Link to NCBI Front Page Taxonomy Logo
Entrez PubMed Nucleotide Protein Genome Structure PMC Taxonomy BioCollections
   
Taxonomy browser (Oryza sativa Japonica Group)

Oryza sativa Japonica Group

Taxonomy ID: 39947 (for references in articles please use NCBI:txid39947)
current name
Oryza sativa Japonica Group
Genbank common name: Japanese 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 (japonica cultivar-group)
heterotypic synonym
Oryza sativa subsp. japonica
common name(s) Japonica 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 1,445,596 1,439,246
Protein 333,036 330,551
Structure 189 189
Genome 1 1
Popset 662 662
Conserved Domains 7 7
GEO Datasets 4,532 4,532
PubMed Central 151 151
Gene 94,898 94,898
SRA Experiments 21,035 20,982
GEO Profiles 22,575 22,575
Protein Clusters 15,558 15,558
Identical Protein Groups 155,791 155,754
BioProject 1,311 1,306
BioSample 44,632 44,613
Assembly 19 16
PubChem BioAssay 42 42
Taxonomy 4 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
Zhao K et al. 2010, doi:10.1371/journal.pone.0010780
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
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.
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.
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.
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.

Genome Information

Genome view: 13 chromosomes
Names 1 2 3 4 5 6 7 8 9 10 11 12 Pltd

External Information Resources (NCBI LinkOut)

LinkOut Subject LinkOut Provider
2 records from this provider 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

Show organism modifiers



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. PubMed: 32761142 PMC: PMC7408187.


Comments and questions to info@ncbi.nlm.nih.gov

[Help] [Search] [NLM NIH] [Disclaimer]