Database maintenance site: The University of Tokyo Graduate School of Frontier Sciences
Organism(s) covered:Oryzias latipes
Description: This is a browser for the Medaka (Oryzias latipes) genome. The site allows users to perform BLAST searches or query by ID. Data is also available for download.Show Details...
Closed
Probe
Database maintenance site: NCBI (National Center for Biotechnology Information)
Description: This database contains information on amino acid sequences and their functions. It is composed of four core databases, UniProtKB, UniRef, UniParc, and Proteomes. UniProtKB conta...Show Details...
Database maintenance site: NCBI (National Center for Biotechnology Information)
Organism(s) covered:All
Description: This database contains sets of transcriptional sequences obtained from the same locus. It includes information such as the homology between transcripts and the reference protein...Show Details...
Description: UCSC Genome Browser is a database which contains the reference sequence and working draft assemblies for a large collection of genomes. It is also a portal site to the ENCODE an...Show Details...
Database maintenance site: Kyushu Institute of Technology
Organism(s) covered:
Description: TRSIG is a database of mRNA sequence elements that influence translation events. The database contains signals such as regulatory elements and caps. The database can be searched...Show Details...
Closed
TraP: Transcription Product Database
Database maintenance site: AIST (National Institute of Advanced Industrial Science and Technology)
Description: This database compares a number of metabolic pathways in a group of seven single-celled microorganisms (also called archaea) namely the citric acid cycle, the energy producing g...Show Details...
Database maintenance site: RIKEN BRC (RIKEN BioResource Research Center)
Organism(s) covered:Arabidopsis thaliana
Description: This database of Arabidopsis transposon mutants can be searched by line ID or gene model ID to locate available mutants, which can be ordered for further study.Show Details...
Description: Transpogene is a database that focusses on how the transcriptome of 7 species are influenced by transposed elements (TEs).It consists of a collection of TEs, which are located i...Show Details...
Database maintenance site: Nara Institute of Science and Technology
Organism(s) covered:Escherichia coli
Description: This database contains three working data tables displaying the effect of genes from a particular category on organismal characteristics, based on transcriptome analysis of the ...Show Details...
Description: TP-Search is an integrated database on drug transporters, which are thought to play an important role in the pharmacokinetics of drugs. This database contains information extrac...Show Details...
Database maintenance site: RIKEN BRC (RIKEN BioResource Research Center)
Organism(s) covered:Nicotiana tabacum
Description: This database of tobacco cDNA clones contains 5' and 3' sequence information for each clone, generated from BY-2 cells. Users can search by gene or clone information, or locate ...Show Details...
Database maintenance site: Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology
Organism(s) covered:Homo sapiens
Description: TMIG-2DPAGE Database is a database of aging-related proteome of human cells. This database contains information for investigating molecular mechanisms involved in cellular aging...Show Details...
Database maintenance site: Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University
Organism(s) covered:Rattus norvegicus
Description: NBRP-Rat is a database for collection, preservation and supply of rat strains with phenotypic and genotypic profiles. NBRP-Rat contains standardized strains as well as many muta...Show Details...
Database maintenance site: Nara Institute of Science and Technology Graduate School of Biological Sciences
Organism(s) covered:Mus musculus
Description: NAISTrap is a database of gene-trapped ES cell lines generated by a gene trapping method termed UPATrap. Each entry consists of following 7 items; the clone number, name of the ...Show Details...
Description: Species 2000 is a collection of all the species in the world (microbes, fungi, plants and animals).The data is obtained, and made available by combining a comprehensive number o...Show Details...
Database maintenance site: Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences
Organism(s) covered:
Description: SPAD is a database of protein signaling cascades with pathway diagrams for a limited number of extracellular signaling pathways in three broad areas: growth factors, cytokines, ...Show Details...
Database maintenance site: NCBI (National Center for Biotechnology Information)
Organism(s) covered:Homo sapiens
Description: dbSNP collects information on polymorphisms based on single and small-scale multi-base substitutions, including insertions and deletions, microsatelites, and non-polymorphic var...Show Details...
Database maintenance site: National Institute of Genetics
Organism(s) covered:Homo sapiens | Pan troglodytes | Pan paniscus | Gorilla gorilla | Pongo pygmaeus | ...
Description: Silver Project: Ape Genome Sequencing is a repository of ape nucleotide sequences maintained by Division of Population genetics, National Institute of genetics (NIG). This datab...Show Details...
Database maintenance site: National Institute of Genetics
Organism(s) covered:Bombyx mori
Description: Silkworm Base is a database of silkworm resources including eggs, larvae, pupas, cocoons and cloned DNA established by Kyushu University and National Institute of genetics. Silk...Show Details...
Database maintenance site: The University of Tokyo
Organism(s) covered:Bombyx mori | Samia ricini | Bombyx mandarina
Description: SilkBase is a database of expressed genes from Bombyx mori and the related species Samia cynthia ricini and Mandarina fosimid. The database contains thousands of EST reads from ...Show Details...
Description: This is an integrated database for budding yeast Saccharomyces cerevisiae. It contains search and analysis tools based on genes, sequences, and functions, as well as information...Show Details...
Description: Sugi Genome Database is a database for genome of sugi (Cryptomeria japonica) and a Japanese conifer (Chamaecyparis obtusa). It provides information about EST, DNA markers, a lin...Show Details...
Database maintenance site: MRC (The Medical Research Council) Laboratory of Molecular Biology
Organism(s) covered:
Description: SCOP2 is a database for organizing structurally characterized proteins according to their structural and evolutionary relationships. In this database, proteins are organized acc...Show Details...
Database maintenance site: The University of Tokyo Graduate School of Frontier Sciences
Organism(s) covered:Saccharomyces cerevisiae
Description: SCMD is a database of micrographs of budding yeast with thousands of images of mutant strains and results from automated data mining analysis of several parameters of these muta...Show Details...
Database maintenance site: The University of Tokyo Research Center for Advanced Science and Technology
Organism(s) covered:Homo sapiens
Description: SBM DB is comprehensive database of gene expression profiles. This database is constructed with three databases; 1) RefExA is a comprehensive gene expression database of Human n...Show Details...
Database maintenance site: RIKEN Tsukuba Institute
Organism(s) covered:Arabidopsis thaliana
Description: SASSC is a search tool for finding Arabidopsis mutant seed lines. The site consists of a search box that can be used to locate genes of interest, retrieve information on mutant ...Show Details...
Database maintenance site: National Institute of Agrobiological Sciences
Organism(s) covered:Oryza sativa
Description: RMOS is a database of comprehensive information for Rice Microarray Project (April 1999 - March 2003). In addition to microarray data, users can also find information of the gen...Show Details...
Database maintenance site: NARO (National Agriculture and Food Research Organization)
Organism(s) covered:Oryza sativa
Description: This site contains information on the mitochondrial genome of rice, including sequences and physical maps.The original site (http: //rmg.rice.dna.affrc.go.jp/) has been closed. ...Show Details...
Database maintenance site: RIKEN BRC (RIKEN BioResource Research Center)
Organism(s) covered:Arabidopsis thaliana
Description: This database contains Arabidopsis thaliana cDNA sequences that users can query to obtain full clone sequences, particularly from AGI-coded data. The sequence coverage is select...Show Details...
Database maintenance site: NARO (National Agriculture and Food Research Organization)
Organism(s) covered:Oryza sativa
Description: This database is a collection of two-dimensional electrophoretic gel spots obtained using various tissues of rice and subcellular organelles. A variety of protocols related to p...Show Details...
Description: RhizoBase is a database of rhizobia sequence resources for users to obtain genomic information and perform searches. There are 22 currently available species, and in addition to...Show Details...
Database maintenance site: Medical College of Wisconsin/Bioinformatics Research Center
Organism(s) covered:Rattus norvegicus
Description: This is a comprehensive site for rat genome researches. In addition to information on rat genes, the site contains information on rat strains, data on rat models for disease, an...Show Details...
Description: RefSeq is a database of standard reference genomic, transcript, and protein sequences. The database contains consensus sequence data for over 20,000 organisms and over 27 millio...Show Details...
Database maintenance site: RIKEN (The Institute of Physical and Chemical Research)
Organism(s) covered:Mus musculus
Description: READ is a database of mouse expression studies that allows users to explore gene expression patterns in up to 49 mouse tissues. In addition to gene data, users can also use READ...Show Details...
Description: REACTOME is a database of human pathways for basic research, genome analysis, pathway modeling, systems biology and education. It contains manually curated and peer-reviewed pat...Show Details...
Database maintenance site: Michigan State University
Organism(s) covered:Archaea | Bacteria
Description: This database is a collection of rRNA sequences for fungai, bacteria and archaea. The site provides a variety of analytical tools, including rRNA sequence alignments, similarity...Show Details...
Database maintenance site: RIKEN CSRS (RIKEN Center for Sustainable Resource Science)
Organism(s) covered:Arabidopsis thaliana
Description: The RARGE database was created to enhance the RIKEN Arabidopsis resource, which provides full-length cDNAs, transposon mutants and microarray experiments. Users can search BLAST...Show Details...
Database maintenance site: NARO (National Agriculture and Food Research Organization)
Organism(s) covered:Oryza sativa
Description: This database contains highly accurate annotations on the rice genome provided by the rice annotation project (RAP). Literature-based annotation data will be updated a few times...Show Details...
Closed
RAD: Rice Annotation Database
Database maintenance site: NARO (National Agriculture and Food Research Organization)
Database maintenance site: National Institutes of Biomedical Innovation, Health and Nutrition
Organism(s) covered:Macaca fascicularis
Description: QFbase is a cDNA database of the crab-eating macaque (Macaca fascicularis). QFbase contains EST and full-length sequences of macaque cDNAs obtained from brain, testis, bone marr...Show Details...
Database maintenance site: NCBI (National Center for Biotechnology Information)
Organism(s) covered:
Description: This database contains bibliographic information from journal articles in the field of life science as well as MEDLINE (title, authors, journal name, abstracts). Links are provi...Show Details...
Description: Pseudogene.org is a comprehensive database of identified pseudogenes, utilities used to find pseudogenes, various publication data sets and a pseudogene knowledgebase. It contai...Show Details...
ProTherm: Thermodynamic Database for Protein and Mutants
Database maintenance site: Kyushu Institute of Technology
Organism(s) covered:
Description: The data in the ProTherm database include thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc., for wild...Show Details...
ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions
Database maintenance site: Kyushu Institute of Technology
Organism(s) covered:
Description: The ProNIT database provides data on experimentally determined thermodynamic interactions between proteins and nucleic acids. The properties of the interacting protein and nucle...Show Details...
Description: ProMode-Elastic is a database of normal mode analysis of PDB data using elastic network model in torsional angle space. Normal mode analysis are performed by unique developed pr...Show Details...
Database maintenance site: Rhone-Alpes Bioinformatics Center
Organism(s) covered:
Description: ProDom is an extensive database providing information on protein domain families.It was created automatically by performing a global comparison of all the protein sequences that...Show Details...
Database maintenance site: Protein Research Foundation
Organism(s) covered:
Description: PRF is a collection of the information related to amino acids, peptides and proteins and making databases. It consists of there databases; Literature Database (PRF/LITDB), Pepti...Show Details...
Database maintenance site: Kyushu University Medical Institute of Bioregulation
Organism(s) covered:Homo sapiens
Description: Polymorphism of Microsatellite Markers is a database of genotypic information on microsatellite loci in the Japanese population. This database contains data on location, heteroz...Show Details...
