This help document describes Phenotypic Allele Detail reports.
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.
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.
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.
| Field |
Description |
| Nomenclature |
|
Mutation origin |
| Mutant Cell Line | Identifies 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 Line | Parent 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. |
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Mutation description |
| Click arrows to toggle between the two views. |
| Allele Type | Type of allele by mode of origin. |
| Mutation | Method that produced this mutation and methodology. When available, a description appears. Any molecular references are linked to MGI Reference Detail reports. |
| Inheritance mode | Phenotypic 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 tag | Click ► to open the display.
Click ▼ to close the display.
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| Genome Context | Click ► 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. |
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| 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 Mutation | Number (in parentheses) of gene expression assay results involving the featured allele, linked to a corresponding Gene Expression Assay Results Summary Report. |
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| Recombinase specificity |
| Specificity in | Recombinase activity was assayed and detected for this allele in all (the high-level terms for the) anatomical systems listed. |
| Not Detected in | Recombinase activity was assayed and not detected for this allele in all (the high-level terms for the) anatomical systems listed. |
| Driver | Name 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 summary | See Interpreting the Phenotype summary table. |
| Phenotypic data by genotype | Phenotypic 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.
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| Allelic Composition | Genotype of each allele, linked to its MGI Allele Detail report. |
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| Genetic Background | Mouse 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 models | List 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. |
| Note | Column 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 Composition | Allele pairs present in the genotype. Each allele is linked to its corresponding Phenotypic Allele Detail report. |
| Genetic Background | Mouse strains involved, if known. |
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| Ref(s) | The supporting reference linked by its MGI reference number to the MGI Reference Detail report containing the full citation. |
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| 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.
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