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Strains and SNPs

MGI integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes.

 Strain Query Help
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Mouse SNP Query
Phenotypes, Alleles & Disease Models Search
Nomenclature Guidelines
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Inbred strains of mice represent unique fixed genotypes that can be repeatedly accessed as homogeneous experimental individuals, with predictable phenotypes and defined allelic composition. Hundreds of inbred strains of mice have been described and new strains continue to be developed, taking advantage of the rich genetic diversity among the existing strains and the ease with which the mouse genome can be manipulated.

MGI serves as a registry for mouse strains worldwide, maintaining the authoritative nomenclature for existing strains. Comparative data on inbred strain characteristics, SNPs, polymorphisms, and quantitative phenotypes are integrated with other genetic, genomic, and biological data in MGI.

SNPs (single nucleotide polymorphisms)

MGI provides comprehensive information about reference SNPs including the reference flanking sequence, assays that define the SNP, and gene/marker associations with their corresponding function class annotations. Each SNP detail page includes links to popular gene browsers including the MGI JBrowse Genome Browser.

Other molecular polymorphisms

MGI includes data on RFLP and PCR based polymorphisms. Probes and restriction enzymes used for RFLP analysis and primer sequences used for PCR are provided, with fragment sizes and variants for each strain tested. Links to these data can be found in the Polymorphisms section of gene and marker detail pages.

Strain characteristics and historical origins

MGI holds information on comparative strain characteristics as originally curated by Dr. Michael Festing. These narratives provide key phenotypic traits of major inbred strains, such as behavior, physiology, anatomy, drug responses, immunology, infection, and reproduction. The Genealogy of Inbred Strains provides a "pedigree" of relationships of strains since their origin. The Genealogy Chart graphically displays the movement and development of inbred strains and is particularly useful in looking at dispersion of strains and how inbreeding (and allele fixation) occurred in relation to conserved sequence blocks observed in SNP analysis Data are fully referenced.

Detailed explanations for using Strains, SNPs & Polymorphisms query forms and tools:
  • Strain Search help
  • SNP Query Form help
  • Guidelines for Nomenclature of Mouse and Rat Strains help
  • Mouse Strain 129 Substrain Nomenclature help
Collaborators and Data Providers:

Mouse SNP data in MGI are obtained from the dbSNP resource at NCBI

The registered mouse strains in MGI include strains
  • in public repositories like the International Mouse Strain Resource (IMSR)
  • held by members of the Federation of International Mouse Resources (FIMRe)
  • described as source material for sequences in NCBI GenBank entries
  • submitted by researchers
  • included in the scientific literature

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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last database update
MGI 6.22
The Jackson Laboratory