RiceGE: Database Sources, Details and Summary

RiceGE: Database Sources, Details and Summary ( Jun. 22, 2017 )

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

1. Postech PFG T-DNA, S. Korea [Publication]
2. Rice Mutant Data, Huazhong Agricultural University, China [Publication]. We have uploaded RMD's newly comprehensive FSTs into our database. They have 85,315 sequences in total and 47,231 mapped onto the japanica genome and 46,481 onto the indica genome. Due to difference of their new names and the old ones, we will keep the old names a while. However, we will remove them later.
3. Taiwan Rice Insertion Mutant (TRIM), Academia Sinica
4. NIAS Tos17 insertion mutants [RTIM], Japan [Publication]
5. CIRAD / Genoplante oryza tag lines, France [Publication]
6. Zhejiang Univ. rice T-DNA, China [Publication]
7. UCD dSpm/Ds, USA
8. CSIRO Ac/Ds, Australia [Publication]
9. PSNU Ds, Korea
10. EU-OSTID Ds, Netherlands
11. SHIP T-DNA, China.

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.
9. 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
11. UC Davis CSRDB rice small RNAs .
12. Rice indica cDNA Database, NCGR, China .

2. Data Details :

Categery	Group	Sequences	v5 Mapped	v6 Mapped	Update
Gene	IRGSP/TIGR/MSU		57,142	57,840	06/03/2010
Insertions	RTIM	77,740	17,937	77,701	07/12/2011
	Eu-CIRAD/Genoplante	29,263	28,324	28,540	06/03/2010
	ZJU T-DNA	741	714		06/03/2010
	UCD FST	17,730	17,683 dSpm: 12,856 Ds: 4,827	17,684 dSpm: 12,857 Ds: 4,827	06/03/2010
	TRIM FST	59,804	11,646	65,701	06/22/2017
	CSIRO FST	611	589	592	06/03/2010
	RMD FST	85,315	33,197	47,231	01/20/2012
	PFG T-DNA	107,171	106,095 67,282 lines	106,100	06/03/2010
	GSNU Ds	1,072	1,046	1,047	06/03/2010
	EU-OSTID Ds	1,315	1,301	1,315	06/03/2010
	SHIP T-DNA	10,381	10,281 (7,759 lines)	10,281	06/03/2010
Full-length cDNAs	KOME	35,786	36,467	36,497	06/03/2010
	RiCD indica	10,083	9,302 (9,155)	9,325	06/03/2010
	Community	3,371	3,079	3,459	02/04/2012
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	269,552 (<=3 hits)	06/08/2010
miRNA	ASRP/Sanger	68	391		04/22/2008
miRNA	miRBase	15,632		1,597	06/08/2010
small RNA	UC Davis CSRDB	11809	16489 (10743)		10/07/2008
small RNA	UC Davis CSRDB	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 cDNA	Wheat		1,159	575	07/06/2010
	Maize		32,226 (27K+ Arizona GI)	45,843	07/06/2010
	Barley		462	631	07/06/2010
	Brassica		879	1,344	07/06/2010
	Arabidopsis coding protein	26,751	22,602	23,039	07/06/2010
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.

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

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