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MGI News
September 7, 2018
MouseMine now includes genomic data for 18 more mouse inbred strains: 16 sequenced and annotated by the Wellcome Institute Sanger Mouse Genomes Project and two wild-derived strains (CAROLI/EiJ and PAHARI/EiJ) published by Paul Flicek and Duncan Odom and others, as well as the C57BL/6J reference genome. Currently only the C57BL/6J annotation is “reference quality.”
In your MouseMine search results for a gene or list of genes, several query templates are automatically run. Four in the Genome section of your results include the new data (Example ):
  • Canonical gene --> CDSs in specific strains
    • A report of the coding sequences for each strain for the genes in your list
  • Canonical gene --> Exons in specific strains
    • A report of the exons for each transcript for each strain for the genes in your list
  • Canonical gene --> Strain-specific IDs, biotypes, and locations
    • A report of the genomic sequences for each strain for the genes in your list
  • Canonical gene --> Transcripts in specific strains
    • A report of each of the transcripts for each strain for the genes in your list
Use the Export button above a report to get your results as a tab or comma-separated file, or as FASTA or GFF3 features. Or click on an identifier to get an individual sequence.
August 21, 2018
The GXD Home Page has been redesigned to make it more intuitive and effective. Graphical tiles provide a quick overview of and access to GXD's search functions, including direct access to each of the three (tabbed) search modes of the Gene Expression Data Query Form. A Highlights section alerts users of newly added features and data.
May 7, 2018
The capabilities of the Differential Expression Search have been expanded. This search allows users to query for genes expressed in some anatomical structures and/or developmental stages but not in others. The new feature allows users to search for genes that have been shown to be expressed in a specified structure (or its substructures) and/or developmental stage(s) but nowhere else.
We have developed interface utilities that allow users to compare gene expression and phenotype data for a given gene. The new Gene Expression + Phenotype Comparison Matrix, accessible from gene detail pages, visually juxtaposes tissues where a gene is normally expressed against tissues where mutations in that gene cause abnormalities. The anatomy axis of the view can be expanded and collapsed, allowing users to interactively explore correlations between gene expression and phenotype at different levels of detail. The Mouse Developmental Anatomy Browser has been enhanced; in addition to providing access to expression data for a given anatomical structure, it now provides access to corresponding phenotype data. On Allele Detail pages we have added links to anatomical structures affected by the mutations and links to wild-type expression data for these structures. As well, links have been added to the term detail section of the Mammalian Phenotype Browser, allowing users to access wild-type expression data in tissues associated with the phenotype.
New interface utilities have been developed to help users find recombinase (cre) reporters with activity in specific tissues. The Recombinase (cre) Activity Search now allows users to narrow their query to reporters whose activity has been detected in the specified structure (or its substructures) but nowhere else. Further, a Matrix View that juxtaposes the endogenous expression pattern of a gene against activity patterns for recombinases driven by the mouse gene promoter is now available. The matrix view is accessible from relevant gene and allele detail pages, as well as from the recombinase allele search summary.

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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