This help document describes Phenotypic Allele Details.
The title on an allele detail page takes the following form:
[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.
|Allele type||Title example|
|Spontaneous||Apoeshl Spontaneous Allele Detail|
|Chemically induced (ENU)||Edn3tmgc48 Chemically induced Allele Detail|
|Radiation induced||Crygenz Radiation induced Allele Detail|
|Transposon induced||Mdc1Tn(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|
|Targeted||Ahrtm1(AHR)Mym Targeted Allele Detail|
|Gene trapped||Alms1Gt(XH152)Byg Gene trapped Allele Detail|
|QTL||Ap7qC57BL/6ByJ QTL Variant Detail|
* See Why aren't all gene traps associated with a gene? for details.)
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.
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.
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.
|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||Unofficial names for this allele.|
|Gene||Some or all of the following: Gene (symbol), Location (chromosome, genome coordinates, strand), Genetic Position.
- 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 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, linked to its strain detail page.|
|Project Collection||For alleles from large scale projects and repositories, the source is indicated. |
|Allele Type||Type of allele by mode of origin.|
|Inducer||For inducible alleles, the agent that initiates expression of the allele is given (e.g., induced by tamoxifen, induced by doxycycline).|
|Mutation||Method 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.
|Organism||The species of origin for the expressed gene.|
|Expressed Gene||The 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 Mouse||If the expressed gene is from an organism other than mouse, this column will show its mouse homolog, linked to its MGI Gene Detail page.|
|Note||Any clarifying details from MGI curators.|
|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.|
|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 NCBI BLAST.|
|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.
|Activity||Recombinase 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.
The age ranges are as follows:
- 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.
|E 0-8.9||Embryonic age from conception to 8.9 days|
|E 9.0-13.9||Embryonic age from 9 to 13.9 days|
|E 14-19.5||Embryonic age from 14 to 19.5 days|
|P 0-21||Postnatal age from birth to 21 days|
|Post-weaning||Postnatal age from 22 to 42 days|
|Adult||Older than 43 days|
|Driver||Name of promoter and:
- a link to a summary of all recombinase alleles that use the driver gene or an orthologous gene from another species. Currently, the species for the driver gene is not displayed.
- 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 is a 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, it will not be displayed in the grid.
|User Notes||If 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.
|Phenotypes||See Interpreting the Phenotype summary table.|
|Disease models||List 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 Disease||All 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, |
- 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.
- 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.
||Miscellaneous data about the allele that does not appear in the above categories such as:
If this field is not present, it means that there is currently no information of this type in the MGI database for this allele.
- 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.
- 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.