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Taxonomy browser (Oryza sativa Japonica Group)

Oryza sativa Japonica Group

Taxonomy ID: 39947
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)
Other names:
synonym: Oryza sativa subsp. japonica
synonym: Oryza sativa (japonica cultivar-group)
common name: Japonica 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; Oryza sativa
   Entrez records   
Database name Subtree links Direct links
Nucleotide 138,435 134,437
Nucleotide EST 987,327 987,327
Nucleotide GSS 309,903 309,903
Protein 278,384 278,191
Structure 115 115
Genome 1 1
Popset 632 632
Domains 10 10
GEO Datasets 2,471 2,471
PubMed Central 285 285
Gene 90,926 90,926
SRA Experiments 2,518 2,518
Probe 101,369 101,369
Assembly 8 8
Bio Project 889 889
Bio Sample 31,350 31,350
Bio Systems 514 514
GEO Profiles 22,575 22,575
PubChem BioAssay 30 30
Protein Clusters 11,761 11,761
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=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 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 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 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 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
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Show Biotic Interactions taxonomy/phylogenetic Global Biotic Interactions
Related Immune Epitope Information gene/protein/disease-specific Immune Epitope Database and Analysis Resource
WebScipio: Oryza sativa Japonica group A123 organism-specific WebScipio - eukaryotic gene identification
WebScipio: Oryza sativa Japonica group organism-specific
diArk: Oryza sativa Japonica group organism-specific diArk a resource for eukaryotic genome research
diArk: Oryza sativa Japonica group HEG4 organism-specific
diArk: Oryza sativa Japonica group Nipponbare organism-specific
diArk: Oryza sativa Japonica group A123 organism-specific
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Information from sequence entries

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