Interpreting Phenotypic Allele Detail Reports
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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 typeTitle example
spontaneousApoeshi Spontaneous Allele Detail
chemically inducedEdn3tmgc48 Chemically induced Allele Detail
radiation inducedCrygenz Radiation induced Allele Detail
transposon inducedMdc1Tn(pb-ZG-s)1.1MrcTransposon induced Allele Detail
transgenicTg(CAG-sb10)1Dla Transgene Allele Detail
transgenic (Transposae)Tg(aP2-SREBF1c)9884Reh Transgenic Allele Detail
targeted alleleAhrtm1(AHR)Mym Targeted Allele Detail
gene trappedAlms1Gt(XH152)Byg Gene trapped Allele Detail
Gene trapped/no gene nomenclature*Gt(pU21)102lmeg Gene trapped Allele Detail
QTLAp7qC57BL/6ByJ QTL Variant Detail
* 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.

Nomenclature | origin | description | Recombinase activity | Phenotypes | Disease models | Expression | Find Mice (IMSR) | 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.
GeneSome or all of the following: Gene (symbol), Location (chromosome, genome coordinates, strand), Genetic Position.
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.
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/Variant/Vector/Transgene description
Allele TypeType of allele by mode of origin.
MutationMethod that produced this mutation and methodology. When available, click the ► to view a description. Any molecular references are linked to MGI Reference Detail reports.
InheritancePhenotypic 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 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 the current NCBI build.
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 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.
Recombinase activity
ActivityRecombinase activity was assayed for this allele in all (the high-level terms for the) anatomical systems listed.

Recombinase activity is displayed in a table of Systems/Structures and ages assayed. The Activity in Systems/Structures column lists anatomical Systems/Structures assayed for recombinase activity.

  • If a structure you are interested in does not appear, it means that currently there are no assay data for this allele in that structure.
  • The sort order is alphabetical (e.g., behavioral/neurological before cardiovascular, skeleton before skin/coat/nails).
  • To expand or collapse all structures, click show or hide (at the top of the Activity in Systems/Structures column).
  • To expand or collapse a single system, click the ► or ▼ beside it.
  • A check mark (✓) means recombinase activity was assayed and detected in the system/structure and age. A minus sign (-) means recombinase activity was assayed and not detected in the system/structure and age.

The age ranges are as follows:
E 0-8.9Embryonic age from conception to 8.9 days
E 9.0-13.9Embryonic age from 9 to 13.9 days
E 14-19.5Embryonic age from 14 to 19.5 days
P 0-21Postnatal age from birth to 21 days
Post-weaningPostnatal age from 22 to 42 days
AdultOlder than 43 days
DriverName of promoter and a link to a summary of all recombinase alleles driven by this promoter.
User NotesIf researchers have submitted additional information to MGI regarding the tissue activity of this allele, this section will be present. Toggle the ► to view the information.

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.

If you have information about this allele that is not displayed on this Allele Detail page, such as ectopic activity observed for the allele or constitutive activity for an inducible allele, click the Your Observations Welcome button to have this information included in MGI.

PhenotypesSee Interpreting the Phenotype summary table.
Disease modelsList 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 DiseaseAll 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.
ExpressionA link to expression data in mice carrying this allele.
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.
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 and candidate genes within the QTL interval.
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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