Rice Gene Index

What's in RGI?

16 rice accessions, 18 annotations
744,233 genes

Average 33,350 gene pairs

119,783 non-redundant homologous groups
112,658 Ortholog Gene Indices
21,418 OGI core genes
51,099 OGI accession-specific genes

116,640 alternative splicing events
398,755 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.

Genomes



Accession Name		Subpopulation	Assembly	Annotation	Locus Tag Prefix	Gene	Reference
	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
	Azucena	Geng-japonica-trop1	AzucenaRS1	Gramene (+IsoSeq)	OsAzu_	36,882	Zhou et al., 2020
	KETAN NANGKA::IRGC 19961-2	Geng-japonica-trop2	Os128077RS1	Gramene (+IsoSeq)	OsKeNa_	37,994	Zhou et al., 2020
	CHAO MEO::IRGC 80273-1	Geng-japonica-subtrp	Os132278RS1	Gramene (+IsoSeq)	OsCMeo_	37,240	Zhou et al., 2020
	ARC 10497::IRGC 12485-1	circum-Basmati	Os117425RS1	Gramene (+IsoSeq)	OsARC_	37,181	Zhou et al., 2020
	PR 106::IRGC 53418-1	Xian-indica-1B2	Os127742RS1	Gramene (+IsoSeq)	OsPr106_	36,720	Zhou et al., 2020
	Minghui 63	Xian-indica-adm	MH63RS3	HZAU	OsMH63_	59,903	Song et al., 2021
	IR64	Xian-indica-1B1	OsIR64RS1	Gramene (+IsoSeq)	OsIR64_	36,925	Zhou et al., 2020
	Zhenshan 97	Xian-indica-1A	ZS97RS3	HZAU	OsZS97_	60,935	Song et al., 2021
	LIMA::IRGC 81487-1	Xian-indica-3A	Os127564RS1	Gramene (+IsoSeq)	OsLima_	37,994	Zhou et al., 2020
	KHAO YAI GUANG::IRGC 65972-1	Xian-indica-3B1	Os127518RS1	Gramene (+IsoSeq)	OsKYG_	37,522	Zhou et al., 2020
	GOBOL SAIL (BALAM)::IRGC 26624-2	Xian-indica-2A	Os132424RS1	Gramene (+IsoSeq)	OsGoSa_	36,467	Zhou et al., 2020
	LIU XU::IRGC 109232-1	Xian-indica-3B2	Os125827RS1	Gramene (+IsoSeq)	OsLiXu_	44,942	Zhou et al., 2020
	LARHA MUGAD::IRGC 52339-1	Xian-indica-2B	Os125619RS1	Gramene (+IsoSeq)	OsLaMu_	37,474	Zhou et al., 2020
	N22	circum-Aus1	OsN22RS2	Gramene (+IsoSeq)	OsN22_	37,598	Stein et al., 2018
	NATEL BORO::IRGC 34749-1	circum-Aus2	Os127652RS1	Gramene (+IsoSeq)	OsNaBo_	36,392	Zhou et al., 2020