RiceGE: Database Sources, Details and Summary ( Aug. 16, 2013 )

1. Data Sources :
    

a. Genome : IRGSP sequenced and TIGR assembled pseudo-molecules/annotation version 5 (01/24/2007) and MSU assembled pseudo-molecules/annotation version 6.1.

b. T-DNA/Ds FST

c. cDNA and others

2. Data Details :
CategeryGroupSequencesv5 Mappedv6 Mapped    Update     
GeneIRGSP/TIGR/MSU 57,14257,84006/03/2010
InsertionsRTIM77,74017,93777,70107/12/2011
Eu-CIRAD/Genoplante29,26328,32428,54006/03/2010
ZJU T-DNA741714 06/03/2010
UCD FST17,73017,683
dSpm: 12,856
Ds: 4,827
17,684
dSpm: 12,857
Ds: 4,827
06/03/2010
TRIM FST38,84011,64638,09708/16/2013
CSIRO FST61158959206/03/2010
RMD FST85,31533,19747,23101/20/2012
PFG T-DNA107,171106,095
67,282 lines
106,10006/03/2010
GSNU Ds1,0721,0461,04706/03/2010
EU-OSTID Ds1,3151,3011,31506/03/2010
SHIP T-DNA10,38110,281 (7,759 lines)10,28106/03/2010
Full-length cDNAsKOME35,78636,46736,49706/03/2010
RiCD indica10,0839,302 (9,155)9,32506/03/2010
Community3,3713,0793,45902/04/2012
Genomic DNACommunity Gene65868008/25/2007
EST jap. contigs 1,040,1401,007,456
ctg: 37,954
08/25/2007
MPSS
(<=2 hits)
mRNA 17bp419,157101,246 08/25/2007
mRNA 20bp35,570076,059 08/25/2007
Small RNA296,201256,790 269,552 (<=3 hits) 06/08/2010
miRNA ASRP/Sanger 68391 04/22/2008
miRBase 15,632   1,597 06/08/2010
small RNA UC Davis CSRDB1180916489 (10743) 10/07/2008
113,196  84,122 (<=3 hits)06/08/2010
SAGE= 1 hit 32,804 08/25/2007
Markers AFLP,RFLP,RAPD,STS  7,845 08/25/2007
Homology cDNAWheat 1,15957507/06/2010
Maize 32,226 (27K+ Arizona GI)45,84307/06/2010
Barley 46263107/06/2010
Brassica 8791,34407/06/2010
Arabidopsis coding protein26,75122,60223,039 07/06/2010
Affymetrix rice genome arraysequence information (SIF)57,38155,088 08/25/2007
gene expression sample (GSM)  155 08/25/2007
Yale Tiling Array  12,896,594 08/25/2007

3. Summary (08/25/2007) :

NOTE :     5' UTR : 300 to ATG     Promoter : 1000 to 300 bases away from ATG.

4. Download Data : http://signal.salk.edu/database/RiceGE.

hits since Jun 15, 2004 | T-DNA Express | Transcriptome | RiceGE japonica | RiceGE indica | Methylome | YeastGE |
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