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Taxonomy browser (Oryza sativa Indica Group)

Oryza sativa Indica Group

Taxonomy ID: 39946
Genbank common name: long-grained rice
Inherited blast name: monocots
Rank: no rank
Genetic code: Translation table 1 (Standard)
Mitochondrial genetic code: Translation table 1 (Standard)
Other names:
synonym: Oryza sativa subsp. indica
synonym: Oryza sativa (indica group)
synonym: Oryza sativa (indica cultivar-group)
common name: Indica rice
common name: Indian rice
includes: Oryza sp. Poi-6
authority: Oryza sativa subsp. indica Kato
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; Oryza sativa
   Entrez records   
Database name Subtree links Direct links
Nucleotide 54,168 52,430
Nucleotide EST 205,482 205,482
Nucleotide GSS 259,694 259,694
Protein 47,025 46,866
Structure 9 9
Genome 1 1
Popset 832 832
GEO Datasets 1,224 1,224
PubMed Central 106 106
Gene 305 305
SRA Experiments 1,837 1,795
Probe 4,812 4,812
Assembly 15 14
Bio Project 122 121
Bio Sample 1,166 1,165
GEO Profiles 57,381 57,381
Protein Clusters 53 53
Taxonomy 2 1

Comments and References:

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

Reference to PubMed documentKovach MJ et al. 2009
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732888/?tool=pubmedKovach 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 documentSweeney M & McCouch S 2007
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759204/?tool=pubmedSweeney M and McCouch S. 2007. The complex history of the domestication of rice. Annals of Botany 100(5): 951-957.

Reference to PubMed documentCaicedo AL et al. 2007
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994709/?tool=pmcentrezCaicedo 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 documentGarris et al. 2005
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449546/?tool=pubmedGarris 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.


Genome Information

   Trace records (raw single-pass reads of DNA sequence)   
Sequencing Center Name
Record counts per type
CHIP SHOTGUN ALL
BGI - Beijing Genome Institute
- 6,423,393 6,423,393
IRRI - The International Rice Research Institute
1,102,237 - 1,102,237
Totals per type
1,102,237 6,423,393 7,525,630

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
dryaddb supplemental materials Dryad Digital Repository
GOLD: Go0017152 organism-specific Genomes On Line Database
GOLD: Go0087562 organism-specific
GOLD: Go0139366 organism-specific
GOLD: Go0139365 organism-specific
GOLD: Go0144231 organism-specific
GOLD: Go0144232 organism-specific
GOLD: Go0139364 organism-specific
GOLD: Go0008025 organism-specific
GOLD: Go0008106 organism-specific
GOLD: Go0008061 organism-specific
GOLD: Go0000696 organism-specific
GOLD: Go0008105 organism-specific
GOLD: Go0008104 organism-specific
GOLD: Go0008060 organism-specific
GOLD: Go0017199 organism-specific
GOLD: Go0008107 organism-specific
GOLD: Go0008825 organism-specific
GOLD: Go0008028 organism-specific
GOLD: Go0017197 organism-specific
GOLD: Go0008064 organism-specific
GOLD: Go0008108 organism-specific
Show Biotic Interactions taxonomy/phylogenetic Global Biotic Interactions
Oryza sativa subsp. indica Kato taxonomy/phylogenetic USDA-ARS GRIN Taxonomy
WebScipio: Oryza sativa Indica group organism-specific WebScipio - eukaryotic gene identification
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.


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