The IMSR glossary provides definitions for terms
used in the IMSR web site. Abbreviations in parentheses following some
terms refer to the abbreviations used in the
data submission files
For additional definitions useful for understanding mouse genetics and
informatics, and for links to other biological glossaries online, see the
Further descriptions of strain/stock types and nomenclature can be found in the
Rules for Nomenclature of Mouse and Rat Strains
- Accession ID
- A unique alphanumeric character string that is used to unambiguously identify a particular record in a database. For example,
MGI:96677 is the accession ID for the kit oncogene (Kit) in the Mouse Genome Informatics database;
Y00864 is the GenBank ID for a mouse Kit mRNA sequence. The format of a MGI Accession ID is MGI:nnnnnn, where n is a number.
- One of the variant forms of a gene, differing from other forms in its nucleotide sequence.
- Allele Name
- A word or phrase that uniquely identifies an allele of a given gene. The allele name has an abbreviation, the allele symbol, added as a superscript to the
gene symbol. For example, one of the alleles of the Kit gene is named "viable dominant spotting," with the symbol KitW-v.
- Allele Symbol
- A unique abbreviation for the allele name. Allele symbols take the form of superscripts added to the gene symbol.
For example, one of the alleles of the Kit gene is named "viable dominant spotting," with the symbol KitW-v.
- Any chromosome that is not a sex chromosome; for mouse, Chromosomes 1-19.
- Chemically Induced Mutation (CI)
- A mutation induced by treatment with a chemical mutagen, for example, ENU (ethyl nitrosourea) or chlorambucil.
- A structural unit within a eukaryotic nucleus that carries genes. A chromosome consists of a long, continuous strand of DNA and associated proteins.
- Chromosomal Aberration (CH)
- A chromosomal rearrangement or a numerical chromosomal aberration.
- Chromosomal Rearrangement
- A kind of mutation in which there is a change to the normal arrangement of the genome into chromosomes.
Usually, but not exclusively, this term applies to those changes that are visible cytogenetically.
Classes of chromosome rearrangements include:
Transpositions. See also these specific terms.
- Closed Colony (CCO)
- Shortened version of "closed colony random bred," meaning a strain propagated by random mating within the stock. No genes are introduced from outside the stock from generation to generation.
- Coisogenic Strain (COI)
- A strain that differs from its progenitor inbred strain at only one locus. A coisogenic strain arises when a mutation occurs in an inbred strain.
- Congenic Strain (CON)
- An inbred strain that contains a small genetic region (ideally a single gene) from another strain, but which is otherwise
identical to the original inbred strain. Congenic strains are derived by backcrossing to a parental inbred strain for at least
ten generations while selecting for retention of a specific locus from the donor strain. For example, CBACa.C3-KitW-x/J
is an inbred strain of CBA/Ca background onto which the KitW-x allele from C3H/HeJ has been placed.
- Consomic Strain (CSS)
- An inbred strain that contains a single entire chromosome from another strain. Consomic (or Chromosome Substitution Strains)
are derived by backcrossing to a parental inbred strain for at least ten generations while selecting for retention of a specific
whole chromosome from the donor strain. For example, C57BL/6J-Chr 4A/NaJ is a consomic strain in which the
Chromosome 4 from the A/J strain has been placed on a C57BL/6J background.
- Cre Recombinase
- A site-specific recombination enzyme that recognizes the 34 base pair loxP sequence.
- Cryoarchived (CA)
- The process by which living cells, organs, or organisms are frozen and maintained with the intent to revive them as functional units in the future.
Cryopreserved embryos (EM): the frozen state of
embryos, usually frozen at the 2- or 8-cell stage.
Cryopreserved ovaries (OV): the frozen state of ovaries (female reproductive organs containing the gametes).
Cryopreserved sperm (SP): the frozen state of sperm.
- Deletion (DEL)
- A type of mutation caused by loss of one or more nucleotides from a DNA segment. Deletions can be very large, encompassing
many genes and megabases of DNA, to the point of producing a visible cytological abnormality in a chromosome. Small deletions
within a gene can alter the reading frame, and thus the amino acid sequence of the encoded protein.
- Duplication (DP)
- An additional copy of a DNA segment present in the genome. Duplications can lead to an increase in the number of genes
carried on a chromosome and may or may not be cytologically visible.
- Embryos, cryopreserved (EM)
- Embryonic Stem (ES) Cells
- Undifferentiated cells derived from blastocyst-stage embryos. ES cells can differentiate in culture to a number of different
cell types. When incorporated into chimeric mouse embryos they are totipotent and can differentiate into any cell type in the mouse.
If these cells become part of the germline, they can mature to gametes and be "rescued" as living mice.
- Endonuclease Mediated Mutation (EMM)
- A type of engineered mutation in which a chromosomal gene is altered by the action of a RNA-guided DNA site-specific
endonuclease, including the actions of the clustered regulatory interspaced short palindromic repeat (CRISPR/Cas9)
system, transcription activator-like effector nucleases (TALENS) or zinc finger nucleases (ZFN). These endonucleases induce
a broad range of mutations by inducing DNA double-strand breaks that stimulate error-prone nonhomologous end joining
(NEJ) or homology-directed repair (HDR) at specified genomic locations.
- The basic unit of heredity; a portion of DNA that (usually) codes for a protein product. The term "gene" also may be used
to refer to a locus in the cytoplasmic or nuclear genome characterized by an altered phenotype or by an effect on an inserted
reporter gene, such as a gene trap or enhancer trap.
- Gene Name
- A gene name is a word or phrase that uniquely identifies a gene. The gene name has an abbreviation that is the gene symbol.
- Gene Symbol
- A gene symbol is a unique abbreviation for the gene name.
- Gene Trap (GT)
- A type of DNA construct containing a reporter gene sequence downstream of a splice acceptor site that is capable of
integrating into random chromosomal locations in mouse. Integration of the gene trap into an intron allows the expression
of a new mRNA containing one or more upstream exons followed by the reporter gene. The reporter gene is therefore expressed
in the same cells and developmental stages as the gene into which the gene trap has inserted.
- Hybrid (HY)
- First-generation progeny of a cross between mice of two inbred strains (F1 hybrid) or progeny of a cross between
F1 progeny of such a cross (F2 hybrid).
- Inbred Strain (IS)
- An inbred strain is essentially homozygous at all loci and each member of the strain is genetically identical to
other members (excepting sex differences). In mice, an inbred strain is produced from brother x sister matings for at
least 20 sequential generations. C57BL/6J is a widely-used inbred strain of mouse.
- Insertion (INS)
- A type of mutation in which one or more nucleotides is inserted into a DNA sequence. Small insertions within a gene
can alter the reading frame, and thus the amino acid sequence of the encoded protein.
- Inversion (INV)
- A type of mutation in which a length of DNA is broken in two positions and repaired in such a way that the medial
segment is now present in reverse order. Inversions range in size from those large enough to be visible cytogenetically
to those involving only a few base pairs.
- Knock in
- A type of targeted mutation in which an alteration in gene function other than a loss-of-function allele is produced.
- Knock out
- A type of targeted mutation in which a loss-of-function (often a null allele) is produced.
- Live Mice
- Living mice that are not in some state of cryopreservation.
- loxP Sequence
- A 34 base pair DNA sequence recognized by the site-specific recombination enzyme Cre.
- Major histocompatibility congenic (MAH)
- A congenic strain in which the donor allele transferred to the host strain background is a major histocompatibility gene.
- Any biological feature that can be positioned with respect to other features on a chromosome, by genetic, physical or other mapping methods. For example, a gene, anonymous DNA segment, mutation, or phenotype.
- MGI Accession ID
- A unique alphanumeric character string that is used to unambiguously identify a particular record in the Mouse Genome Informatics database. The format of a MGI Accession ID is MGI:nnnnnn, where n is a number.
- Minor histocompatibility congenic (MIH)
- A congenic strain in which the donor allele transferred to the host strain background is a minor histocompatibility gene.
- Mitochondrial Gene
- A gene contained within the mitochondrial genome of a eukaryote, transmitted independently of the nuclear genome. The mitochondrial genome is transmitted maternally (from the female parent).
- A term applied to a gene or phenotype altered by mutation or to an individual carrying a mutation.
- Mutant Strain (MSR)
- An inbred strain carrying one or more phenotypic mutations. For example, the mutant strain
C3H/H3eSn-bc3J/J carries the bouncy 3 Jackson phenotypic mutation.
- Mutant Stock
- A stock carrying one or more phenotypic mutations. The term "STOCK" is used for a mutant strain, incipient or inbred,
derived from more than two progenitor strains or having genetic contribution from an unknown genetic background source and
is considered a "mixed" inbred. For example, the mutant stock named STOCK Col2a1sedc/J carries the
spondyloepiphyseal dysplasia congenita phenotypic mutation of the procollagen, type II, alpha 1 gene.
- Any permanent change in DNA, i.e., in its nucleotide sequence. Examples include chromosome rearrangements and
point mutations. The term mutation also is used for the process through which genes undergo a structural change.
- Mutation Type
- A classification of alleles, usually representing how a mutant allele arose.
- Noninbred Stock
- A stock that is known to be noninbred, or intentionally kept noninbred.
- Ovaries, cryopreserved (OV)
- See cryopreservation.
- Outbred Stock (OUT)
- A closed population (for at least four generations) of genetically variable animals that is bred to maintain maximal heterozygosity.
- A description of the observable state of an individual with respect to some inherited characteristic.
Often, individuals with different genotypes display the same phenotype.
- Pseudoautosomal Gene
- A gene in the small region of homology shared between the X chromosome and the Y chromosome in mammals. All crossovers between the X and Y chromosomes occur in this region.
- Radiation Induced Mutation (RAD)
- A mutation induced by irradiation, in mouse usually gamma-ray or X-ray.
- Recombinant Congenic Strains (RC)
- Strains formed by crossing two inbred strains, followed by a few backcrosses to one of the parental strains,
with subsequent inbreeding without selection.
- Recombinant Inbred Strains (RI)
- Inbred strains created by crossing two different inbred strains, followed by brother x sister matings for at least
20 generations. A panel of recombinant inbred strains derived from a cross between the same original parental strains
can be used to establish linkage between any marker that is polymorphic between the parental strains and other polymorphic
markers that have been typed in each strain in the panel.
- Robertsonian Translocation (RB)
- A particular type of translocation in which the breakpoints in the two chromosomes occur at or near the centromere,
followed by centric fusion such that the long arms now form a metacentric chromosome with a single centromere.
Any small fragments generated in the exchange are usually lost. See also
- Segregating Inbred Strain (SEG)
- An inbred strain that is kept in forced heterozygosity for one or more loci. For example, the SM/J strain segregates
for an agouti allele and animals are either Aw/a (white bellied agouti) or a/a (black) in color.
- Sex Chromosome
- Either of two chromosomes that are sexually dimorphic in species with chromosomal (as opposed to genic) sex determination.
In mammals, males are the heterogametic sex, having an X chromosome and a Y chromosome, while females are the homogametic sex, having two X chromosomes.
- Site-specific Recombination
- Reciprocal recombination between specific target sequences catalyzed by a
specific recombination enzyme, as opposed to general homologous recombination.
One example is recombination at loxP sites catalyzed by Cre recombinase.
- Spontaneous Mutation (SM)
- Spontaneous mutations are those that occur in the absence of any experimental mutagenic treatment, such as irradiation or treatment with chemical mutagens.
- A synonym is an alternate symbol for a gene or allele that has appeared in the scientific literature or
in public databases such as GenBank, or a formerly official symbol, withdrawn to conform to new nomenclature procedures.
- Targeted Mutation (TM)
- A type of mutation in which a chromosomal gene is altered by the substitution of a DNA construct assembled
in vitro. These constructs are "targeted" to a specific gene and may cause deletion, insertion, or substitution
in the endogenous gene. In mouse, the constructs are frequently designed to eliminate gene function; such targeted
mutations are often referred to as knock outs. Some DNA constructs are designed to alter gene function through
replacement of native DNA sequence; such targeted mutations are referred to as knock ins.
- Transgenic Mouse
- A mouse that contains stably inherited DNA which has been experimentally inserted at random into the genome.
The inserted gene sequence (the transgene) may or may not be derived from mouse sequence.
- Translocation (TL)
- A type of chromosome rearrangement in which two nonhomologous chromosomes are each broken and then repaired in such a way
that the resulting chromosomes each contain material from the other chromosome (a reciprocal translocation). See also
- Transposition (TP)
- A type of chromosome rearrangement in which a segment of a chromosome is moved to a different location on the same chromosome
or to a different chromosome, without reciprocal exchange.
- Trisomy (TS)
- The condition of having three chromosomes of a particular type. Trisomy for a complete extra chromosome of the standard complement is
referred to as primary trisomy, such as in Down Syndrome in human where individuals are trisomic for Chromosome 21.
- Unclassified Strain/Stock (UN)
- Strains or Stocks that cannot be classified into any of the categories supported by the IMSR.
- In MGI, a map location of "unknown" means that the marker has not yet been assigned to a chromosome.
- Wild-Derived Inbred Strains (WDS)
- Strains formed by brother x sister matings or other inbreeding schemes from mice originally caught in the wild.
The IMSR Glossary was originally written by Rachael Selley (1998) of the MRC Genetics Unit, Harwell, and has subsequently been updated and expanded by the IMSR staff.
Some definitions derive directly from the