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Taxonomy browser (Oryza sativa Indica Group)

Oryza sativa Indica Group

Taxonomy ID: 39946 (for references in articles please use NCBI:txid39946)
current name
Oryza sativa Indica Group
includes:
Oryza sp. Poi-6
Genbank common name: long-grained rice
NCBI BLAST name: monocots
Rank: no rank
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:
heterotypic synonym
Oryza sativa (indica cultivar-group)
heterotypic synonym
Oryza sativa (indica group)
heterotypic synonym
Oryza sativa subsp. indica Kato
common name(s) Indian rice, Indica rice
Lineage( abbreviated )
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
   Entrez records   
Database name Subtree links Direct links
Nucleotide 520,235 518,320
Protein 47,649 47,418
Structure 13 13
Genome 1 1
Popset 872 872
Conserved Domains 1 1
GEO Datasets 1,640 1,631
PubMed Central 42 42
Gene 305 305
SRA Experiments 4,332 4,258
GEO Profiles 57,381 57,381
Protein Clusters 56 56
Identical Protein Groups 41,656 41,647
Bio Project 243 241
Bio Sample 3,411 3,384
Assembly 28 25
Probe 4,813 4,813
Taxonomy 2 1

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, 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
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.
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.
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.
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.

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
dryaddb supplemental materials Dryad Digital Repository
24 records from this provider organism-specific Genomes On Line Database
Show Biotic Interactions taxonomy/phylogenetic Global Biotic Interactions
OMA taxonomy/phylogenetic OMA Browser: Orthologous MAtrix
Oryza sativa subsp. indica Kato taxonomy/phylogenetic USDA-ARS GRIN Taxonomy
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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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