RGAP 7 Summary


Gene Annotation

Total loci55,986
Non-TE Loci
Number39,045
Gene models49,066
Gene size2,853 bp
Exons/gene4.9
Introns/gene3.9
TE Loci
Number16,941
Gene models17,272
Gene size3,223 bp
Exons/gene4.2
Introns/gene3.2

Genome Browser

83 tracks of annotation

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RGAP Updates


February 6, 2013
– A paper describing the unified Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules and MSU Rice Genome Annotation Project Release 7 has been published.

February 7, 2012
–The GFF3 and brief info files were updated on the FTP site. The update corrects issues with the UTR feature type and several cases where the mRNA coordinates were incorrect. The sequence files and other features in the GFF3 files were not changed.

October 31, 2011
–Release 7 of the MSU Rice Genome Annotation Project is available.
–This release is based on a new pseudomolecule assembly (Os-Nipponbare-Reference-IRGSP-1.0) made in collaboration with the Agrogenomics Research Center at the National Institute of Agrobiological Sciences, Tsukuba, Japan. This set of pseudomolecules unifies the previous MSU with the IRGSP/RAP effort.
–Genome browser has been updated with 81 tracks of data.
Orthologous group analysis has been updated to include Zea mays release 5b filtered gene models.


Maintenance Notice


We have planned server maintenance on the first Wednesday of every month. The Rice Genome Annotation Project web pages may be unavailable or only partially functional during server maintenance.

Introduction to the Rice Genome Annotation Project

Feb 6, 2013 - A paper describing the unified Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules and MSU Rice Genome Annotation Project Release 7 has been published in the journal Rice.

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.

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 the Agrogenomics 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 MSU Rice Genome Annotation Project 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 the MSU and RAP-DB projects. Gene loci, gene models and associated annotations created by MSU-RAP 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 MSU Rice Gene Models by Other Websites/Databases

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. Please note that while we can not prevent users from downloading our entire Genome Browser, we do not sponsor or approve of public re-display of our rice genome browser.





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


NSF Logo This work is supported by grants (DBI-0321538/DBI-0834043) from the National Science Foundation.