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Rice Databases

Information Commons for Rice (IC4R) is a rice knowledgebase based on an extensible and sustainable architecture that achieves data integration through community-contributed modules. IC4R is designed for scalability and sustainability, integrating data from remote resources through web APIs and featuring collaborative integration of rice data from multiple committed modules and low costs for database update and maintenance.

OryGenesDB is an interactive tool for rice reverse genetics.The aim of this Oryza sativa database was first to display sequence information resulting from the activities of our group, such as the T-DNA and Ds flanking sequence tags (FSTs) produced in the framework of the French genomics initiative Genoplante and the EU consortium Cereal Gene Tags. Later, we decided to link this information with related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data).

Gramene

Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Our goal is to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations.

The Oryzabase is a comprehensive rice science database established in 2000 by 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 MSU Rice Genome Annotation Project Database and Resource is a National Science Foundation project and provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes.

The Rice Annotation Project (RAP) was conceptualized in 2004 upon the completion of the Oryza sativa ssp.  japonica cv.  Nipponbare genome sequencing by the International Rice Genome Sequencing Project  with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence. One of the major objectives of this project is to facilitate a comprehensive analysis of the genome structure and function of rice on the basis of the annotation.

Rice Mutant Database (RMD) is developed by the Wuhan group of a joint national program, the National Special Key Program on Rice Functional Genomics of China, and maintained by the National Center of Plant Gene Research (Wuhan) at Huazhong Agricultural University. RMD currently (RMD update information) contains the information of approximate 129,000 rice T-DNA insertion (enhancer trap) lines generated by an enhancer trap system. Comprehensive information about mutant phenotypes, reporter-gene expression patterns, flanking sequences of T-DNA insertional sites, seed availability, and others are collected in the database. RMD can be searched by keywords, nucleotide sequence or protein sequence. This database provides three classes of functions: (1) identifying novel genes, (2) identifying regulatory elements, and (3) identifying pattern lines for ectopic expression (misexpression) of target gene at specific tissue or at specific growth stage.

The Rice TE Database has been developed at Arizona Genomics Institute. It collects repeated sequences and transposable elements (TEs) of several species of the Oryza (rice) genus, and the closely-related Leersia perrieri. Its goal is to assist and ease the repeat annotation - and consequent genomic analyses - of a multi-genome dataset developed for the Oryza Genome Evolution project, part of the International Oryza Map Alignment Project.

RiceVarMap provides comprehensive information of 6,551,358 single nucleotide polymorphisms (SNPs) and 1,214,627 insertions/deletions (INDELs) identified from sequencing data of 1,479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online queries and downloading. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various sub-populations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database provides a tool to compare any two accessions and identify the polymorphisms between them. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations.

RiceFREND is a gene coexpression database in rice based on a large collection of microarray data derived from various tissues / organs at different stages of growth and development under natural field conditions, and rice plants treated with various phytohormones. The gene expression data used for coexpression analysis can be accessed in the RiceXPro, a repository of gene expression profiles obtained by microarray analysis. RiceFREND is aimed at providing a platform for identification of functionally related genes in various biological pathways and/or metabolic processes.
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