RGP gmap

2014/10/31

Web Site: http://rgp.dna.affrc.go.jp/E/publicdata/naturegenetics/ricegmap.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/rgp-gmap/

The database of DNA markers that were used to create the rice genetic map.

README Content

Database Component
Data Description
License
Update History
Literature
Contact address

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2. Data Description

2.1 README

Data name	README
Description of data contents	HTML file to describe "RGP gmap" data.
File	README_e.html(English)

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2.2 Statistics of DNA Markers

Data name	Statistics of DNA Markers
Description of data contents	Statistics of DNA markers that were used to create the rice genetic map.
File	rgp_gmap_main.zip (1 KB)

Data items are the following:

Data item	Description
Chrom. No.	Number of chromosome (In Simple search site, the chromosome number link to the site of "Detailed information of DNA markers", and the image file name link to the map image.)
No. of callus cDNA clones	Number of callus cDNA clones
No. of root cDNA clones	Number of root cDNA clones
No. of random genomic clones	Number of random genomic clones
No. of NotI-linking clones	Number of NotI-linking clones
No. of YAC end clones	Number of YAC end clones
No. of telomere-associated clones	Number of telomere-associated clones
No. of RAPD markers	Number of RAPD markers
No. of STS markers	Number of STS markers
No. of wheat clones	Number of wheat clones
No. of other clones	Number of other clones
Total marker number	Total marker number
Total length in error detection off mode	Total length in Kosambi map function by error detection off mode of MAPMAKER/EXP
Total length in error detection on mode	Total length in Kosambi map function by error detection on mode of MAPMAKER/EXP
Difference between error detection on and off mode (cM)	Difference between error detection on and off mode (cM)
Difference between error detection on and off mode (%)	Difference between error detection on and off mode (%)
No. of candidate errors by MAPMAKER/EXP	Number of the candidate errors shown by MAPMAKER/EXP 3.0
Total number of observed genotypes	The total number of the observed genotypes to calculate the map
Average number of observed genotypes per marker	An avarege of the number of the observed genotypes per marker

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2.3 Detailed information of DNA markers

Data name	Detailed information of DNA markers
Description of data contents	Detailed information of DNA markers that were used to create the rice genetic map.
File	rgp_gmap_marker.zip (28.3 KB)

Data items are the following:

Data item	Description
Chrom. No.	Chromosome number
Two-point distance (cM)	The two-point distances to the previous markers (cM)
Position (cM)	Marker position in the chromosome (cM)
Locus name	Locus name
DDBJ accession No.	DDBJ accession number(s) of the marker sequence
Restriction enzyme	Names of restriction enzymes to detect the polymorphism between Nipponbare and Kasalath
Nipponbare band size (kb)	Southern band size of Nipponbare (kb)
Kasalath band size (kb)	Southern band size of Kasalath (kb)
Probe size (kb)	Probe size
Vector	Cloning vector
Cloning site	Cloning site
Special primers or restriction enzymes for NotI-linking clone	Special primer set or restriction enzyme set for the preparation of NotI-linking marker
RAPD primer sequence 1	RAPD marker primer sequence 1
RAPD primer sequence 2	RAPD marker primer sequence 2
PCR protocol for RAPD and STS markers	PCR protocol of RAPD and STS markers
Image file name	Southern image file name

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2.4 Southern images

Data name	Southern images
Description of data contents	Parents Southern hybridization image files.
File	rpg_gmap_southern_image.zip (37.3 MB)

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3. License

Last updated : 2014/10/31

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: "RGP : RICE GENETIC MAP IN NATURE GENETICS © 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

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4. Update History

Date	Update contents
2014/10/31	RGP gmap English archive site is opened.
2013/04/01	The URL of RGP gmap is changed to "http://rgp.dna.affrc.go.jp/E/publicdata/naturegenetics/ricegmap.html."
1994/08/08	RGP gmap (http://rgp.dna.affrc.go.jp/publicdata/naturegenetics/ricegmap.html) is opened.

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5. Literature

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, Y. Minobe
A 300 kilobase interval genetic map of rice including 883 expressed sequences.
Nature Genetics, 8: 365-372 (1994)
PMID: 7894488

6. Contact address

When you have any question about "RGP gmap", contact the following:

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