Selecting Phenotypic Allele Categories

If you do not check any of the boxes (in the Categories section of the Phenotypes, Alleles, and Disease Models Query Form), the search includes every allele type in the list. You can limit your search by making selections in any or all of the three category sections. Category definitions for the three sections are as follows:

Generation Method | Allele Attributes | Collections

Generation Method Definitions for the origination of the allele
Chemically induced (ENU)Exposure of mice to the N-ethyl-N-nitrosourea (ENU) chemical mutagen results in germline-transmissible mutations.
Chemically induced (other)Exposure of mice to a chemical mutagen — excluding ENU and other common chemical agents such as ethyl methanesulfonate (EMS), bleomycin, and chlorambucil — results in germ-line transmissible mutations.
Chemically and radiation induced Exposure of mice to X-ray or other types of radiation result in germ-line transmissible mutations. Also included are mutations produced by a combination of chemical and radiation exposure.
Endonuclease-mediatedThese are targeted mutations generated in pluripotent or totipotent cells by an endonuclease joined to sequence-specific DNA binding domains. The mutation is introduced during homology-directed or non-homologous end-joining repair of the induced DNA break(s).
Gene trapped The integration of a reporter construct into a putative gene is selected by virtue of its expression. The trapped gene is usually (though not necessarily) mutated by the integration. Gene trapped alleles differ from targeted mutations in that the integration event is random (as opposed to targeted through homologous recombination). Gene trapped alleles usually have nomenclature that includes a traditional Gt prefix and cell line ID of the creator in the superscripted portion of the allele symbol. Gene trapped alleles are not included in the transgenic (all) search.
QTLQuantitative Trait Locus. A polymorphic locus having alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually, a QTL is a marker described by statistical association to quantitative variation in the particular phenotypic trait thought to be controlled by the cumulative action of alleles at multiple loci. Note: MGI does not define major modifier loci as QTL, although the literature often refers to these as QTL.
Radiation induced Exposure of mice to X-ray or other types of radiation result in germ-line transmissible mutations.
SpontaneousNo laboratory manipulation took place to generate the mutations or mutant phenotypes. Annotations are to naturally occurring mutants displaying abnormal phenotypes. Note: Naturally occurring variants, such as alleles identified based on electrophoretic mobility differences, antigen specificity, and noted polymorphisms, are annotated to Not applicable and these types of variants do not usually have an associated phenotype.
TargetedIncludes several targeted types such as floxed/frt, reporter, knock-out and knock-in, whereby the process of homologous recombination in ES cell lines results in an allele.
TransgenicThese alleles involve DNA that has been stably introduced into the germline. All transgenic types (such as random, expressed, gene disruptions and reporter transgenes) appear in query results.
Transposon inducedThe random insertion of a transposable element induced by the expression of transposase in any mouse tissue that results in a germline transmissible mutation.

Allele Attributes Definitions for the allele subtypes of the Generation Methods
Conditional readyConditional ready alleles are those in which a region of DNA is flanked with recombinase recognition sites sites (e.g. LoxP, FRT). Subsequent interaction with a recombinase will remove or invert the flanked region, resulting in a deletion or alteration in expression of the target gene or transgene.
RMCE-ReadyRecombinase Mediated Cassette Exchange (RMCE)-Ready mutations contain acceptor recombination sites for targeting expression constructs to a defined genomic region, thus avoiding possible positional effects of transgene expression.
Inserted expressed sequenceInserted expressed sequences are experimentally introduced and expressed in at least one cell type. This categorical set includes only those mutations that are not included in other sets of introduced sequences (i.e. Reporter, Transposase, Recombinase).
Humanized sequenceHumanized sequences are non-human sequences that have been altered to introduce one or more changes intended to make the sequence closer to that of the homologous gene in humans.
ReporterA reporter is an experimentally introduced expressed gene whose product is easily detected and not ordinarily present in the organism or cell type under study. Bacterial beta-galactosidase (LacZ), whose activity can be detected using a staining reaction, is a commonly used reporter gene; as is green fluorescent protein (GFP), which is detected by immunofluorescence.
TransposaseTransposases are expressed enzymes that bind to the ends of a transposon and catalyze the transposition of the transposon DNA segment to another part of the genome.
Transposon concatemerTransposon concatemers are multiple copies of transposon sequences inserted at a single site. Transposon concatamers serve as donor sites in transposase mutagenesis.
Constitutively activeAn enzyme or protein product is constitutively active if its activity level is constant over time and independent from normal regulatory controls.
Dominant negativeDominant negative alleles produce mutant gene products that disrupt the activity of the wild-type gene when co-expressed. These mutations result in an altered molecular function (usually inactivity) and result in a dominant or semi-dominant phenotype.
HypomorphA hypomorphic mutation has reduced gene expression and/or reduced gene product activity.
InducibleAn allele is inducible if its activation or expression occurs in the presence of a particular external stimulus, or by the removal of a particular external stimulus.
KnockdownA knockdown is a specific class of hypomorph in which the affected gene’s DNA sequence is not directly modified. A common technique to knockdown a gene’s expression is through RNA interference (RNAi).
Modified isoform(s)Isoforms are different gene products encoded by the same gene sequence as a result of alternative splicing. Alleles with modified isoform(s) are those in which at least one wild-type isoform is produced, while others are mutant or missing.
Null/knockoutA null or knockout mutation is amorphic, producing no gene product, or one with complete loss-of-function.
No functional changeNo functional change describes a mutation in which no discernible effect on the expression or function of the gene has been demonstrated. An example is the introduction of loxP sites to flank a critical exon, which usually has no effect on gene expression or function until cre recombinase is applied. This set also includes reporter alleles when the endogenous gene product is not modified.

Collections Use this section to limit your search to alleles from specific large scale projects and repositories.
Australian PhenomeBankA repository of genetically modified mouse strains held in Australia either as live or cryopreserved stock.
B2B/CvDCThe National Heart, Lung, and Blood Institute (NHLBI) Bench to Bassinet (B2B) Program of translational research in pediatric cardiovascular disease
Beutler MutagenixResource of phenotypes and mutations produced through random germline mutagenesis with ENU
DeltagenDeltagen targeted knock-outs
EUCOMMThe European Conditional Mouse Mutagenesis Program contributes conditionally trapped and targeted genes in mouse C57BL/6N embryonic stem (ES) cells to the International Knockout Mouse Consortium (IKMC).
GENSATGene Expression Nervous System Atlas of the developing and adult central nervous system of the mouse reporter and recombinase lines
Harwell ENU MutagenesisStocks with random ENU-induced mutations
KOMP-CSDCSD: CHORI (Children's Hospital Oakland Research Institute), the Wellcome Trust Sanger Institute, and the University of California at Davis. Knockout-first alleles created in C57BL/6N embryonic stem cells.
KOMP-RegeneronNull alleles from the VelociGene group at Regeneron, Inc.
LexiconTargeted gene knock-outs and gene trapped alleles
Mutagenesis for Dev. DefectsFacility for Mouse Mutagenesis for Developmental Defects at Baylor College of Medicine
Neuroscience Blueprint creC57BL6/J mouse strains for the tissue and cell-type-specific perturbation of gene function in the nervous system
NorCOMMThe North American Conditional Mouse Mutagenesis project develops and distributes a library of mouse embryonic stem (ES) cell lines carrying single gene trapped or targeted mutations.
Pleiades Promoter ProjectHuman MiniPromoters that drive region- and cell-specific gene expression in the mouse brain
RIKEN GSC ENU ProjectENU induced mouse mutants
Sanger Inst. Gene Trap Res.The Sanger Institute Gene Trap Resource (SIGTR) characterized reporter-tagged, loss of function gene trapped mouse embryonic stem (ES) cell lines.
Sanger miRNA knockoutsmicroRNA reporter knockouts in ES cell lines created using recombinase mediated cassette exchange (RMCE)

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