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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., 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)
Plastid genetic code: Translation table 11 (Bacterial, Archaeal and Plant Plastid)
Other names:
common name(s) red rice, 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 2,295,123 322,848
Protein 448,369 62,313
Structure 321 95
Genome 1 1
Popset 1,335 1,150
Conserved Domains 13 6
GEO Datasets 25,660 18,495
PubMed Central 41,664 41,664
Gene 95,609 218
HomoloGene 9,787 9,787
SRA Experiments 128,499 91,072
GEO Profiles 670,939 670,939
Protein Clusters 15,559 -
Identical Protein Groups 203,248 44,251
BioProject 7,733 5,969
BioSample 139,843 81,723
Assembly 118 60
PubChem BioAssay 495 461
Taxonomy 11 1

Comments and References:

image:Oryza sativa
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, 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://dx.doi.org/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://dx.doi.org/10.1371/journal.pone.0010780
Kovach MJ et al. 2009, other link:http://www.ncbi.nlm.nih.gov/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://www.ncbi.nlm.nih.gov/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://www.ncbi.nlm.nih.gov/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://www.ncbi.nlm.nih.gov/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
GOLD: 2983 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
5 records from this provider 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
16 records from this provider organism-specific diArk - a resource for eukaryotic genome research
Wikipedia taxonomy/phylogenetic iPhylo
Notes:
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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. PubMed: 32761142 PMC: PMC7408187.


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