RGP physicalmap
2015/07/07Web Site: http://rgp.dna.affrc.go.jp/E/publicdata/physicalmap/physicalmap.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/rgp-physicalmap/
Physical mapping of rice YAC clones selected with the RGP DNA markers.
README Content
1. Database Component
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "RGP physicalmap" data. |
| File | README_e.html(English) |
2.2 YAC contig information
| Data name | YAC contig information |
| Description of data contents | YAC contigs on the rice chromosomes |
| File | rgp_physicalmap_yac_contigs.zip (1 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Chrom. No. | Chromosome number |
| Region | Region number |
| Physical map image | The file name of rice physical map |
| First marker | First DNA marker |
| Distance of first marker (cM) | Distance of the first marker from the top of each chromosome (cM) |
| Last marker | Last DNA marker |
| Distance of last marker (cM) | Distance of the last marker from the top of each chromosome (cM) |
2.3 YAC clone information
| Data name | YAC clone information |
| Description of data contents | YAC clones selected with DNA markers |
| File | rgp_physicalmap_yac_clones.zip (18.7 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Chrom. No. | Chromosome number |
| Region | Region number |
| Physical map image | The file name of rice physical map |
| Order | Linkage order |
| Marker | Marker name |
| Distance (cM) | The genetic distance from the previous marker (cM) |
| YAC clone1 | YAC clone 1 The YAC name followed by "c" shows that the YAC is a chimera. |
| YAC clone2 | YAC clone 2 |
| YAC clone3 | YAC clone 3 |
| YAC clone4 | YAC clone 4 |
| YAC clone5 | YAC clone 5 |
| YAC clone6 | YAC clone 6 |
| YAC clone7 | YAC clone 7 |
| YAC clone8 | YAC clone 8 |
| YAC clone9 | YAC clone 9 |
| YAC clone10 | YAC clone 10 |
| YAC clone11 | YAC clone 11 |
| YAC clone12 | YAC clone 12 |
| YAC clone13 | YAC clone 13 |
| YAC clone14 | YAC clone 14 |
| YAC clone15 | YAC clone 15 |
| YAC clone16 | YAC clone 16 |
| YAC clone17 | YAC clone 17 |
| YAC clone18 | YAC clone 18 |
| YAC clone19 | YAC clone 19 |
| YAC clone20 | YAC clone 20 |
| YAC clone21 | YAC clone 21 |
| YAC clone22 | YAC clone 22 |
| YAC clone23 | YAC clone 23 |
| YAC clone24 | YAC clone 24 |
| YAC clone25 | YAC clone 25 |
| YAC clone26 | YAC clone 26 |
| YAC clone27 | YAC clone 27 |
| YAC clone28 | YAC clone 28 |
| YAC clone29 | YAC clone 29 |
| YAC clone30 | YAC clone 30 |
2.4 Insert size of YAC clones
| Data name | Insert size of YAC clones |
| Description of data contents | Insert size of YAC clones in the physical map |
| File | rgp_physicalmap_insert_size.zip (3.4 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| YAC No. | YAC clone number |
| YAC insert size (kb) | Insert size of each YAC clone (kb) |
3. License
Last updated : 2015/07/07
You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "Rice Genome Mapping and Sequencing Data from RGP, STAFF/NIAR, Japan © National Institute of Agrobiological Sciences licensed under CC Attribution-Share Alike 2.1 Japan".
The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.
With regard to this database, you are licensed to:
- freely access part or whole of this database, and acquire data;
- freely redistribute part or whole of the data from this database; and
- freely create and distribute database and other derivative works based on part or whole of the data from this database,
under the license, as long as you comply with the following conditions:
- You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
- You must distribute any derivative work based on part or whole of the data from this database under the license.
- You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
Takashi Matsumoto
E-mail: mat[at]affrc[dot]go[dot]jp
Yuichi Katayose
E-mail: katayose[at]affrc[dot]go[dot]jp
4. Update History
| Date | Update contents |
|---|---|
| 2015/07/07 | RGP physicalmap English archive site is opened. |
| 2013/04/01 | The URL of RGP physicalmap is changed to "http://rgp.dna.affrc.go.jp/E/publicdata/physicalmap/physicalmap.html". |
| 1997/07/09 | RGP physicalmap (http://rgp.dna.affrc.go.jp/publicdata/physicalmap/physicalmap.html) is opened. |
5. Literature
Yosuke Umehara, Akiko Inagaki, Hiroshi Tanoue, Yuji Yasukochi, Yoshiaki Nagamura, Shoko Saji, Yoshiaki Otsuki, Tatsuhito Fujimura, Nori Kurata, Yuzo MinobeConstruction and characterization of a rice YAC library for physical mapping
Molecular Breeding (1995) 1(1): 79-89.
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,
A 300 kilobase interval genetic map of rice including 883 expressed sequences
Nature Genetics (1994) 8: 365-372.
PMID:7894488
Zi-Xuan Wang, Atsuko Idonuma, Yosuke Umehara, Wim Van Houten, Ikuo Ashikawa, Yuzo Minobe, Nori Kurata and Takuji Sasaki
Physical Mapping of Rice Chromosome 1 with Yeast Artificial Chromosomes (YACs)
DNA Research (1996) 3(5): 291-296.
PMID:9039498
Yosuke Umehara, Nori Kurata, Ikuo Ashikawa and Takuji Sasaki
Yeast Artificial Chromosome Clones of Rice Chromosome 2 Ordered Using DNA Markers
DNA Research (1997) 4(2): 127-131.
PMID:9205839
Hiroshi Tanoue, Takanori Shimokawa, Jianzhong Wu, Norio Sue, Yosuke Umehara, Ikuo Ashikawa, Nori Kurata and Takuji Sasaki
Ordered YAC Clone Contigs Assigned to Rice Chromosomes 3 and 11
DNA Research (1997) 4(2): 133-140.
PMID:9205840
Kazuhiro Koike, Katsuhiko Yoshino, Norio Sue, Yosuke Umehara, Ikuo Ashikawa, Nori Kurata and Takuji Sasaki
Physical Mapping of Rice Chromosomes 4 and 7 Using YAC Clones
DNA Research (1997) 4(1): 27-33.
PMID:9179493
Shoko Saji, Yosuke Umehara, Nori Kurata, Ikuo Ashikawa and Takuji Sasaki
Construction of YAC Contigs on Rice Chromosome 5
DNA Research (1996) 3(5): 297-302.
PMID:9039499
Y Umehara, H Tanoue, N Kurata, I Ashikawa, Y Minobe, and T Sasaki
An ordered yeast artificial chromosome library covering over half of rice chromosome 6
Genome Research (1996) 6(10): 935-942.
PMID:8908512
Baltazar A. Antonio, Makiko Emoto, Jianzhong Wu, Ikuo Ashikawa, Yosuke Umehara, Nori Kurata and Takuji Sasaki
Physical mapping of rice chromosomes 8 and 9 with YAC clones
DNA Research (1996) 3(6): 393-400.
PMID:9097041
Takanori Shimokawa, Nori Kurata, Jianzhong Wu, Yosuke Umehara, Ikuo Ashikawa and Takuji Sasaki
Assignment of YAC Clones Spanning Rice Chromosomes 10 and 12
DNA Research (1996) 3(6): 401-406.
PMID:9097042
6. Contact address
When you have any question about "RGP physicalmap", contact the following:2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
National Institute of Agrobiological Sciences
Takashi Matsumoto
E-mail: mat[at]affrc[dot]go[dot]jp
Yuichi Katayose
E-mail: katayose[at]affrc[dot]go[dot]jp