Overview

This is TIGR Release 5 of the annotation of the genome of the japonica subspecies of O.sativa. Please see TIGR and Ouyang, et. al. for more information.

Statistics

This release of Phytozome include TIGR release 5 of the Oryza sativa genome.

Genome

372Mb arranged in 12 chromosomes

Loci

56278 loci containing protein-coding transcripts

Transcripts

56470 protein-coding transcripts

Exploring Rice

Rice in the context of Green Plant evolution

Rice genes will be found in clusters defined at the Viridiplantae, Embryophyte, Tracheophyte, Angiosperm, and Grass nodes. If you know something about the rice gene you're interested in (e.g., its TIGR or RefSeq name, its gene symbol, a descriptive phrase), you can select "search" from the menu at the top of the page, enter your search terms, pick one of the above nodes (or All nodes), and search. The gene clusters you find can then be examined in detail, with summary pages that include descriptive and functional (domain) annotation, syntenic context, and links to each cluster's ancestors and descendants. If you don't have keyword information but do have a gene or gene product sequence, you can search for related gene clusters using BLAST (click on "search" and then select the BLAST tab).

The Rice Genome

Use the Browse the Genome button at the top of this page to view rice gene models in their full genomic context. Alternatively, if you'd like to search the genome for regions homologous to a particular sequence, use the BLAST against the genome button. The browsing environment, Gbrowse, provides overview and detailed views of gene structure. Gbrowse provides a search interface allowing you to look up rice models by TIGR name, RefSeq identifier, or location. Once you've located a gene model of interest, click on it to go to its detail page (e.g, here). The detail page provides sequence information on the model and its translated peptide. From the detail page you can also jump to viewing rice genes in their evolutionary context. To see this gene's orthologs at the Angiosperm node, click on the Cluster link on the detail page. If you'd like to see what other ancestral gene's share sequence similarity with this gene, click on the detail page's Phytozome BLAST link, which will pull up similar gene clusters at whichever Phytozome node you choose.

Downloading Data

CDS and peptide sequence for individual genes is available from the details page of the rice Gbrowse environment. To get there from a Cluster Summary page, however, you'll need to click the "Display Options" tab and make sure that "Reference ID" column is selected. Then expand all the "Genes in the Cluster" rows (by clicking on the icon near the Org heading) and click on the "[PAC]" link, which will take you to the detail page for that model. You can also get gene sequences for all the members of one or more clusters from any Cluster Summary, Phytozome BLAST results, or Search Results page, by launching Jalview (by clicking links for Multiple Sequence Alignments"), which will provide access to CDS sequence or peptide sequence of the members of the gene clusters you selected. If you're are interested in bulk downloads of all data (gene models, proteomes, genomic sequence), this is available directly from TIGR.