Gene Nomenclature System for Rice

The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative has revised the gene nomenclature system for rice (Oryza) to take advantage of the completion of the rice genome sequence and the emergence of new methods for detecting, characterizing, and describing genes in the biological community. This paper outlines a set of standard procedures for describing genes based on DNA, RNA, and protein sequence information that have been annotated and mapped on the sequenced genome assemblies, as well as those determined by biochemical characterization and/or phenotype characterization by way of forward genetics. With these revisions, we enhance the potential for structural, functional, and evolutionary comparisons across organisms and seek to harmonize the rice gene nomenclature system with that of other model organisms. Newly identified rice genes can now be registered on-line at http://shigen.lab.nig.ac.jp/rice/oryzabase_submission/gene_nomenclature/.

• Publication year

  2008

• Venue

  Rice

• Publication date

  2008-08-15

• Fields of study

  Biology, Agricultural and Food Sciences

• Identifiers
  DOI 10.1007/s12284-008-9004-9
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

  2007cited by this paper
• Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes

  2006cited by this paper
• Gramene: a bird's eye view of cereal genomes

  2005cited by this paper
• The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza.

  2005cited by this paper
• The map-based sequence of the rice genome

  2005cited by this paper
• The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

  2005cited by this paper
• The Institute for Genomic Research Osa1 Rice Genome Annotation Database1

  2005cited by this paper
• Genew: the Human Gene Nomenclature Database, 2004 updates

  2004cited by this paper
• InterPro, progress and status in 2005

  2004cited by this paper
• A guide to naming sequenced plant genes

  2004cited by this paper
• BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

  2004cited by this paper
• The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists

  2003cited by this paper
• MOsDB: an integrated information resource for rice genomics

  2003cited by this paper
• Gramene: Development and Integration of Trait and Gene Ontologies for Rice

  2002cited by this paper
• A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)

  2002influential reference
• A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).

  2002cited by this paper
• Genew: the Human Gene Nomenclature Database

  2002cited by this paper
• A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

  2002cited by this paper
• Toward a cytological characterization of the rice genome.

  2001cited by this paper
• Guidelines for genetic nomenclature and community governance for the model legume Medicago truncatula.

  2001cited by this paper
• IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) and Nomenclature Committee of IUBMB (NC-IUBMB).

  1997cited by this paper
• Report of committee on gene symbolization, nomenclature and linkage groups

  1995cited by this paper
• Enzyme nomenclature — Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology: Academic Press Ltd, London, UK, 1992. xiii + 862 pp. Price £40.00. ISBN 0-12-227165-3

  1994cited by this paper
• Guidelines

  1994cited by this paper
• On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA".

  1992cited by this paper
• Rice karyotype, marker genes, and linkage groups.

  1991cited by this paper

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