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Entrez PubMed Nucleotide Protein Genome Structure PMC Taxonomy BioCollections
   
   Entrez records   
Database name Direct links Subtree links Links from type
BioProject 1,711 1,720 -
BioSample 57,487 58,876 -
Conserved Domains 7 7 -
GEO DataSets 5,787 5,819 -
Gene 101,437 101,437 -
Identical Protein Groups 155,622 155,658 -
Nucleotide 1,441,663 1,448,019 -
PubChem BioAssay 41 41 -
PMC 178 178 -
Protein 331,247 333,732 -
SRA 35,195 36,683 -
Structure 241 241 -
Taxonomy 4 4 -

Oryza sativa Japonica Group

Taxonomy ID: 39947 (for references in articles please use NCBI:txid39947)
current name
Oryza sativa Japonica Group
Genbank common name: Japanese rice
NCBI BLAST name: monocots
Rank: no rank
Genetic code: Translation table 1 (Standard)
Mitochondrial genetic code: Translation table 1 (Standard)
Other names:
heterotypic synonym Oryza sativa subsp. japonica
heterotypic synonym Oryza sativa (japonica cultivar-group)
common name(s) Japonica rice

Lineage(full)
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa

Comments and References:

The 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
Huang 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: http://dx.doi.org/10.1038/nature11532
Zhao K et al. 2010
Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali M, Tung C, Reynolds A, Bustamante C, SR McCouch. 2010. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One 24:e10780. Published online 2010 May 24. DOI: http://dx.doi.org/10.1371/journal.pone.0010780
Kovach 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.
Caicedo 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.
Sweeney 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.
Garris 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.

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
dryaddb supplemental materials Dryad Digital Repository
dryaddb supplemental materials Dryad Digital Repository
GOLD: 24 Organisms organism-specific Genomes On Line Database
Show Biotic Interactions taxonomy/phylogenetic Global Biotic Interactions
Related Immune Epitope Information gene/protein/disease-specific Immune Epitope Database and Analysis Resource
OMA taxonomy/phylogenetic OMA Browser: Orthologous MAtrix
WebScipio: Oryza sativa Japonica group organism-specific WebScipio - eukaryotic gene identification
diArk: Oryza sativa Japonica group HEG4 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Japonica group Nipponbare organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Japonica group organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Japonica group A123 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Japonica group Suijing18 organism-specific diArk - a resource for eukaryotic genome research
Notes:
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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.

Reference: How to cite this resource - Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062. PubMed: 32761142 PMC: PMC7408187.


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