of Rice Chromosome 1 with Yeast Artificial Chromosomes (YACs)
Author name(s):
Zi-Xuan Wang, Atsuko Idonuma, Yosuke Umehara, Wim Van Houten, Ikuo Ashikawa, Yuzo Minobe, Nori Kurata and Takuji Sasaki
Journal:
DNA Research (1996) 3(5): 291-296.
External Links:
 
Article title:
Yeast Artificial Chromosome Clones of Rice Chromosome 2 Ordered Using DNA Markers
Author name(s):
Yosuke Umehara, Nori Kurata, Ikuo Ashikawa and Takuji Sasaki
Journal:
DNA Research (1997) 4(2): 127-131.
External Links:
 
Article title:
Ordered YAC Clone Contigs Assigned to Rice Chromosomes 3 and 11
Author name(s):
Hiroshi Tanoue, Takanori Shimokawa, Jianzhong Wu, Norio Sue, Yosuke Umehara, Ikuo Ashikawa, Nori Kurata and Takuji Sasaki
Journal:
DNA Research (1997) 4(2): 133-140.
External Links:
 
Article title:
Physical Mapping of Rice Chromosomes 4 and 7 Using YAC Clones
Author name(s):
Kazuhiro Koike, Katsuhiko Yoshino, Norio Sue, Yosuke Umehara, Ikuo Ashikawa, Nori Kurata and Takuji Sasaki
Journal:
DNA Research (1997) 4(1): 27-33.
External Links:
 
Article title:
Construction of YAC Contigs on Rice Chromosome 5
Author name(s):
Shoko Saji, Yosuke Umehara, Nori Kurata, Ikuo Ashikawa and Takuji Sasaki
Journal:
DNA Research (1996) 3(5): 297-302.
External Links:
 
Article title:
An ordered yeast artificial chromosome library covering over half of rice chromosome 6
Author name(s):
Y Umehara, H Tanoue, N Kurata, I Ashikawa, Y Minobe, and T Sasaki
Journal:
Genome Research (1996) 6(10): 935-942.
External Links:
 
Article title:
Physical mapping of rice chromosomes 8 and 9 with YAC clones
Author name(s):
Baltazar A. Antonio, Makiko Emoto, Jianzhong Wu, Ikuo Ashikawa, Yosuke Umehara, Nori Kurata and Takuji Sasaki
Journal:
DNA Research (1996) 3(6): 393-400.
External Links:
 
Article title:
Assignment of YAC Clones Spanning Rice Chromosomes 10 and 12
Author name(s):
Takanori Shimokawa, Nori Kurata, Jianzhong Wu, Yosuke Umehara, Ikuo Ashikawa and Takuji Sasaki
Journal:
DNA Research (1996) 3(6): 401-406.
External Links:
 

Original website information

info Database maintenance site 

info URL of the original website (Suspended)http://rgp.dna.affrc.go.jp/E/publicdata/physicalmap/physicalmap.html
info Operation start date 1997/07/09
info Last update date 1998/08/24
info URL of the portal site 
info Whole data download -
info Referenced database 

DDBJ

info Entry list Available
info Query search Not available
info Web services Not available
info URL of Web services -
info Need for user registration Not available