RiceGE: Database Sources, Details and Summary

RiceGE: Database Sources, Details and Summary ( May. 7, 2008 )

1. Data Sources :

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

b. T-DNA/Ds FST

c. cDNA and others

1. KOME, Japan
2. community cDNAs from NCBI.
3. IRGSP BACs/PACs.
4. rice ESTs and markers from NCBI.
5. microRNA (miRNA) from ASRP and Sanger.
6. Long SAGE Tags.
7. MPSS mRNA 17bp, 20bp and small RNA from UDel.
8. Microarray data from Japan. [1] [2]
9. Affy genome array data [GPL2025] and Gene Expression Samples (GSM) from GEO, NCBI.
10. The tiling array jap from GEO, NCBI

2. Data Details :

Categery	Group	Sequences	Mapped	Update
Gene	IRGSP/TIGR		57,142	01/26/2007
Insertions	RTIM	18,024	17,937	08/25/2007
	Eu-CIRAD/Genoplante	29,263	28,324	10/22/2007
	ZJU T-DNA	741	714	08/25/2007
	UCD FST	12,950	12,711 dSpm: 8,416 Ds: 4,295	01/03/2008
	TRIM FST	7,053	6,965	08/25/2007
	CSIRO FST	611	589	08/25/2007
	RMD FST	16,158	15,971	08/25/2007
	PFG T-DNA	85,267	84,680 58,943 lines	04/28/2008
	GSNU Ds	1,072	1,046	08/25/2007
	EU-OSTID Ds	1,315	1,301	08/25/2007
	SHIP T-DNA	6,962	6,761	08/25/2007
Full-length cDNAs	KOME	37,036	35,644	05/07/2008
Full-length cDNAs	Community	2,596	2,619	04/08/2008
Genomic DNA	Community Gene	658	680	08/25/2007
EST jap. contigs		1,040,140	1,007,456 ctg: 37,954	08/25/2007
MPSS (<=2 hits)	mRNA 17bp	419,157	101,246	08/25/2007
	mRNA 20bp	35,5700	76,059	08/25/2007
	Small RNA	296,201	256,790	04/22/2008
miRNA	ASRP/Sanger	68	391	04/22/2008
SAGE	= 1 hit		32,804	08/25/2007
Markers AFLP,RFLP,RAPD,STS			7,845	08/25/2007
Homology cDNA	Wheat		1,159	02/27/2008
	Maize		6,252	02/27/2008
	Barley		462	02/27/2008
	Brassica		879	02/27/2008
	Arabidopsis coding protein	26,751	22,602	08/25/2007
Affymetrix rice genome array	sequence information (SIF)	57,381	55,088	08/25/2007
Affymetrix rice genome array	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.

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