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Taxonomy browser (Oryza sativa Japonica Group)

Oryza sativa Japonica Group

Taxonomy ID: 39947 (for references in articles please use NCBI:txid39947)
Scientific name: Oryza sativa Japonica Group
Genbank common name: Japanese rice
Inherited 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:
synonym: Oryza sativa (japonica cultivar-group)
synonym: Oryza sativa subsp. japonica
common name: Japonica rice
Lineage( abbreviated )
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
   Entrez records   
Database name Subtree links Direct links
Nucleotide 142,949 138,792
Nucleotide EST 987,327 987,327
Nucleotide GSS 309,903 309,903
Protein 280,224 279,973
Structure 132 132
Genome 1 1
Popset 638 638
Conserved Domains 10 10
GEO Datasets 2,862 2,862
PubMed Central 97 97
Gene 94,869 94,869
SRA Experiments 3,677 3,677
GEO Profiles 22,575 22,575
Protein Clusters 15,558 15,558
Identical Protein Groups 142,340 142,321
Bio Project 963 963
Bio Sample 32,202 32,202
Bio Systems 514 514
Assembly 10 10
Probe 101,370 101,370
PubChem BioAssay 30 30
Taxonomy 4 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

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.


Genome Information

Genome view: 13 chromosomes
Names 1 2 3 4 5 6 7 8 9 10 11 12 Pltd
   Trace records (raw single-pass reads of DNA sequence)   
Sequencing Center Name
Record counts per type
CHIP OTHER PRIMERWALK SHOTGUN ALL
GSC - Genoscope
- 22,528 40,949 371,149 434,626
IRRI - The International Rice Research Institute
881,786 - - - 881,786
RGP - Rice Genome Research Program
- - - 6,285,199 6,285,199
SBI - Syngenta Biotechnology Inc
- - - 7,798,053 7,798,053
Totals per type
881,786 22,528 40,949 14,454,401 15,399,664

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
dryaddb supplemental materials Dryad Digital Repository
22 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
OMA taxonomy/phylogenetic OMA Browser: Orthologous MAtrix
WebScipio: Oryza sativa Japonica group organism-specific WebScipio - eukaryotic gene identification
5 records from provider organism-specific diArk - a resource for eukaryotic genome research
Notes:
Groups interested in participating in the LinkOut program should visit the LinkOut home page.
A list of our current non-bibliographic LinkOut providers can be found here.

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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