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Taxonomy browser (Oryza sativa Indica Group)

Oryza sativa Indica Group

Taxonomy ID: 39946 (for references in articles please use NCBI:txid39946)
Scientific name: Oryza sativa Indica Group
includes: Oryza sp. Poi-6
Genbank common name: long-grained rice
NCBI BLAST® name: monocots
Rank: no rank
Genetic code: Translation table 1 (Standard)
Mitochondrial genetic code: Translation table 1 (Standard)
Plastid genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid)
Other names:
heterotypic synonym: Oryza sativa (indica cultivar-group)
heterotypic synonym: Oryza sativa (indica group)
heterotypic synonym: Oryza sativa subsp. indica Kato
common name: Indian rice
common name: Indica rice
Lineage( full )
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
   Entrez records   
Database name Subtree links Direct links
Nucleotide 519,768 517,958
Protein 47,116 46,944
Structure 11 11
Genome 1 1
Popset 845 845
GEO Datasets 1,438 1,429
PubMed Central 37 37
Gene 305 305
SRA Experiments 2,507 2,457
GEO Profiles 57,381 57,381
Protein Clusters 56 56
Identical Protein Groups 41,344 41,343
Bio Project 176 175
Bio Sample 1,770 1,761
Assembly 18 17
Probe 4,813 4,813
Taxonomy 2 1

Comments and References:

Nota BeneThe 3,000 rice genomes project
The 3,000 rice genomes project. GigaScience 2014, 3:7. DOI: http://dx.doi.org10.1186/2047-217X-3-7

Nota BeneHuang X et al. 2012
Huang X et al. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature 490: 497-501. doi:

Reference to PubMed documentKovach MJ et al. 2009
Kovach MJ, Calingacion MN, Fitzgerald MA, McCouch SR. 2009. The origin and evolution of fragrance in rice (Oryza sativa L.). Proceedings of the National Academy of Sciences U.S.A. 106(34): 14444-9.

Reference to PubMed documentSweeney M & McCouch S 2007
Sweeney M and McCouch S. 2007. The complex history of the domestication of rice. Annals of Botany 100(5): 951-957.

Reference to PubMed documentCaicedo AL et al. 2007
Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, and Purugganan MD. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics 2007 September; 3(9): e163. Prepublished online 2007 August 6. Published online 2007 September 28. doi: 10.1371/journal.pgen.0030163.

Reference to PubMed documentGarris et al. 2005
Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S. 2005. Genetic structure and diversity in Oryza sativa L. Genetics. 2005 Mar;169(3):1631-8. Epub 2005 Jan 16.

Genome Information

   Trace records (raw single-pass reads of DNA sequence)   
Sequencing Center Name
Record counts per type
BGI - Beijing Genome Institute
- 6,423,393 6,423,393
IRRI - The International Rice Research Institute
1,102,237 - 1,102,237
Totals per type
1,102,237 6,423,393 7,525,630

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
dryaddb supplemental materials Dryad Digital Repository
24 records from this provider organism-specific Genomes On Line Database
Show Biotic Interactions taxonomy/phylogenetic Global Biotic Interactions
OMA taxonomy/phylogenetic OMA Browser: Orthologous MAtrix
Oryza sativa subsp. indica Kato taxonomy/phylogenetic USDA-ARS GRIN Taxonomy
Groups interested in participating in the LinkOut program should visit the LinkOut home page.
A list of our current non-bibliographic LinkOut providers can be found here.

Information from sequence entries

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Disclaimer: The NCBI taxonomy database is not an authoritative source for nomenclature or classification - please consult the relevant scientific literature for the most reliable information.

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