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Taxonomy browser (Oryza sativa)

Oryza sativa

Taxonomy ID: 4530 (for references in articles please use NCBI:txid4530)
Scientific name: Oryza sativa L.
Genbank common name: rice
Inherited 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: red 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
   Entrez records   
Database name Subtree links Direct links
Nucleotide 869,415 217,718
Nucleotide EST 898,978 23,846
Nucleotide GSS 584,859 75,163
Protein 352,244 21,921
Structure 199 51
Genome 2 1
Popset 1,173 1,020
Conserved Domains 19 9
GEO Datasets 16,555 12,447
UniGene 44,118 44,118
PubMed Central 20,501 20,476
Gene 95,489 149
HomoloGene 9,787 9,787
SRA Experiments 55,707 49,406
GEO Profiles 670,939 670,939
Protein Clusters 15,559 -
Identical Protein Groups 178,581 7,950
Bio Project 3,734 2,607
Bio Sample 68,925 34,715
Bio Systems 1,265 751
Assembly 35 3
Clone DB 226,350 172,043
Probe 186,169 92,681
PubChem BioAssay 470 440
Taxonomy 10 1

Comments and References:

Nota BeneGRIN (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.

Nota BeneTROPICOS (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/

Nota BeneFlora 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

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: http://dx.doi.org/10.1038/nature11532

Nota BeneZhao 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

Reference to PubMed documentKovach MJ et al. 2009
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.

Reference to PubMed documentCaicedo AL et al. 2007
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.

Reference to PubMed documentSweeney M & McCouch S 2007
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.

Reference to PubMed documentGarris et al. 2005
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
   Trace records (raw single-pass reads of DNA sequence)   
Sequencing Center Name
Record counts per type
CHIP CLONEEND ALL
IRRI - The International Rice Research Institute
220,449 - 220,449
JGI - Joint Genome Institute, U.S. Department of Energy
- 71,342 71,342
Totals per type
220,449 71,342 291,791

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
Oryza sativa taxonomy taxonomy/phylogenetic Arctos Specimen Database
5 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 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
Oryza sativa taxonomy/phylogenetic electronic Plant Information Centre
Wikipedia taxonomy/phylogenetic iPhylo
Notes:
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Information from sequence entries

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