RGP estmap2001
2015/04/02Web Site: http://rgp.dna.affrc.go.jp/E/publicdata/estmap2001/index.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/rgp-estmap2001/
The database of EST sites that were used to create the YAC-based rice transcript map.
README Content
1. Database Component
- README
- Statistics information of rice EST mapping results
- Details of rice EST mapping results
- The rice transcript map
2. Data Description
2.1 README
| Data name | README |
| Description of data contents | HTML file to describe "RGP estmap2001" data. |
| File | README_e.html(English) |
2.2 Statistics information of rice EST mapping results
| Data name | Statistics information of rice EST mapping results |
| Description of data contents | Summary of Rice EST Mapping Results per each chromosome. The map is composed of 2782 YAC clones, containing 364 YAC contigs with 6591 assigned EST sites from 6421 unique sequences, and covers 80.8% of the rice genome. |
| File | rgp_estmap2001_main.zip (597 B) |
Data items are the following:
| Data item | Description |
|---|---|
| Chrom. No. | Chromosome number (UN: Chromosome unknown) |
| YAC Clones | Number of YAC clones |
| YAC Contigs | Number of YAC contigs |
| Total Length of YAC Contigs (Mb) | Total length of YAC contigs (Mb) |
| Coverage (%) | Coverage (%) = Total length (Mb) of YAC contigs / ( genetic length of chromosome (cM) x 430 (Mb) / 1530.4 (cM) ) x 100 |
| EST Sites | Number of EST sites |
| Ave EST Density (EST/100 kb) | Average EST density (EST/100 kb) = Number of ESTs / total length of YAC contigs |
| Contig Image File | Image file name of chromosomal distribution |
2.3 Details of rice EST mapping results
| Data name | Details of rice EST mapping results |
| Description of data contents | The data contains the detailed results of PCR-based YAC screening with the clone-specific EST primers. |
| File | rgp_estmap2001_detail.zip (242 KB) |
Data items are the following:
| Data item | Description |
|---|---|
| Anchor | Genetic markers used for YAC landing |
| Chrom. No. | Chromosome number |
| Position (cM) | Genetic distance (cM) |
| EST Clone | EST Clone (sites) name |
| DDBJ Acc FW | DDBJ accession of the EST clone (Forward sequence) |
| DDBJ Acc RV | DDBJ accession of the EST clone (Reverse sequence) |
| Positive YACs | Positive YAC names |
| PCR Primer | PCR primer name |
| Amplified Band Size | Amplified PCR band size (kb) |
| Ann T | Annealing temperature (℃) |
| 5'-Primer Sequence | Primer sequence (5' primer, each 20 bases) |
| 3'-Primer Sequence | Primer sequence (3' primer, each 20 bases) |
| Map Image File | Image file name of the rice transcript map |
2.4 The rice transcript map
| Data name | The rice transcript map |
| Description of data contents | Images of a YAC-Based rice transcript map containing 6591 EST Sites. |
| File | rgp_estmap2001_map_image.zip (4.9 MB) |
3. License
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 : A YAC-Based Rice Transcript Map Containing 6591 EST Sites © 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 |
|---|---|
| 2015/04/02 | RGP estmap2001 English archive site is opened. |
| 2013/04/01 | The URL of RGP estmap2001 is changed to "http://rgp.dna.affrc.go.jp/E/publicdata/estmap2001/index.html". |
| 2002/02/16 | RGP estmap2001 (http://rgp.dna.affrc.go.jp/publicdata/estmap2001/index.html) is opened. |
5. Literature
Wu J, Maehara T, Shimokawa T, Yamamoto S, Harada C, Takazaki Y, Ono N, Mukai Y, Koike K, Yazaki J, Fujii F, Shomura A, Ando T, Kono I, Waki K, Yamamoto K, Yano M, Matsumoto T, Sasaki T.A comprehensive rice transcript map containing 6591 expressed sequence tag sites.
The Plant Cell / 2002 Mar / 14(3):525-535
PMID:11910001
6. Contact address
When you have any question about "RGP estmap2001", 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