Introduction to the Rice Genome Annotation Project

September 3, 2024 - The Rice Genome Annotation Project website has been updated. The genome browser has been updated to Jbrowse2. The gene expression and coexpression data and webpages have also been updated. There is also a new syntelogs page with data for two new syntelog data sets. A new data download page has been released with the updated datasets and user friendly filenames and formats. The website has also been upgraded to use HTTPS for security and better compatibility with modern web browsers.

The Rice Genome Annotation Project Database was initially funded by the National Science Foundation project to provide sequence and annotation data for the rice genome. The September 2024 update was made through funding from the Georgia Research Alliance, Georgia Seed Development, and the University of Georgia

This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and our Genome Browser that provides an integrated display of annotation data.

Release 7 - Unified Rice Pseudomolecules

In cooperation with researchers at theAgrogenomics Research Center at the National Institute of Agrobiological Sciences, Tsukuba, Japan, we have prepared a final assembly of the rice pseudomolecules. These pseudomolecule sequences are now common to both the Rice Genome Annotation Project (RGAP) and the Rice Annotation Project Database (RAP-DB)/International Rice Genome Sequencing Project. This effort was undertaken in order to allow researchers to easily compare annotations from both projects. Gene loci, gene models and associated annotations created by RGAP and RAP-DB were independently derived, but the pseudomolecules used by the two rice annotation projects to generated those annotations are now identical and can be easily compared. A manuscript describing the generation of the final rice pseudomolecule assembly is in preparation.

Use of the Rice Genome Annotation Project (RGAP) Rice Gene Models by Other Websites/Databases

While many researchers utilize the RGAP loci, gene models and transcripts in their own databases and genome browsers, these sites may have outdated annotation and may have modified or further annotated our official gene set. All RGAP rice gene names are of the form LOC_Os##g##### as explained on our nomenclature page. RGAP rice genes are created using de novo gene predictions from Fgenesh followed by improvements and/or modifications by the PASA program which uses other de novo gene prediction software and rice full length cDNA and EST alignments. Our gene set is constructed entirely "in house" and is not equivalent to annotation from RefSeq, RAP, SwissProt or UniProt. Because we can not guarantee that data that is labeled as MSU/TIGR RGAP genes at other websites are really our data, we suggest that users always refer back to the Rice Genome Annotation Project for our genuine and current RGAP rice gene data.