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Taxonomy browser (Oryza sativa)

Oryza sativa

Taxonomy ID: 4530 (for references in articles please use NCBI:txid4530)
current name
Oryza sativa L.
Genbank common name: rice
NCBI BLAST name: monocots
Rank: species
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:
common name(s) 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
   Entrez records   
Database name Subtree links Direct links
Nucleotide 2,280,951 319,428
Protein 438,488 61,746
Structure 248 69
Genome 1 1
Popset 1,171 1,021
Conserved Domains 12 5
GEO Datasets 20,175 14,863
PubMed Central 27,900 27,900
Gene 91,440 149
HomoloGene 9,787 9,787
SRA Experiments 84,211 64,095
GEO Profiles 670,939 670,939
Protein Clusters 15,559 -
Identical Protein Groups 204,549 44,047
Bio Project 6,250 4,864
Bio Sample 92,365 49,166
Bio Systems 1,265 751
Assembly 89 43
Probe 186,169 92,681
PubChem BioAssay 478 448
Taxonomy 9 1

Comments and References:

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.
TROPICOS (Aug 27, 2015)
Name accessed on 27 August 2015 in: Tropicos.org. Missouri Botanical Garden, 2008 - 4344 Shaw Boulevard, Saint Louis, Missouri 63110, U.S.A. on line at: http://www.tropicos.org/
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, doi:10.1038/nature11532
Huang X et al. 2012. A map of rice genome variation reveals the origin of cultivated rice. Nature 490: 497-501. doi: http://0-dx.doi.org.brum.beds.ac.uk/10.1038/nature11532
Zhao K et al. 2010, doi:10.1371/journal.pone.0010780
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://0-dx.doi.org.brum.beds.ac.uk/10.1371/journal.pone.0010780
Kovach MJ et al. 2009, other link:http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/pmc/articles/PMC2732888/?tool=pubmed
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, other link:http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/pmc/articles/PMC1994709/?tool=pmcentrez
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, other link:http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/pmc/articles/PMC2759204/?tool=pubmed
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, other link:http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/pmc/articles/PMC1449546/?tool=pubmed
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.

Genome Information

Go to NCBI genomic BLAST page for Oryza sativa

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
Oryza sativa taxonomy taxonomy/phylogenetic Arctos Specimen Database
6 records from this provider supplemental materials Dryad Digital Repository
Oryza sativa L. taxonomy/phylogenetic Encyclopedia of life
1512 records from this provider 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
5 records from this provider taxonomy/phylogenetic NCBI taxonomy bookmarks
Oryza sativa taxonomy/phylogenetic PLANTS Database (USDA/NRCS)
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
16 records from this provider organism-specific diArk - a resource for eukaryotic genome research
Wikipedia taxonomy/phylogenetic iPhylo
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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.
Reference: How to cite this resource - Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062. [Full text] [PubMed]


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