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Understanding Phenotypic Allele Detail Reports

This help document describes Phenotypic Allele Detail reports.

See also:

Title

The title on an allele detail report takes the following form:

[allele symbol]
[allele type] Detail

As examples:

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Your Input Welcome

The Your Input Welcome button appears (top right) as part of the detailed query results for an allele. Click the button to bring up a form for submitting updates and additions to the allele data on view. This provides an easy way to help keep data current.

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Images

If the MGI database contains multiple images for the mouse, a representative image appears on the Phenotypic Allele Detail page (top right). Click anywhere on the image to see the Image Detail page for the representative image or click Show the # image(s) involving this allele to view them all.

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Fields

The table below describes the possible fields in an allele detail report. When information for a field is not available or is not pertinent to a given allele, it does not appear.

Nomenclature | Mutation origin | Mutation description | Find Mice (IMSR) | Expression | Recombinase specificity | Phenotype summary | Phenotypic data by genotype | Disease models | Additional information | References
Field Description
Nomenclature
SymbolThe symbol of the allele. The allele symbol is composed of the gene symbol and the allele designation. If the gene is unknown, only the allele designation appears.
NameThe allele name appears beneath the symbol. See Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat for details.
MGI IDThe MGI accession identifier for this allele.
SynonymsOther names for this allele.
Mutation
origin
Mutant Cell LineIdentifies the stem cell line where a mutation occurred. Lists the mutant stem cell line accession ID and (in parentheses) the organization that generated the cell line (e.g., Lexicon, BayGenomics, Texas Institute for Medical Genetics, etc.).
Germline Transmission Either the status of a mouse created from this cell line, if germ line or chimera transmission reference is known, or an indication that the transmission status is unknown.
Parent Cell LineParent name, and, in parentheses, the cell type (for example, ES Cell). If Parent Cell Line appears as Other (see notes), there is more information in the Additional information section of this report.
Strain of Origin Mouse strain that the allele originated from.
Mutation
description
Click arrows to toggle between the two views.
Allele TypeType of allele by mode of origin.
MutationMethod that produced this mutation and methodology. When available, a description appears. Any molecular references are linked to MGI Reference Detail reports.
Inheritance modePhenotypic effect of the allele when heterozygous with the wild type allele. Note: This information is primarily entered for spontaneous and chemically or radiation-induced alleles.
Sequence tagClick ► to open the display. Click ▼ to close the display.
Tag IDCell line sequence tag identifier, assigned by the creator. The link goes to the external resource for this sequence (for example, IGTC, dbGSS).
GenBank IDThe dbGSS identifier assigned to this sequence tag.
MethodSequencing technique.
Tag Location (strand)Chromosome location, genome coordinates in base pairs, and the indicator of how the strand is oriented to the genome (+ or -), based on NCBI build 37.
SelectClick the check box to select a sequence for downloading in FASTA format or forwarding to MGI MouseBLAST.
Genome ContextClick ► to open the display. Click ▼ to close the display.
The genome browser view of the mutation and a link (that includes the number of available traps) to MGI GBrowse for additional information. When numerous gene traps appear, use the GBrowse zoom feature to locate a given trap.
Find Mice (IMSR)Information about the availability of mouse strains and/or cell lines of this allele in the International Mouse Strain Resource (IMSR). There is also an indicator of whether or not there are any strains or lines available for any mutation of this gene.
Expression
In Mice Carrying this MutationNumber (in parentheses) of gene expression assay results involving the featured allele, linked to a corresponding Gene Expression Assay Results Summary Report.
Recombinase specificity
Specificity inRecombinase activity was assayed and detected for this allele in all (the high-level terms for the) anatomical systems listed.
Not Detected inRecombinase activity was assayed and not detected for this allele in all (the high-level terms for the) anatomical systems listed.
DriverName of promoter and a link to a summary of all recombinase alleles driven by this promoter.
Each listed system links to a Recombinase Specificity Detail page associating expression assays of type Recombinase reporter, In situ reporter (knock in) and In situ reporter (transgene) with genotypes.
Phenotype summarySee Interpreting the Phenotype summary table.
Phenotypic data by genotypePhenotypic details for all genotypes that include at least one copy of the specified allele.

Colored boxes,
abbreviations,
numbers
  • A Key decodes the information.
  • Each column heading contains a color, an abbreviation, and a number.
  • Colors correspond to genotypic "states."
  • Abbreviations are "shorthand" for those states (e.g., hm stands for homozygous).
  • Numbers are sequential; there is one for each genotype.
  • The colors make it easy to distinguish genotypes from one another, especially when the summary extends horizontally.
  • Identical colors, abbreviations, and numbers appear in the Phenotypic data by genotype and Disease models sections, offering alternate (or more specific) views of the data.
Allelic CompositionGenotype of each allele, linked to its MGI Allele Detail report.
Genetic BackgroundMouse strains involved, if known.

Click ► to open a display of any high-level phenotypic terms (e.g., behavior/neurological), in the phenotype descriptions. Beneath the terms are:

  • subterms linked to Mammalian Phenotype Browser Term Detail reports
  • J: numbers, linked to MGI References Query Results Detail reports.
  • Disease model and image indicators, when pertinent and/or available.
Click ▼ to close the display.
Disease modelsList of all mouse genotypes annotated to a disease. Results are sorted into five categories (if there is no result, a category does not appear) for models with:
  • phenotypic similarity to human disease and etiologies involving orthologs (the human ortholog of the mouse gene is associated with the same disease). If a genotype appears in this category, it will not be associated with any of the other four categories except transgenes or other mutation types<.
  • phenotypic similarity to human disease but a distinct etiology (that is, human genes are associated with this disease, but orthologs of those genes do not appear in the mouse genotype).
  • phenotypic similarity to human diseases with unknown etiology or involving genes where the human ortholog is unknown.
  • transgenes or other mutation types (appears only if there are diseases annotated to an allele of a non-gene marker).
  • no similarity to the expected human disease phenotype (that is, one or more human genes may be associated with the human disease; the mouse genotype may involve mutations in orthologous genes; but the phenotype does not resemble the human disease).
Mouse Models of
Human Disease		All human diseases annotated to any mouse genotype containing the allele. Full disease term (e.g., Aniridia, TypeII; Peters Anomaly; Frasier Syndrome; Wilms Tumor 1), linked to the (MGI) Human Disease and Mouse Model Detail report. The OMIM accession identifier appears beneath the term (e.g., 106210; 60387), linked to its OMIM record.
NoteColumn containing a number if there is additional information about the disease or model. This information appears below the table, beside the number. If the word Not appears, it means that the reference's author(s) looked for but found no similarity to the expected human disease phenotype in the mouse genotype specified.
Colored boxes,
abbreviations,
numbers
  • A Key decodes the information.
  • Each column heading contains a color, an abbreviation, and a number.
  • Colors correspond to genotypic "states."
  • Abbreviations are "shorthand" for those states (e.g., hm stands for homozygous).
  • Numbers are sequential; there is one for each genotype.
  • The colors make it easy to distinguish genotypes from one another, especially when the summary extends horizontally.
  • Identical colors, abbreviations, and numbers appear in the Phenotypic data by genotype and Disease models sections, offering alternate (or more specific) views of the data.
Genotype
Allelic CompositionAllele pairs present in the genotype. Each allele is linked to its corresponding Phenotypic Allele Detail report.
Genetic BackgroundMouse strains involved, if known.
Ref(s)The supporting reference linked by its MGI reference number to the MGI Reference Detail report containing the full citation.
Notes Miscellaneous data about the allele that does not appear in the above categories such as:
  • GenBank accession identifier for the mutation.
  • Other origin information.
  • Additional information for the parent cell line.
  • Mapping data for QTL variants.
If this field is not present, it means that there is currently no information of this type in the MGI database for this allele.
References
  • Original is a J: number (MGI identifier) link to an MGI Reference Detail report containing the full citation for the original allele reference.
  • All references (#) links to a Reference Summary report on all MGI papers examining the phenotype of the allele.

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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11/20/2009
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