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Gene nomenclature

Rice gene nomenclature

Since the International Rice Genome Sequencing Project (IRGSP) completed the genome sequencing of Oryza sativa L. ssp. japonica cultivar Nipponbare, it was anticipated to decipher all of the genic regions in the genome. Systematic locus identifiers were assigned to the RAP loci on the IRGSP genome assembly. An ID (OsXXg#######) consists of the species name (Os for Oryza sativa), a two-digit number for chromosomes, the type of an identifier (g for genes), and a seven-digit number that indicates a sequential order of loci in a chromosome. This nomenclature was proposed by the Committee on Gene Symbolization, Nomenclature and Linkage in the First and Second Rice Annotation Project Meetings, modified on the basis of intensive discussions, and then approved by IRGSP/RAP. The RAP annotations with the Os identifiers were submitted to DDBJ/EMBL/Genbank under the accession numbers of AP008207-AP009218, and used in RefSeq. The Os code is used also in UniProtKB/Swiss-Prot as a locus identifier. For details, see the following paper.

Susan R. McCouch and CGSNL "Gene nomenclature system for rice" Rice (2008)

Please note that the MSU rice database (formerly known as TIGR osa1) employs a similar system (LOC_Os IDs), but they differ from our Os identifiers. The IDs can be converted at the ID Converter page. A table of the LOC_Os IDs corresponding to the Os IDs is available at the data download page. However, the MSU loci were determined by a different method on a different genome assembly (MSU's genome), so that the corresponding RAP and MSU transcripts may not have the same nucleotide sequence.