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Rice Genome Annotation

Database and resource that 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. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes

URL: http://rice.plantbiology.msu.edu/

Resource ID: nif-0000-31459     Resource Type: Resource     Version: Latest Version

Keywords

rice, oryza sativa, maize, corn, zea mays, wheat, triticum aestivum, gene, genome, annotation

Additional Resource Types

Database, Data Analysis Service

Availability

Acknowledgement requested

Old URLs

http://rice.plantbiology.msu.edu/pseudomolecules/info.shtml

Species

rice

Abbreviation

Osa1

Synonyms

Rice Genome Annotation Project, MSU Rice Genome Annotation Project Database and Resource

Parent Organization

Supercategory

Resource

Funding Information

NSF, DBI-0321538, DBI-0834043

Listed By

OMICtools

Alternate URLs

http://rice.tigr.org

Alternate IDs

OMICS_01563

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 21, 2010

Originated From

SciCrunch

Changes from Previous Version

  • Description was changed
  • Additional Resource Types was changed

Version 2

Created 3 weeks ago by Christie Wang

Version 1

Created 5 years ago by Anonymous

The TIGR Rice Genome Annotation Resource: improvements and new features.

  • Ouyang S
  • Nucleic Acids Res.
  • 2007 4

In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42,653 non-transposable element-related genes encoding 49,472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13,237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31,739 gene models), representing approximately 50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.