NAR Molecular Biology Database Collection entry number 90
Yamazaki, Y.1, Yoshimura, A.3, Nagato, Y.2, Yamakawa, T.1, Kurata, N.4
1Center for Genetic Resource information, National Institute of Genetics
2University of Tokyo
3Kyushu University
4Genetic Strain Research Center, National Institute of Genetics

Database Description

The Oryzabase is a comprehensive rice science database established in collaboration with the rice researcher's committee in Japan. The database is originally aimed to gather as much knowledge as possible ranging from classical rice genetics to recent genomics and from fundamental information to hot topics. The current Oryzabase consists mainly of six components: (1) genetic resource stock information, (2) gene dictionary, (3) genetic maps, (4) mutant phenotype collection, (5) developmental stage and gene expression, and (6) fundamental knowledge of rice science. The database is a compilation of around 11000 strains collected or developed by classical breeding and/or new molecular biological methods, as a result of a long history of rice breeding in Japan. Oryzabase also provides "Core Collections of Wild Rice" to show representative wild rice accessions, which cover nine different genomes and nineteen different species. Oryzabase provides several linkage maps and physical maps, including the latest information published by the Rice Genome Project. Common genes and/or markers located on two or more maps are automatically updated with a link to new release genomic sequences. The gene dictionary has been constantly updated by specialists coupled with the activity of the Rice Gene Cooperative. All genes in the dictionary have GO-ID (Gene Ontology ID). In the database, developmental stages for each organ have been defined precisely according to the stage-specific events and information about the expressed genes for each stages have bene compiled, although this project is still in the trial stage. Oryzabase is available from http://www.shigen.nig.ac.jp/rice/oryzabase/.

Category: Plant databases
Subcategory: Rice

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