Documentation

Rice Genes and Alleles Database (RGAD) Help Document

Rice Genes and Alleles Database Search

Search: You can search rice genes and alleles database using gene symbol, gene name or Gramene accession number. You can also do browse search using gene symbol shown in alphabetical order.

Rice Genes and Alleles Page

General information:
- Gene name: Traditional gene name has been used. Some gene names have been modified according to the Gene Nomenclature system.
- Gene symbol: Gene symbol has been assigned following the Gene Nomenclature System.
- Gene synonym: List of names or symbols that have been used for a specific gene.
- Phenotypic description: Text defines the primary visual feature used to detect mutant phenotype for particular gene and distinguish it from wild type.
- Mutant image: Display image(s) and text explanation of mutant for a particular gene, if available.

Gene identity and gene product:
- Gene identity: Provide the link to NCBI, if related GI number available.
- Gene product: Provide the link to Rice Protein Database, if link available.

Allele: show one or multiple allele name(s) for the particular gene. The detail information for specific allele can be displayed while you chick that allele name.
- Allele designation: Different alleles of the same mutant gene are distinguished by a point between the name of the gene and the number that follows, e.g., gle1.1. The synonyms for that allele are also listed following allele designation.
- Allele description: If alleles give phenotypic differences.
- Description of allelic interaction: If information about the interaction with other alleles or loci is available.
- Study: List of one or several study (studies) or assay(s) for that particular allele. The detail information for specific study can be displayed while you chick that study name.
  - Study name: Constructed of [name of first auther, principal investigator, or institution] + [year of publication or data submission] + [a, b, c . . .] to differentiate among multiple studies for the same investigator and year.
  - Year: The year study was done. If not available in "Materials and Methods," the year of the publication will be used.
  - Season: The seasons in which the study was done.
  - Location: The nearest city, town or university and institute name where the study was done. If not available in "Materials and methods," first author or principal investigator's address will be used to derive the location.
  - Study type: Choices include field, greenhouse, growth chamber, and laboratory.
  - Environmental factors: Text description of environmental conditions for particular study, including temperature, light quality and intensity, moisture and nutrients, etc.

Map position: show closely linked markers, map name, chromosome number, start position and stop position on particular map.

Associated feature: One or multiple composite associated term(s) are used to define associated feature for the particular gene. The composite associated term consists of:
- Trait ontology term (TO)
- Developmental stage (PO)
- Anatomy location term (PO)
- Biological process term (GO)
- Evidence code

Oryzabase link: Provide the link to the curation page for same gene in Oryzabase , if available.

References Used for Curation: A list of all references related to the gene. It also gives an option to search in Gramene Literature database for all the references that may be associated with this entry.

Last modified: Tue Aug 7 17:44:38 2007