Rice Gene Index

What's in RGI?

50 rice accessions, 52 annotations
2,119,189 genes

Average 31,690 gene pairs

561,681 non-redundant homologous groups
156,598 Ortholog Gene Indices
12,257 OGI core genes
60,292 OGI accession-specific genes

116,640 alternative splicing events
1,130,998 genes in the Swiss-Prot database

Ortholog Gene Index

Cite RGI:

Yu Z, Chen Y, Zhou Y, Zhang Y, Li M, Ouyang Y, Chebotarov D, Mauleon R, Zhao H, Xie W, McNally K, Wing R, Guo W and Zhang J. Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice. Molecular Plant, 2023, 16(5):798-801. DOI: 10.1016/j.molp.2023.03.012

Resources

Homologues

Search annotation, location, and homolog of genes by gene ID.

Genes

Gene basic information, visualization of transcript structure, AS events and homologs.

Accessions

Comprehensive information of accessions in Asian rice.

GenePair

Optimal mathing genes between rice accessions.

MacroCollinearity

Visualization of gene collinearity in macro-region between rice accessions.

MicroCollinearity

Visualization of gene collinearity in micro-region between rice accessions.

Structural Variations

Visualization of structural variations between rice accessions.

Genomes



Accession Name		Subpopulation	Assembly	Annotation	Locus Tag Prefix	Gene	Reference
	OglaRS2	O.glaberrima	OglaRS2	DIADE	Oglab	37,833	Ntakirutimana et al 2023
	Basmatil1	circum-Basmati	Basmatil1	SICAU	OsBasmatil1	42,098	Qin et al 2021
	ARC 10497::IRGC 12485-1	circum-Basmati	Os117425RS1	Gramene (+IsoSeq)	OsARC_	37,181	Zhou et al., 2020
	KETAN NANGKA::IRGC 19961-2	Geng-japonica-trop2	Os128077RS1	Gramene (+IsoSeq)	OsKeNa_	37,994	Zhou et al., 2020
	Lemont	Geng-japonica-trp	Lemont	SICAU	OsLemont	39,479	Qin et al 2021
	Azucena	Geng-japonica-trop1	AzucenaRS1	Gramene (+IsoSeq)	OsAzu_	36,882	Zhou et al., 2020
	NamRoo	Geng-japonica-sbtp	NamRoo	SICAU	OsNamRoo	41,293	Qin et al 2021
	CHAO MEO::IRGC 80273-1	Geng-japonica-subtrp	Os132278RS1	Gramene (+IsoSeq)	OsCMeo_	37,240	Zhou et al., 2020
	02428	Geng-japonica-temp	02428	SICAU	Os02428	39,133	Qin et al 2021
	LJ	Geng-japonica-adm	LJ	SICAU	OsLJ	38,981	Qin et al 2021
	DHX2	Geng-japonica-temp	DHX2	SICAU	OsDHX2	41,060	Qin et al 2021
	KY131	Geng-japonica-temp	KY131	SICAU	OsKY131	37,247	Qin et al 2021
	ZH11	Geng-japonica-temp	ZH11	SICAU	OsZH11	37,338	Qin et al 2021
	Nipponbare	Geng-japonica-temp	IRGSP1.0	Gramene (+IsoSeq)	OsNip_	38,404	Yoshihiro et al., 2013
				MSU	LOC_Os	55,801	Yoshihiro et al., 2013
				RAP-db	Os	37,859	Yoshihiro et al., 2013
	Kosh	Geng-japonica-temp	Kosh	SICAU	OsKosh	40,888	Qin et al 2021
	NATEL BORO::IRGC 34749-1	circum-Aus2	Os127652RS1	Gramene (+IsoSeq)	OsNaBo_	36,392	Zhou et al., 2020
	N22	circum-Aus1	OsN22RS2	Gramene (+IsoSeq)	OsN22_	37,598	Stein et al., 2018
	LARHA MUGAD::IRGC 52339-1	Xian-indica-2B	Os125619RS1	Gramene (+IsoSeq)	OsLaMu_	37,474	Zhou et al., 2020
	LIU XU::IRGC 109232-1	Xian-indica-3B2	Os125827RS1	Gramene (+IsoSeq)	OsLiXu_	44,942	Zhou et al., 2020
	XL628S	Xian-indica-adm	XL628S	PKU	OsXL628S	43,527	Zhang et al 2022
	LK638S	Xian-indica-adm	LK638S	PKU	OsLK638S	41,090	Zhang et al 2022
	D62	Xian-indica-1A	D62	SICAU	OsD62	38,880	Qin et al 2021
	CN1	Xian-indica-1A	CN1	SICAU	OsCN1	42,047	Qin et al 2021
	DG	Xian-indica-1A	DG	SICAU	OsDG	41,009	Qin et al 2021
	FS32	Xian-indica-1A	FS32	SICAU	OsFS32	41,317	Qin et al 2021
	G46	Xian-indica-1A	G46	SICAU	OsG46	40,682	Qin et al 2021
	Zhenshan 97	Xian-indica-1A	ZS97RS3	HZAU	OsZS97_	60,935	Song et al., 2021
	II32	Xian-indica-1A	II32	SICAU	OsII32	41,887	Qin et al 2021
	TM	Xian-indica-2	TM	SICAU	OsTM	40,082	Qin et al 2021
	GOBOL SAIL (BALAM)::IRGC 26624-2	Xian-indica-2A	Os132424RS1	Gramene (+IsoSeq)	OsGoSa_	36,467	Zhou et al., 2020
	KHAO YAI GUANG::IRGC 65972-1	Xian-indica-3B1	Os127518RS1	Gramene (+IsoSeq)	OsKYG_	37,522	Zhou et al., 2020
	Tumba	Xian-indica-3	Tumba	SICAU	OsTumba	41,535	Qin et al 2021
	LIMA::IRGC 81487-1	Xian-indica-3A	Os127564RS1	Gramene (+IsoSeq)	OsLima_	37,994	Zhou et al., 2020
	Y58S	Xian-indica-1B	Y58S	SICAU	OsY58S	42,521	Qin et al 2021
	J4155S	Xian-indica-adm	J4155S	PKU	OsJ4155S	43,237	Zhang et al 2022
	J4155	Xian-indica-1B	J4155	SICAU	OsJ4155	40,137	Qin et al 2021
	G8	Xian-indica-1B	G8	SICAU	OsG8	40,228	Qin et al 2021
	WSSM	Xian-indica-adm	WSSM	SICAU	OsWSSM	39,193	Qin et al 2021
	HZ	Xian-indica-adm	HZ	PKU	OsHZ	42,992	Zhang et al 2022
	IR64	Xian-indica-1B1	OsIR64RS1	Gramene (+IsoSeq)	OsIR64_	36,925	Zhou et al., 2020
	YX1	Xian-indica-adm	YX1	SICAU	OsYX1	40,093	Qin et al 2021
	R9311	Xian-indica-adm	R9311	AGIS	R9311C	40,345	Wamg et al 2022
	PR 106::IRGC 53418-1	Xian-indica-1B2	Os127742RS1	Gramene (+IsoSeq)	OsPr106_	36,720	Zhou et al., 2020
	G630	Xian-indica-adm	G630	SICAU	OsG630	38,306	Qin et al 2021
	FH838	Xian-indica-adm	FH838	SICAU	OsFH838	37,555	Qin et al 2021
	Y3551	Xian-indica-1B	Y3551	SICAU	OsY3551	39,913	Qin et al 2021
	R498	Xian-indica-1B	R498	SICAU	OsR498	43,063	Qin et al 2021
	S548	Xian-indica-1B	S548	SICAU	OsS548	43,074	Qin et al 2021
	Minghui 63	Xian-indica-adm	MH63RS3	HZAU	OsMH63_	59,903	Song et al., 2021
	R527	Xian-indica-1B	R527	SICAU	OsR527	36,893	Qin et al 2021