Other Useful Links
- Rice Genome Annotation Project
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. These data are available through search pages and Genome Browser that provides an integrated display of annotation data.
- RAP-DB | Home
- Rice Database
This database is part of NIAS DNA Bank which was established in 1994 as a section of the MAFF Genebank System in-charge of the management of DNA materials and information. The major thrust of its activities focuses on the collection and distribution of DNA materials from agricultural organisms (both plants and animals), materials derived from researches in molecular genetics, and associated genomics information.
- Gramene: A comparative resource for plants | Gramene
Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. This databaase 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.
- TIGR Rice Genome Annotation
The TIGR Rice Genome Project BLAST server has a collection of databases for use in searching with the BLAST programs blastn, blastx, tblastn, or tblastx. There are a total of 24 databases to search.
- RiceGE: Rice Functional Genomic Express Database
The TIGR Rice Genome Project BLAST server has a collection of databases for use in searching with the BLAST programs blastn, blastx, tblastn, or tblastx. There are a total of 24 databases to search.
- MOsDB: rice genome database - Mips
The MOsDB is a resource for publicly available sequences of the rice (Oryza sativa L.) genome. Rice is an experimental model for the cereal crops research and an agriculturally important plant, providing food for more than half of the world population. MOsDB provides all available data about rice genes and genomics, including (in the future) mutant information and expression profiles. At this moment, the MOsDB database includes current (updated on daily basis) published sequences and gene annotation information of two Oryza sativa subspecies: japonica and indica.
- OryGenesDB: a database 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...).
- Rice DB | Oryza Portal | Home
Rice DB Oryza sativa database, lets you search and display gene identifiers, functional & proteomic annotations, subcellular localisation, phenotypes and upstream transcription motifs.
- Rice Oligonucleotide Array Database
Rice Oligonucleotide Array Database (ROAD) is a public resource for gene expression and coexpression analysis in rice, the most important staple food over the world. Over 1,000 microarray slides were incorporated and several kinds of analysis tools are available in ROAD.
- BGI Rise Rice Genome Database
The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis, and biological research of the rice genome. Our Rice Information System (BGI-RIS) is targeted to be the most up-to-date integrated information resource for rice genomes as well as a workbench for comparative genomic analysis among cereal crops.
- Oryza sativa Genome DB - PlantGDB
The plantgdb.org web resource is currently being managed as part of an NSF-funded project (IOS-1126267) to develop robust genome annotation methods, tools, and standard training sets for the plethora of plant genomes currently or soon to be sequenced.
- RiceChip Annotation Site
Support for Annotation & Functional Analysis of the Oryza sativa (Rice) Genome
- Rice Mutant Database
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.
- RiceSRTFDB - National Institute of Plant Genome Research
The Rice Stress-Responsive Transcription Factor Database (RiceSRTFDB) has been developed with the view to provide most comprehensive information about the expression patterns of rice TFs during water-deficit and salinity stress conditions and various stages of development. The database provides information about the cis-regulatory elements located in the promoters of TFs and Tos17 mutant information.
- DRTF - Database of Rice Transcrption Factor
The Database of Rice Transcription Factors (DRTF) is a collection of known and predicted transcription factors of Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. DRTF currently contains 2,025 putative transcription factors (TF) gene models in indica and 2,384 in japonica, distributed in 63 families.
- Oryzabase - SHIGEN
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.