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


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

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

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Comprehensive information of accessions in Asian rice.

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Optimal mathing genes between rice accessions.

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

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

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Structural Variations

Visualization of structural variations between rice accessions.


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
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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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