RGP gmap2000

2015/03/10

Web Site: http://rgp.dna.affrc.go.jp/E/publicdata/geneticmap2000/index.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/rgp-gmap2000/

The database of RFLP markers that were used to create the year 2000 version of the high-density rice genetic map.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. High-density linkage map information
  3. Detailed information of DNA markers
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "RGP gmap2000" data.
File README_e.html(English)
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2.2 High-density linkage map information

Data name High-density linkage map information
Description of data contents Information of High-density linkage maps of rice RFLP (Restriction Fragment Length Polymorphism).
File rgp_gmap2000_main.zip (30.0 KB)

Data items are the following:
Data itemDescription
Chrom. No. Chromosome number
Floating marker Floating marker.
"F" in this column indicates that the segregation data of the locus did not show any recombination to the loci with the different positions.
If "F" is indicated in the column, the minimum position is shown in column "position" and the maximum position is shown in column "max".
Position The genetic distance of the locus from the short arm end.
If "F" is indicated in "Floating marker" column, the minimum position is shown in this column.
Max If "F" is indicated in "Floating marker" column, the maximum position is shown in this column.
Marker name Marker name: The "Marker name" corresponds to the "Real name" in "Detailed information of DNA markers".
Accession 5'_1 The DDBJ sequence accession number for 5' end of insert fragment that was used as a probe.
Accession 5'_2 If there are two accession numbers for 5' end, another number is shown in this column.
Accession 3' The DDBJ sequence accession number for 3' end
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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_gmap2000_marker.zip (46.7 KB)

Data items are the following:
Data itemDescription
Chrom. No. Chromosome number
Locus name Locus name
Real name If the polymorphism is detected at multiple locations, the locus name of marker that match the original sequence information is referred to as "Real name". The "Real name" corresponds to the "Marker name" in ""High-density linkage map information".
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
Primer sequence 1 Primer sequence 1 of marker
Primer sequence 2 Primer sequence 2 of marker
PCR protocol PCR protocol for markers
Image file name Parental Southern image file name
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3. License

Last updated : 2015/03/10

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.

Creative Commons License

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: The Latest High-Density Rice Genetic Map, Including 3267 Markers © 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:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. 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:

  1. 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.
  2. You must distribute any derivative work based on part or whole of the data from this database under the license.
  3. 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

DateUpdate contents
2015/03/10 RGP gmap2000 English archive site is opened.
2013/04/01 The URL of RGP gmap2000 is changed to "http://rgp.dna.affrc.go.jp/E/publicdata/geneticmap2000/index.html".
2000/11/30 RGP gmap2000 (http://rgp.dna.affrc.go.jp/publicdata/geneticmap2000/index.html) is opened.
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5. Literature

-
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6. Contact address

When you have any question about "RGP gmap2000", 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

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