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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 6,941 8,917 -
BioSample 121,809 190,587 -
Conserved Domains 6 13 -
GEO DataSets 21,325 29,043 -
Gene 218 102,125 -
Identical Protein Groups 44,406 203,057 -
Nucleotide 323,993 2,298,390 -
PubChem BioAssay 464 498 -
PMC 43,196 43,196 -
Protein 62,608 448,940 -
SRA 120,618 167,019 -
Structure 105 351 -
Taxonomy 12 12 -

Oryza sativa

Taxonomy ID: 4530 (for references in articles please use NCBI:txid4530)
current name
Oryza sativa L., 1753
Genbank common name: Asian cultivated rice
NCBI BLAST name: monocots
Rank: species
Genetic code: Translation table 1 (Standard)
Mitochondrial genetic code: Translation table 1 (Standard)
Other names:
common name(s) rice, red 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

Comments and References:

image:Oryza sativa
Image by Augustus Binu from Wikimedia Commons under a CC BY-SA 4.0 license.
* Image may not have been verified for accuracy by NCBI Taxonomy.
GRIN (Oct 18, 2016)
Name accessed on 18 October 2016 in: USDA, ARS, National Genetic Resources Program. Germplasm Resources Information Network - (GRIN) [Online Database]. National Germplasm Resources Laboratory, Beltsville, Maryland.
Flora of China - Poaceae
Chen S-L et al. 2006. Poaceae (R. Brown) Barnhart. In Wu, Z. Y., P. H. Raven & D. Y. Hong, eds. Flora of China. Vol. 22 (Poaceae). Science Press, Beijing, and Missouri Botanical Garden Press, St. Louis. Online at Flora of China: www.efloras.org
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.
Vaughn LK et al. 2001
Vaughn LK, Ottis BV, Prazak-Havey AM, Bormans, CA, Sneller C, Chandler JM and Park WD. 2001. Is all red rice found in commercial rice really Oryza sativa? Weed Science 49(4): 468-476.

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
Oryza sativa taxonomy taxonomy/phylogenetic Arctos Specimen Database
dryaddb supplemental materials Dryad Digital Repository
dryaddb supplemental materials Dryad Digital Repository
dryaddb supplemental materials Dryad Digital Repository
dryaddb supplemental materials Dryad Digital Repository
dryaddb supplemental materials Dryad Digital Repository
dryaddb supplemental materials Dryad Digital Repository
Oryza sativa L. taxonomy/phylogenetic Encyclopedia of life
GOLD: 3018 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
Oryza sativa L. taxonomy/phylogenetic Integrated Taxonomic Information System
Oryza sativa taxonomy/phylogenetic Lifemap
US Rice Genome Project taxonomy/phylogenetic NCBI taxonomy bookmarks
Monsanto taxonomy/phylogenetic NCBI taxonomy bookmarks
Oryzabase taxonomy/phylogenetic NCBI taxonomy bookmarks
Rice Genome Project taxonomy/phylogenetic NCBI taxonomy bookmarks
Gramene taxonomy/phylogenetic NCBI taxonomy bookmarks
OMA taxonomy/phylogenetic OMA Browser: Orthologous MAtrix
Oryza sativa taxonomy/phylogenetic PLANTS Database (USDA/NRCS)
Oryza sativa (L.) herbarium/museum collections PlantaeDB, University of Bucharest
Oryza sativa taxonomy/phylogenetic Plants of the World Online
Oryza sativa taxonomy/phylogenetic The International Plant Names Index
Oryza sativa L. taxonomy/phylogenetic USDA-ARS GRIN Taxonomy
search W3TROPICOS taxonomy/phylogenetic Vascular Tropicos
WebScipio: Oryza sativa Indica group organism-specific WebScipio - eukaryotic gene identification
diArk: Oryza sativa Indica group organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group Minghui 63 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group DJ123 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group PA64s organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group Tetep organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group IR8 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group IR64 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group Co39 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group Tadukan organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group HR-12 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group 93-11 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa KMR3 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa IL50-13 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group RP Bio-226 organism-specific diArk - a resource for eukaryotic genome research
diArk: Oryza sativa Indica group Zhenshan 97 organism-specific diArk - a resource for eukaryotic genome research
Wikipedia taxonomy/phylogenetic iPhylo
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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