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


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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.


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
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National Key Laboratory of Crop Genetic Improvement

Huazhong Agricultural University

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