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, reporter, knock-out, knock-in) or QTL.

As examples:

Allele typeTitle example
SpontaneousApoeshl Spontaneous Allele Detail
Chemically induced (ENU)Edn3tmgc48 Chemically induced Allele Detail
Radiation inducedCrygenz Radiation induced Allele Detail
Transposon inducedMdc1Tn(pb-ZG-s)1.1Mrc Transposon induced Allele Detail
Transgenic (Transposase)Tg(CAG-sb10)1Dla Transgene Allele Detail
Transgenic (Inserted expressed sequence)Tg(aP2-SREBF1c)9884Reh Transgene Detail
TargetedAhrtm1(AHR)Mym Targeted Allele Detail
Gene trappedAlms1Gt(XH152)Byg 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 phenotypic 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 Mutation description section may also contain images that define the mutation. Click on an image for a larger view.

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Fields

The table below describes the fields in an allele detail report.

Summary | origin | description | Recombinase activity | Phenotypes | Disease models | Expression | Find Mice (IMSR) | Additional information | References
Field Description
Summary
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.
SynonymsUnofficial names for this allele.
GeneSome or all of the following: Gene (symbol), Location (chromosome, genome coordinates, strand), Genetic Position.
AllianceA link to the Alliance of Genome Resources page for this allele.
IMPCA link to the International Mouse Phenotyping Consortium page for the gene which may include raw phenotyping data and images for alleles of the gene.
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 OriginMouse strain that the allele originated from, linked to its strain detail page.
Project CollectionFor alleles from large scale projects and repositories, the source is indicated.
Mutation/Variant/Vector/Transgene description
Allele TypeType of allele by mode of origin.
InducerFor inducible alleles, the agent that initiates expression of the allele is given (e.g., induced by tamoxifen, induced by doxycycline).
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. For some chemically induced mutations, the mutation causing the phenotype may be described and there may also be a link to a file of other, incidental mutations, in the stock that may or may not have phenotypic affects.

Alleles that involve multiple genes display links to up to three of the affected genes in this section along with the option to View all the affected genes with their feature types, genome coordinates, associated references and curatorial notes.

If the allele is a knock-in with an expressed component, this section will show the allele symbol followed by the number of expressed genes. Click the blue ► to see a table of the expressed genes.

OrganismThe species of origin for the expressed gene.
Expressed GeneThe gene symbol for the expressed gene. Mouse genes link to their MGI Gene Detail Pages. For other organisms, there is a link to EntrezGene.
Homolog in MouseIf the expressed gene is from an organism other than mouse, this column will show its mouse homolog, linked to its MGI Gene Detail page.
NoteAny clarifying details from MGI curators.

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 NCBI BLAST.
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 colored cell means recombinase activity was assayed. Click on a cell to launch a popup window from which you can then access assay details and view images. See also: What do the colors in a Matrix mean?
The age ranges are as follows:
Embryonic (E0-8.9)Embryonic age from conception to 8.9 days
Embryonic (E9.0-13.9)Embryonic age from 9 to 13.9 days
Embryonic (E14-21)Embryonic age from 14 to 21 days
Newborn (P0-3.9)Postnatal age from birth to 3.9 days
Pre-weaning (P4-21.9)Postnatal age from 4 - 21.9 days
Post-weaning (P22-42.9)Postnatal age from 22 - 42.9 days
Adult (P>43)Older than 43 days
Postnatal (age unspecified)Details about the exact postnatal age are unknown to us
DriverName of promoter and:
  • a link to a summary of all recombinase alleles that use the driver gene or an orthologous gene from another species.
  • a link to a Comparative matrix view of recombinase activities. The matrix shows wild-type expression data for the gene and reported recombinase activity for recombinase alleles driven by the gene. This link will be present only if the allele's driver has corresponding mouse gene and only if we have activity data for alleles with this driver. If this allele has reported activity data, it will be highlighted in the grid column header. If there are no activity data for this allele, the link to a Comparative matrix view of recombinase activities will not be shown and it will not be displayed in the grid.
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.

What do the colors in a Matrix mean?

The colors in the grid, blues for recombinase activity detected and reds for recombinase activity not detected, get progressively darker when there are more supporting annotations. The darker colors do not denote higher or lower levels of recombinase activity, just more evidence.

Grey bars indicate the only annotations for the tissue are ones for which the researchers examined the tissue but did not definitively state whether recombinase activity was present or absent, i.e. their description was ambiguous.

Cells with a red corner indicate that recombinase activity has been reported as being both present and absent in that tissue. Although this may be because different labs made conflicting observations, it may also be due to other factors, such as differences in the genotype or sex of the specimen, sensitivity of the assay used, or a difference in the transcript variant assayed.

A white cell with a gold corner indicates that although there are no annotations where recombinase activity was reported as being present in either the tissue or its substructures, there are recombinase activity results for substructures of the tissue that were reported as being either absent or ambiguous. See How are expression results propagated through the matrix anatomy hierarchy?

A circle in a cell indicates the tissue exists at that Theiler stage but we have no recombinase activity data for it, whereas a blank cell indicates that the tissue does not exist at that stage.

Clicking in any box in the grid will open a dialogue box. For blue cells, this box will indicate the number of annotations where recombinase activity was reported as being present in either the tissue or its substructures. It may also indicate additional recombinase activity results annotated to this tissue that were reported as being either absent or ambiguous; absent or ambiguous annotations to substructures will not be reported. See How are expression results propagated through the matrix anatomy hierarchy?

A blue cell with a gold corner indicates the structure has both present and absent and/or ambiguous results in substructures.

For red cells, this box will indicate the number of annotations where recombinase activity was reported as being absent in the tissue; annotations to substructures will not be reported. See How are expression results propagated through the matrix anatomy hierarchy?

For grey bars, this box will indicate the number of annotations to the tissue where the recombinase activity levels were reported in an ambiguous fashion. It may also indicate additional recombinase activity results annotated to this tissue that were reported as being absent. In neither case will absent and/or ambiguous annotations to substructures be reported. See How are expression results propagated through the matrix anatomy hierarchy?

Since cells with a gold corner indicate that all the recombinase activity results are absent or ambiguous annotations to substructures (rather than the structure represented by the cell) the number of annotations is not indicated in the dialogue box.

In all cases, clicking "View All Result Details and Images" in a cell's pop-up for the recombinase activity column will take you to the assay results tab of the recombinase activity summary where these recombinase activity results can be reviewed in detail. If there are annotations where recombinase activity was reported as being absent or ambiguous in a substructure, they will be shown on this tab (although they will not be included in the counts on the dialogue box).

PhenotypesSee Interpreting the Phenotype summary table.
Disease modelsList of all diseases modeled, or attempted to be modeled with this allele. 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; Peters Anomaly; Frasier Syndrome; rheumatoid arthritis), linked to the (MGI) Human Disease Ontology (DO) Browser record. The IDs links to a popup of IDs associated with the disease, linked to the appropriate source, when possible. Examples are DO IDs, OMIM IDs, and ICD-9 codes.
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.
Expression
  • A link to expression data in mice carrying this mutation
  • A link to the Mouse Developmental Anatomy Browser to view all the anatomical structures mapped to phenotype terms annotated to the mutant. These structures are listed on the left hand section of the Anatomy Browser with the first structure listed selected. In the main body of the page, the Anatomical Tree View links to all expression results annotated to the selected structure and all genotypes with phenotypes involving the structure.
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. The International Mouse Strain Resource (IMSR) is a searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide. The IMSR does not house any stocks but if you follow these links to the IMSR it will search for stocks from several providers. In your IMSR search results, the Strain Name links to the repository's site, the Repository links to an e-mail form so you can ask about or order the stock and the Allele Symbol links to the MGI Allele Detail page. The IMSR search may also find stocks with incidental mutations in this and many other genes.
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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