Users can research the phenotypic description of important rice genetically identified genes such as dwarfism, pest/disease resistance, cold/drought/salinity/nutrient deficiency tolerance, sterility, grain size/shape, seed dormancy and shattering. You can also determine how many alleles a particular gene has, research which germplasms contain a gene of interest, and also determine which traits and which anatomy parts and growth stages a particular gene has. Users can get nucleotide and protein sequence information via GenBank and Gene Product external and internal links. You can also determine a gene's position on a genetic map(s) and then further your research by determining which markers are most closely linked to it.

The major source that Gramene uses to select genes to curate is "List of the genes assigned to the respective linkage groups" in the publication: "Report of the Committee on Gene Symbolization, Nomenclature and Linkage Groups" found in the Rice Genetics Newsletter, volume 15, pp. 13-74, 1998. (see "http://www.gramene.org/newsletters/rice_genetics/rgn15/table_of_contents.html"). Gramene also works closely with Dr. Kinoshita and Oryzabase to add recently published genes into Gramene. (see http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp)

Gramene currently only contains information on rice genes, as well as maize genes integrated from MaizeGDB and a few sorghum genes.

Currently, Gramene covers most genes in rice found in publications through the year 2004, together with some cloned rice genes curated based on recent publications.

Gramene does not currently present gene information from non-published sources, such as personal communication.

You can find this by going to the Summary page for a gene of interest. You can find the "Allele" section by selecting "Allele and Germplasm" from the navigation bar above the "Summary for Rice Gene" section at the top of the page, or by scrolling down to the "Allele" section. Selecting any of the listed alleles will provide detailed information.

You can find this by going to the Summary page for a gene of interest and selecting "Allele and Germplasm" from the navigation bar above the "Summary for Rice Gene" section at the top of the page, or by scrolling down to the "Germplasm" section. Selecting any of the listed germplasms will provide detailed information.

The most rice genes identified from classical genetic studies have not been displayed on Gramene's rice Genomes. However, for some cloned genes, their associated TIGR loci have been annotated based on the sequence similarity comparision, and they have further been displayed on the Gramene TIGR sequence map.

Based on the phenotypic description and information from related publications, Gramene assigns the associated features using trait ontology (TO) terms and plant ontology(PO) terms (PO includes anatomy and growth stage) to describe the trait name, developmental stage and anatomy location. (see http://www.gramene.org/plant_ontology/)

You can find this by going to the Summary page for a gene of interest and selecting "References" from the navigation bar above the "Summary for Rice Gene" section at the top of the page, or by scrolling down to the "Reference" section.

No, Gramene does not provide seed stocks of germplasm with gene alleles. See "germplasm" on our resource page (http://www.gramene.org/resources/#germplasm).

Yes. Please see http://www.gramene.org/tutorials/genes.html

For gene names, we take annotations directly from TIGR. When we update to the newest TIGR some gene locii are lost, and others gained. An explanation of TIGRs gene nomenclature can be found at http://www.tigr.org/tdb/e2k1/osa1/tigr_gene_nomenclature.shtml