RGP caps

2015/05/12

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

The database of EST sites that were used to create the YAC-based rice transcript 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. Information of the markers in each chromosome
  3. Images of gel electrophoresis
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "RGP caps" data.
File README_e.html(English)
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2.2 Information of the markers in each chromosome

Data name Information of the markers in each chromosome
Description of data contents Information of the STS and CAPS markers in each chromosome.
File rgp_caps_main.zip (18.5 KB)

Data items are the following:
Data itemDescription
Chrom. No. Chromosome number
Position in a YAC physical map (cM) Position in a YAC physical map (genetic distance, cM)
Marker name Marker name
Type of marker Type of marker.
Polymorphism between Nipponbare and Kasalath were revealed by STS, CAPS, or dCAPS.
NP indicates that no polymorphism was detected between Nipponbare and Kasalath.
Enzyme Restriction enzymes used for CAPS and dCAPS to detect polymorphism between Nipponbare and Kasalath. No digestion is needed for STS markers.
Amplified band size (bp) Amplified band size in Nipponbare (bp)
5' primer sequence 5' primer sequence
3' primer sequence 3' primer sequence
Mapping population Mapping population
Position Chromosomal location of each marker is shown by either the RFLP marker co-segregated or the interval of flanking RFLP markers on the previously reported linkage map (Harushima et al. 1998 Genetices 148: 479-494, Lin et al.1998 Theor Appl Genet 96: 997-1003).
Comment Comment
Image file name 1 Image file name 1 of gel electrophoresis
Image file name 2 Image file name 2 of gel electrophoresis
Image file name 3 Image file name 3 of gel electrophoresis
Image file name 4 Image file name 4 of gel electrophoresis
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2.3 Images of gel electrophoresis

Data name Images of gel electrophoresis
Description of data contents Detailed information and images of gel electrophoresis of each marker.
File rgp_caps_electrophoresis_image.zip (28.7 MB)

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3. License

Last updated : 2015/05/12

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: 332 PCR-based genetic markers on rice chromosomes © 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
2015/05/12 RGP caps English archive site is opened.
2013/04/01 The URL of RGP caps is changed to "http://rgp.dna.affrc.go.jp/E/publicdata/caps/index.html".
2002/02/10 RGP caps (http://rgp.dna.affrc.go.jp/publicdata/caps/index.html) is opened.
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5. Literature

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6. Contact address

When you have any question about "RGP caps", 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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