• Submitted GenBank assembly : GCA_001305255.1
  • Taxon : Oryza sativa Indica Group (long-grained rice)
  • Cultivar : RP Bio-226
  • Assembly type : haploid
  • Submitter : OSMANIA UNIVERSITY
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  • Submitted GenBank assembly : GCA_014636035.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : 9311
  • Assembly type : haploid
  • Submitter : GrandOmics Biosciences
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  • Submitted GenBank assembly : GCA_019137765.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : Jiayu 253
  • Assembly type : haploid
  • Submitter : China national rice research institute
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  • Submitted GenBank assembly : GCA_009829375.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : LIU XU::IRGC 109232-1
  • Assembly type : haploid
  • Submitter: : University of Arizona
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  • Submitted GenBank assembly : GCA_037179205.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : CSA-Pi9
  • Assembly type : haploid
  • Submitter : Sejong University
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  • Submitted GenBank assembly : GCA_037179195.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : CSA
  • Assembly type : haploid
  • Submitter : Sejong University
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  • Submitted GenBank assembly : GCA_014636015.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : 9311
  • Assembly type : haploid
  • Submitter : GrandOmics Biosciences
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  • Submitted GenBank assembly : GCA_030179985.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : IRRI2K_91
  • Assembly type : haploid
  • Submitter : GuangDong Academy of Agricultural Sciences
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  • Submitted GenBank assembly : GCA_030179975.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : IRRI2K_86
  • Assembly type : haploid
  • Submitter : GuangDong Academy of Agricultural Sciences
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  • Submitted GenBank assembly : GCA_003865215.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : 93-11
  • Assembly type : haploid
  • Submitter : Chinese Academy of Agricultural Sciences
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  • Submitted GenBank assembly : GCA_009914875.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Cultivar : IR64 (IRRI)

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_009829725.1
  • Taxon : Oryza sativa (Asian cultivated rice)
  • Cultivar : R600
  • Assembly type : haploid
  • Submitter : Sichuan Agricultural University
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  • Submitted GenBank assembly : GCA_004007595.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Cultivar : Carolina Gold Select

  • Assembly type : haploid

  • Submitter : Cornell University

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  • Submitted GenBank assembly : GCA_018853525.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Cultivar : Taichung Native 1 (TN1)

  • Assembly type : haploid

  • Submitter : Academia Sinica

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  • Submitted GenBank assembly : GCA_004348155.2

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Cultivar : Tetep

  • Assembly type : haploid

  • Submitter : Nanjing University,China

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  • Submitted GenBank assembly

    GCA_951799355.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : center for research in agricultural genomics (crag

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  • Submitted GenBank assembly : GCA_009830595.1
  • Taxon : Oryza sativa Japonica Group (Japanese rice)
  • Cultivar : Azucena
  • Assembly type : haploid
  • Submitter: : University of Arizona
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  • Submitted GenBank assembly : GCA_003865235.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : Nipponbare

  • Assembly type : haploid

  • Submitter : Chinese Academy of Agricultural Sciences

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  • Submitted GenBank assembly : GCA_014526345.1
  • Taxon : Oryza sativa Japonica Group (Japanese rice)
  • Cultivar : Zhonghua 11
  • Assembly type : haploid
  • Submitter : Institute of Genetics and Developmental Biology
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  • Submitted GenBank assembly : GCA_009797565.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : Kitaake

  • Assembly type : haploid

  • Submitter : DOE Joint Genome Institute

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  • Submitted GenBank assembly : GCA_000817635.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : A123

  • Assembly type : haploid

  • Submitter : University of California, Riverside

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  • Submitted GenBank assembly : GCA_000817615.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : HEG4

  • Assembly type : haploid

  • Submitter : University of California, Riverside

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  • Submitted GenBank assembly : GCA_000149285.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : Nipponbare

  • Assembly type : haploid

  • Submitter : Beijing Genomics Institute

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  • Submitted GenBank assembly : GCA_000321445.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : Hitomebore

  • Assembly type : haploid

  • Submitter : Iwate Biotechnology Research Center

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  • Submitted GenBank assembly : GCA_000164945.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : Koshihikari

  • Assembly type : haploid

  • Submitter : QTL Genomics Research Center, National Institute of Agrobiological Sciences

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  • Submitted GenBank assembly : GCA_009831355.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Assembly type : haploid -Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_009831025.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_009829395.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Assembly type : haploid -Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_001623365.2

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : Minghui 63

  • Assembly type : haploid

  • Submitter : Huazhong Agricultural University

  • Download

  • Submitted GenBank assembly : GCA_009831045.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_009831295.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_001889745.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : IR8

  • Assembly type : haploid

  • Submitter : The University of Arizona

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  • Submitted GenBank assembly : GCA_001618795.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : Zhenshan 97

  • Assembly type : haploid

  • Submitter : Huazhong Agricultural University

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  • Submitted GenBank assembly : GCA_000725085.2

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : HR-12

  • Assembly type : haploid

  • Submitter : Centre for Cellular and Molecular Platforms

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  • Submitted GenBank assembly : GCA_001618785.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : Minghui 63

  • Assembly type : haploid -Submitter : Huazhong Agricultural University

  • Download

  • Submitted GenBank assembly : GCA_019338905.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Assembly type : haploid

  • Submitter : BGI

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  • Submitted GenBank assembly : GCA_000004655.2

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : 93-11

  • Assembly type : haploid

  • Submitter : Beijing Institute of Genomics, Chinese Academy of Sciences

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  • Submitted GenBank assembly : GCA_009831335.1

  • Taxon : Oryza sativa aus subgroup

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_009831275.1

  • Taxon : Oryza sativa tropical japonica subgroup

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_009831255.1

  • Taxon : Oryza sativa aromatic subgroup

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_001952365.3

  • Taxon : Oryza sativa aus subgroup

  • Cultivar : N 22::IRGC 19379-1 (IRGC 117534)

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_009831315.1

  • Taxon : Oryza sativa tropical japonica subgroup

  • Assembly type : haploid

  • Submitter : University of Arizona

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  • Submitted GenBank assembly : GCA_022834795.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : Kitaake

  • Assembly type : haploid

  • Submitter : Kazusa DNA Research Institute

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  • Submitted GenBank assembly : GCA_011764405.2

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : IR64

  • Assembly type : haploid

  • Submitter : Breeding Informatics Research Unit, Division of Basic Research, Institute of Crop Science, NARO

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  • Submitted GenBank assembly : GCA_936158435.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936157615.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936145055.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936153055.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936157035.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936150925.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936157175.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936154975.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936157125.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_936157995.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Assembly type : haploid

  • Submitter : University of Zurich

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  • Submitted GenBank assembly : GCA_001648735.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Cultivar : KMR3

  • Assembly type : haploid

  • Submitter : Centre for Cellular and Molecular Biology

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  • Submitted GenBank assembly : GCA_001648745.1

  • Taxon : Oryza sativa (Asian cultivated rice)

  • Cultivar : IL50-13

  • Assembly type : haploid

  • Submitter : Centre for Cellular and Molecular Biology

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  • Submitted GenBank assembly : GCA_034317485.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : Early Geng

  • Assembly type : haploid

  • Submitter : Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Ch

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  • Submitted GenBank assembly : GCA_003449065.1

  • Taxon : Oryza sativa Japonica Group (Japanese rice)

  • Cultivar : Shennong 265

  • Assembly type : haploid

  • Submitter : Shenyang Agricultural University

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  • Submitted GenBank assembly : GCA_003449045.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : R99

  • Assembly type : haploid

  • Submitter : Shenyang Agricultural University

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  • Submitted GenBank assembly : GCA_028584105.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : CR071

  • Assembly type : haploid

  • Submitter : Huazhong Agricultural University

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  • Submitted GenBank assembly : GCA_028584095.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : J23B

  • Assembly type : haploid

  • Submitter : Huazhong Agricultural University

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  • Submitted GenBank assembly

    GCA_001611195.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : Tetep

  • Assembly type : haploid

  • Submitter : Centre for Cellular and Molecular Platforms

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  • Submitted GenBank assembly : GCA_001611255.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : Tadukan

  • Assembly type : haploid

  • Submitter : Centre for Cellular and Molecular Platforms

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  • Submitted GenBank assembly : GCA_001611235.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : Co39

  • Assembly type : haploid

  • Submitter : Centre for Cellular and Molecular Platforms

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  • Submitted GenBank assembly : GCA_006992885.1

  • Taxon : Oryza sativa Indica Group (long-grained rice)

  • Cultivar : Co39

  • Assembly type : haploid

  • Submitter : Fujian Agriculture and Forest University

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  • Submitted GenBank assembly

    GCA_006942195.1

  • Taxon : Oryza sativa f. spontanea

  • Assembly type : haploid

  • Submitter : Shenyang Agricultural University, China

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  • Varieties

    02428，9311，Basmati1，CG14，CN1，D62，DG，DHX2，FH838，FS32，G46，G8，G630，II32，IR64，J4155，KY131，Lemont，LJ NIP(MSU)，N22，NamRoo，Y3551，R498，R527，S548，TM，Tumba，WSSM，Y58S，Kosh，YX1，ZH11

  • download

  • Data Information

    RTFRD collected 149 rice unique RNA-seq datasets from NCBI GEO database.

  • Promoter Sequences

    Promoter sequence of rice geneFasta file header format:e.g. LOC_Os06g05820 [Chr6 2650068 2652068 + 2000bp](gene name [ chromosome start end strand length ])

  • TF information

    This file mainly corresponds to the information of the BROWSE module

  • Promoter sequence analysis results

    Analyzing Software: FIMO,command: fimo -oc fimo_res Osj_TF_binding_motifs.meme promoter.fa,Osj_TF_binding_motifs.meme: download from PlantTFDB

  • Expression matrix of the total datasets

    Expression matrix of 150 uniqre samples,Genome and annotation file versions: msu 7.0

  • Expression matrix of the anatomy datasets

    Expression matrix of 23 tissues,Genome and annotation file versions: msu 7.0

  • download

  • We corrected 152 and 8,347 gene annotation errors in Nip and 93-11, respectively. These annotations included corrections of gene orientation and gene structure, and identified a number of new genes.
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