About This Database

Details of rice EST mapping results

Data description

Data name

DOI

10.18908/lsdba.nbdc00318-04-002

Description of data contents

The data contains the detailed results of PCR-based YAC screening with the clone-specific EST primers.

Data file

File name :

rgp_estmap2001_detail.zip

File URL :

https://dbarchive.biosciencedbc.jp/data/rgp-estmap2001/LATEST/rgp_estmap2001_detail.zip

File size :

242 KB

Simple search URL

http://togodb.biosciencedbc.jp/togodb/view/rgp_estmap2001_detail#en

Data acquisition method

We used clone-specific primer pairs designed from 6713 unique EST sequences (3' end) derived from 19 cDNA libraries.

Data analysis method

SEGMAP (version 3.48) was used for the analysis of YAC screening data and the establishment of the EST map.
DNA gel blot hybridization of YAC or rice genomic DNA with genetic markers or EST clones was conducted using the enhanced chemiluminescence system (Amersham, Buckinghamshire, UK).

Notes
#; floating markers on the genetic map
c; chimeric YAC clones
*; PCR band size longer than predicted
Ann T; 60 ℃ unless otherwise indicated
NI; YACs with unknown insert

Number of data entries

6,760 entries

Data detail

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