Welcome to the GenomeWeb
Rodent Genome Databases

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This is a collection of rodent genome databases

Mouse and Rat Genome Databases

[info] Mouse Genome Informatics (MGI)
[info] The dysmorphic human and mouse homology database
[info] Mouse Genome Informatics Project (Jackson Labs)
[info] Genome Navigator: Whitehead/MIT Mouse Genome Map
[info] Gene Expression Database (GXD)
[info] RATMAP
[info] RIKEN Genomic Sciences Center
[info] The Mouse UniGene Collection
[info] The German Mouse ENU Project
[info] NIH Mouse Initiative Web site
[info] The Whole Mouse Catalog
[info] Rat Strain Information and Lab Code Names

Transgenic and Targeted Mutation Databases

[info] TBASE Transgenic and Targeted Mutation Animal Database
[info] Transgenic Systems for Mutation Analysis
[info] ORNL Transgenic and Targeted Mutant Animal Database

Other Databases

[info] Mouse Cytogenetic Map Image
[info] Whitehead Institute/MIT Genome Center Mouse Genetic Map
[info] Whitehead Institute/MIT Genome Center Rat SSLP Data

Detailed information on the above options

Mouse Genome Informatics (MGI)
MGI is produced by the Jackson Laboratory, in Bar Harbor, Maine. This is a copy at the HGMP for public use.

MGI is a comprehensive database of genetic information on the laboratory mouse. It includes:

Plus information on:

The dysmorphic human and mouse homology database
This consists of three separate databases of human and mouse malformation syndromes together with a database of mouse/human syntenic regions. The mouse and human malformation databases are linked together through the chromosome synteny database. The purpose of the system is to allow retrieval of syndromes according to detailed phenotypic descriptions and to be able to carry out homology searches for the purpose of gene mapping. Thus the database can be used to search for human or mouse malformation syndromes in different ways:-

Mouse Genome Informatics Project (Jackson Labs)
is maintained by Jackson Laboratory, in Bar Harbor, Maine. This site holds much information on mouse genetics. It is the home site of MGD, which is mirrored at the HGMP.

Genome Navigator: Whitehead/MIT Mouse Genome Map
Genome Navigator is an attempt to provide a visual interactive gateway to major databases containing physical and genetic mapping information about the mouse genome.

Genomic maps of these organisms are displayed using DerBrowser, a Java applet, designed as a universal tool to display and navigate various types of maps. Among other features, it allows a user to query external databases about any map object.

Gene Expression Database (GXD)
The GXD Index is an index of research reports documenting data on endogenous gene expression during mouse development that have been published from May 1993 to present.

The GXD Index includes references, genes and embryonic stages analyzed, and expression assays used, and enables database queries such as: What expression assays have been used to study the expression of a given gene, what stages of mouse development have been analyzed, and what references contain the respective data? Or: Tell me all the genes for which expression studies (or specific assays) have been done at a specific time period of mouse development.

The Gene Expression Database project aims for a comprehensive annotation of these expression data and for much more sophisticated storage, display and analysis tools (see online info).

The GXD Index is integrated with the Mouse Genome Database to foster a close link between genotype, expression and phenotype information.

is a database covering genes physically mapped to chromosomes in the laboratory rat. In addition to chromosomal localisation of genes and anonymous DNA sequences, RATMAP gives information about methods and accuracy of localisation (Mode and Status) and a short description of the genes. Appropriate literature references to each mapped rat gene are also given. Furthermore, RATMAP supports comparative mapping to several species. At present, comparative mapping data is given for bovine, human and the mouse.

RIKEN Genomic Sciences Center
They have developed a unique system for synthesis of full-length cDNA clones and have sequenced the 3'-ends in order to catalogue the 107,088 cDNA clones. Approximately 5,000 unknown partial sequences were identified by comparing sequence data with the sequence data registered in various human and mouse databases.

The Mouse UniGene Collection
Expressed sequence tag (EST) approaches have been used in several organisms as a cost-effective means of identifying a remarkable number of novel genes. In the mouse, over 400,000 EST sequences have been generated, primarily through an initiative funded by the Howard Hugues Medical Institute and carried out at the Washington University Genome Sequencing Center. The Mouse UniGene collection is an attempt to partition these ESTs into sets or"clusters" that correspond to distinct mouse genes. The reduced accuracy and partial nature of ESTs makes this a challenging task, but methods have been developed to generate UniGene in a mostly automated fashion. The UniGene set has proven useful for the selection of candidates for high-throughput gene mapping and gene expression studies.

The German Mouse ENU Project
The German Human Genome Project has established a research center to perform a large ENU mutagenesis screen in the mouse. The research center consists of a core facility and several associated laboratories. The core facility will generate mutagenized F1 mice which will then be analyzed by the associated laboaratories. Additional screens will be (can be) performed by other research groups that are not participants of the German Human Genome Project.

NIH Mouse Initiative Web site
In March 1998, the NIH convened a group of scientists to develop priorities for mouse genomics and genetics resources. In response to the community's recommendations, the NIH has created a Trans NIH Mouse Genomics and Genetics Resources Coordinating Group and a strategic implementation plan. For the convenience of all interested investigators, we have established this Web site as a central information resource. It will contain all relevant information from all parts of the NIH, including summaries of the original planning meetings, publications about the NIH action plan, funding opportunities, progress reports, etc.

The Whole Mouse Catalog
This serves as a central place to find resources of particular interest to scientific researchers using mice or rats in their work. In addition to a somewhat exhaustive listing of especially useful internet resources, you'll also find conference announcements and other information.

Rat Strain Information and Lab Code Names

TBASE Transgenic and Targeted Mutation Animal Database
TBASE is a database of organisms (Mouse, Fruitfly, Pig) and gene sequences which have undergone artificially introduced genetic transformations. Data may be searched by accession number, animal, name of line, method used, DNA introduced, genetic background, gene expression, phenotype, integration site, notes, author(s) and citation.

Transgenic Systems for Mutation Analysis
This gives information on transgenic animals, in particular BigBlue and MutaMouse, used for the study of mutations in mammals by means of a recoverable mutation target gene.

ORNL Transgenic and Targeted Mutant Animal Database
This displays data which researchers have provided about their lines of animals, therefore information that is not necessarily available from published literature is found in the database. The Transgenic and Targeted Mutant Animal Database is a powerful research tool which covers topics including methods used to generate each line, a detailed description of the DNA construct used, expression of the transgene or targeted mutation, and the resulting phenotypes

Mouse Cytogenetic Map Image
This gives a clickable interface to the mouse chromosome ideograms.

Whitehead Institute/MIT Genome Center Mouse Genetic Map
This holds the latest release of the Whitehead Institute/MIT Center for Genome Research mouse genetic map. View genetic maps and physical maps with STS-content data.

Whitehead Institute/MIT Genome Center Rat SSLP Data
This consists of polymorphic rat microsatellite repeats mapped on a SHRxBN F2 intercross using PCR probes. The average spacing between markers on these maps is approximately 3.7 cM.

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