Oryza sativa has two major cultivated species; indica, a variety of long grain rice and japonica, a short grain variety. O. sativa indica was domesticated within a region south of the Himalaya mountains and O. sativa japonica was domesticated in southern China. Both cultivars share another feature in that each have been the subject of large scale genome sequencing projects.

The Beijing Genomics Institute initiated a whole genome shotgun sequencing project in 2000 with the working draft produced in late 2001. We have downloaded the draft sequence from Rice GD to search for putative orthologs of japonica chromatin-associated proteins. We started with the predicted proteins available at that site and improved transcript models using fgenesh+ licensed from Softberry.

The set of indica proteins is not complete, as compared to japonica (use the “Protein Group Counts” on the homepage side tool bar to make a comparison). In addition, we have posted a number of partial proteins. The partial dataset is due, in part, to gaps in the genomic sequence draft and sequence errors. We will continue to update indica proteins as new sequence information is available.