This help document describes Phenotypic Allele Details.
See also:
Title
The title on an allele detail page takes the following form:
[allele symbol]
[allele type] Detail
[allele type] is the
category used to narrow the allele search. The category can be spontaneous, induced (chemically, radiation, or transposon), transgenic (random, expressed; random, gene disruption; Cre/Flp; transposase), gene trapped, targeted (floxed/frt, reporte, knock-out, knock-in) or QTL.
As examples:
| Allele type | Title example |
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| spontaneous | Apoeshi Spontaneous Allele Detail |
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| chemically induced | Edn3tmgc48 Chemically induced Allele Detail |
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| radiation induced | Crygenz Radiation induced Allele Detail |
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| transposon induced | Mdc1Tn(pb-ZG-s)1.1MrcTransposon induced Allele Detail |
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| transgenic | Tg(CAG-sb10)1Dla Transgene Allele Detail |
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| transgenic (Transposae) | Tg(aP2-SREBF1c)9884Reh Transgenic Allele Detail |
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| targeted allele | Ahrtm1(AHR)Mym Targeted Allele Detail |
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| gene trapped | Alms1Gt(XH152)Byg Gene trapped Allele Detail |
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| Gene trapped/no gene nomenclature* | Gt(pU21)102lmeg Gene trapped Allele Detail |
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| QTL | Ap7qC57BL/6ByJ QTL Variant Detail |
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* See Why aren't all gene traps associated with a gene? for details.)
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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 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 names vary depending on the type of allele.
- a Transgene Detail report has field names titled Transgene origin and Transgene description as well as transgene name and location information in the Nomenclature section.
- a QTL detail report has field names entitled Variant origin and Variant description. The Nomenclature section may contain information about the QTL name, location, and genetic position, and/or a QTL note.
| Field
| Description
|
| Nomenclature
|
| Symbol | The 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. |
| Name | The allele name appears beneath the symbol. See
Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, & Mutations in Mouse & Rat for details. |
| MGI ID | The MGI accession identifier for this allele. | | Synonyms | Other names for this allele. |
| Gene | Some or all of the following: Gene (symbol), Location (chromosome, genome coordinates, strand), Genetic Position. |
|
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| Mutation/Variant/Transgene origin
|
| Mutation/Variant/Transgene origin |
- If a mutant cell line has an accession identifier, this appears. If it does not have an accession ID, the name appears (e.g., ES62, EX65). The organization that generated the cell line (e.g., Lexicon, BayGenomics, Texas Institute for Medical Genetics, etc.) appears in parentheses.
- Variant information may include the Strain of Specimen, and allele (QTL) and mutation type.
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| 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. |
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| 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. |
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| Strain of Origin
| Mouse strain that the allele originated from. |
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|
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| Mutation/Variant/Vector/Transgene description
|
| 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. Long molecular descriptions are hidden. Click the ► to view them. |
| Inheritance | 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 and QTLs. |
| Sequence tag | Click ► to open the display.
Click ▼ to close the display.
| Tag ID | Cell line sequence tag identifier, assigned by the creator. The link goes to the external resource for this sequence (for example, IGTC, dbGSS). |
| GenBank ID | The dbGSS identifier assigned to this sequence tag. |
| Method | Sequencing 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 the current NCBI build. |
| Select | Click the check box to select a sequence for downloading in FASTA format or forwarding to MGI MouseBLAST. |
|
| Genome Context | Click ► to open the display.
Click ▼ to close the display.
The image that appears is a genome browser view of the mutation and contains a link to the MGI Mouse Genome Browser and all the genome sequence tags in the region. When numerous gene traps appear, use the Scroll/Zoom feature (yellow arrows, middle of the page) to locate a given trap. |
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| Recombinase activity
|
| Activity 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 Activity Detail page associating expression assays of type Recombinase reporter, In situ reporter (knock in) and In situ reporter (transgene) with genotypes. |
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| Phenotypes | See Interpreting the Phenotype summary table. |
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| Disease models | List of all mouse genotypes annotated to a disease. These annotations may be of the following types:
- phenotypic similarity to human disease.
- 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). These are noted by the ∅ symbol.
| 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 follows the term (e.g., 106210; 60387) and is linked to its OMIM record. |
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.
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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. |
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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. |
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| 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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Interpreting Phenotypic Allele Detail Reports