The MSU Rice Genome Annotation Project Database and Resource is a National Science Foundation project and provides sequence and annotation data for the rice genome. Through these pages, you can view, search, and download our annotation of the rice genome. All of the data is freely available and comments on the data or improvements to these pages are welcome.

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.

A video tour of the MSU Rice Genome Annotation website is now available. The tour gives an introduction to the MSU Rice Genome Annotation Project and website, provides an overview of the Rice Genome Annotation and Community Annotation, and demonstrates the use of the Search Tools, Rice Genome Browser and Expression Tools.

While many researchers utilize the MSU 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 MSU rice gene names are of the form LOC_Os##g##### as explained on our nomenclature page. MSU 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 genes at other websites are really our data, we suggest that users always refer back to the MSU Rice Genome Annotation Project for our genuine and current MSU rice gene data.

We are please to announce release 6.1 of the Rice Pseudomolecules and Genome Annotation. The official release date for this version was June 3, 2009. Release 6.1 contains a number of minor improvements relative to release 6.0.

• A small set of genes (33) that had been classified as TE-related but that had been annotated by Community Annotators as being non-TE functional genes are no longer classified as TE-related.
• In Release 6.0, 121 TE-related genes were not properly flagged as being TE-related. Those genes have been reclassified as being TE-related.
• A new set of download files are available on the FTP site.
• The JGI Sorghum bicolor gene set has become available. Gene orthologs have been reanalyzed to include the new Sorghum bicolor genes. The Sorghum bicolor genes have been aligned to the rice pseudomolecules, and the Sorghum bicolor proteins were aligned to the rice proteome to determine best hit relationships. These data are displayed in the rice genome browser.

Release 6.0 contained numerous major improvements compared to release 5. Release 6.0 had been made public on January 30, 2009.

• The pseudomolecules had been reconstructed and improved by using newly updated BAC/PAC sequences and sequence reads from the Syngenta rice genome project. Additionally, information from the optical mapping work of Zhou et al. (2007) had been used to correct misassembled regions of the pseudomolecules from release 5.
• Updates to the structural and functional annotation of loci and gene models had been made.
• All tracks on the Rice Genome Browser had been updated and new tracks had been added to the Rice Genome Browser.
• Nuclear insertions of the organellar genome had been annotated.
• Orthologous gene relationships between rice, arabidopsis, poplar and grapevine had been predicted with OrthoMCL, and these data can be searched or viewed in the Rice Genome Browser.
• Pack MULEs identiied by Hanada et al. (2009) had been annotated on all chromosomes.

The Pseudomolecule Information Page has more information about the Release 6.1 pseudomolecules. The What's New page has a summary of the updates for the Rice Genome Annotation project web site and for the Rice Genome Browser.

The annotation of the rice genome is a continuing process. Because researchers who are directly involved in researching specific groups of genes are often the most capable of providing structural and/or functional annotation of those genes, we have an active community annotation project. We encourage rice scientists who would like to contribute functional or structural annotation data to contact us. Detailed information about contributing data can be found on the Community Annotation Information page. Detailed pages highlighting the annotation by gene family can be found on the Community Annotation Gene Families page. If you would like to participate or have questions/comments, please send an email to us: rice@plantbiology.msu.edu.

Researchers who wish to cite the Rice Genome Annotation Project website are encouraged to refer to our recent publications:

• Ouyang, S., Zhu, W., Hamilton, J., Lin H., Campbell, M., Childs, K., Thibaud-Nissen, F., Malek, R.L., Lee, Y., Zheng, L, Orvis, J., Haas, B., Wortman, J. and Buell, C.R. 2007. The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Research 35:D883-D887


• Yuan, Q., Ouyang, S., Wang, A., Zhu, W., Maiti, R., Lin, H., Hamilton, J., Haas, B., Sultana, R., Cheung, F., Wortman, J., and Buell, C.R. 2005. The Institute for Genomic Research Osa1 Rice Genome Annotation Database. Plant Physiology 138: 18-26