Oryza sativa Indica Assembly and Gene Annotation

About Oryza sativa Indica

Oryza sativa Indica is one of the two most commonly cultivated sub-species of rice (along with O. sativa Japonica) and is the most widely grown in the hot climates of Southern Asia. The genome of Indica is very similar to that of Japonica, which is generally restricted to temperate climes such as Japan.


The genome of Oryza sativa Indica Group cultivar 93-11 was sequenced by the Beijing Genome Institute (BGI) following a whole-genome shotgun strategy [1].


Gene annotations were predicted by BGI using Glean as released on 10-28-2008. This browser presents data from the 2010 release of the BGI RISe Rice Information System[2].


  • Probes from the Rice Genome Array for two rice cultivars were aligned to the genome.


Two sources of variation data from NCBI dbSNP has been mapped onto the genome assembly:

  1. SNPs called from the comparison of Oryza sativa Indica and Oryza sativa Japonica, and
  2. SNPs resulting from OMAP project alignments between O. glaberrima, O. punctata, O. nivara, and O. rufipogon agains O. sativa Japoinca mapped to O. sativa indica.



  1. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
    Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al. 2002. Science. 296:79-92.
  2. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
    Zhao W, Wang J, He X, Huang X, Jiao Y, Dai M, Wei S, Fu J, Chen Y, Ren X et al. 2004. Nucleic Acids Res.. 32:D377-82.

More information

General information about this species can be found in Wikipedia.



AssemblyASM465v1, INSDC Assembly GCA_000004655.2, Jan 2005
Database version93.2
Base Pairs411,710,190
Golden Path Length427,004,890
Genebuild byBGI
Genebuild methodImported from BGI
Data sourceRIS

Gene counts

Coding genes40,745
Non coding genes48,978
Small non coding genes43,562
Long non coding genes240
Misc non coding genes5,176
Gene transcripts89,723


FGENESH gene prediction59,695
Short Variants5,045,108

About this species