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The terminology that is used in biomedical research may be new to students or to readers who do not have previous exposure to this arena. To assist readers with some of the language that they may encounter at this site, or in some of the publications they may explore, a glossary has been assembled and is provided here.  Additional depth and other terms may be found at the original sources, or from other biomedical vocabulary providers. Such sources include: The Mouse Genome Informatics Glossary, The National Cancer Institute Thesaurus, and The National Human Genome Research Institute’s Talking Glossary of Genetic Terms. Many types of biomedical ontologies are accessible from the National Center for Biomedical Ontology’s repositories.

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3' (3-prime)

A term that identifies one end of a single-stranded nucleic acid molecule. The 3' end is that end of the molecule which terminates in a 3' phosphate group. The 3' direction is the direction toward the 3' end. Nucleic acid sequences are written with the 5' end to the left and the 3' end to the right, in reference to the direction of DNA synthesis during replication (from 5' to 3'), RNA synthesis during transcription (from 5' to 3'), and the reading of mRNA sequence (from 5' to 3') during translation.

Reference: MGI

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3' UTR

3' Untranslated Region. That portion of an mRNA from the 3' end to the position of the last codon used in translation. See also 5' UTR.

Reference: MGI

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5' (5-prime)

A term that identifies one end of a single-stranded nucleic acid molecule. The 5' end is that end of the molecule which terminates in a 5' phosphate group. The 5' direction is the direction toward the 5' end. Nucleic acid sequences are written with the 5' end to the left and the 3' end to the right, in reference to the direction of DNA synthesis during replication (from 5' to 3'), RNA synthesis during transcription (from 5' to 3'), and the reading of mRNA sequence (from 5' to 3') during translation.

Reference: MGI

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5' UTR

5' Untranslated Region. That portion of an mRNA from the 5' end to the position of the first codon used in translation. See also 3' UTR.

Reference: MGI

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Ab initio

Formulated without experimental data. Latin. From the beginning.

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Accession ID

A unique alphanumeric character string that is used to unambiguously identify a particular record in a database. Examples include MGI accession IDs, GenBank accession IDs, and PubMed accession IDs.

Reference: MGI

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Adenine (A)

A purine base that is a component of nucleotides and thus a normal component of DNA and RNA. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Adenocarcinoma

A common cancer characterized by the presence of malignant glandular cells. Morphologically, adenocarcinomas are classified according to the growth pattern (e.g., papillary, alveolar) or according to the secreting product (e.g., mucinous, serous). Representative examples of adenocarcinoma are ductal and lobular breast carcinoma, lung adenocarcinoma, renal cell carcinoma, hepatocellular carcinoma (hepatoma), colon adenocarcinoma, and prostate adenocarcinoma.

Reference: NCI-Thesaurus

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Adenovirus

A group of DNA containing viruses which infect mammals and are capable of causing respiratory disease, including one form of the common cold.

Reference: NCI-Thesaurus

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Adult Mouse Anatomical Dictionary

A controlled vocabulary providing standardized nomenclature for anatomical structures in the postnatal mouse (Theiler stage 28). See the Open Biological Ontologies (OBO) site for further information about structured, shared vocabularies for use within genomic and proteomic domains.

Reference: MGI

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Agonist

An agent that has affinity for a receptor and intrinsic activity at that receptor.

Reference: NCI-Thesaurus

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Agouti

A characteristic of the coat color of wild-type mice and other mammals in which an individual hair has black pigment (eumelanin) at the tip and the base, and a band of yellow pigment (phaeomelanin) in the middle. This coloration has the effect of softening the visual outline of a mammal in the wild, making it harder to see than an animal of solid color.

Reference: MGI

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Alias

An alternative symbol or name for part of the sequence of a known gene that resembles names for other anonymous DNA segments. For example, D6Mit236 is an alias for Cftr.

Reference: MGI

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Allele

One of the variant forms of a gene, differing from other forms in its nucleotide sequence.

Reference: MGI

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Allele Combination

A designation of the specific alleles present on the two homologous chromosomes for all relevant loci of a mouse (i.e., all allele pairs of a genotype). An allele combination can be composed of one or more allele pairs.

Reference: MGI

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Allele Name

An "allele name" is a word or phrase that uniquely identifies an allele of a given gene. The allele name has an abbreviation that is the allele symbol added as a superscript to the gene symbol.

Reference: MGI

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Allele Pair

A designation of the specific alleles present on the two homologous chromosomes for a given locus.

Reference: MGI

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Allele Symbol

An allele symbol is a unique abbreviation for the allele name. Allele symbols take the form of superscripts added to the gene symbol.

Reference: MGI

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Allele Type

A classification of alleles. Biologically, allele types represent how mutant alleles arose (for example, spontaneous, chemically induced, and so on).

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Allograft

A graft transferred from a donor of one species to a recipient of the same species but different genetic makeup.

Reference: NCI-Thesaurus

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Alternative Splicing

The production of two or more distinct mRNAs from RNA transcripts having the same sequence via differences in splicing (by the choice of different exons).

Reference: MGI

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Amino Acid

A molecule of the general formula NH2-CHR-COOH, where "R" is one of a number of different side chains. Amino acids are the building blocks of proteins. The sixty-four codons of the genetic code allow the use of twenty different amino acids (the primary amino acids) in the synthesis of proteins. Other nonprimary amino acids occur in proteins by enzymatic modification of amino acids in mature proteins, and as metabolic intermediates. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Amino Terminus

A term that identifies one end of a protein molecule. The amino terminus is that end of the molecule which terminates in a free amino group.

Reference: MGI

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Amorphic Mutation

A type of mutation in which the altered gene product lacks the molecular function of the wild-type gene. Synonyms: Loss-of-function Mutation, Null Mutation.

Reference: MGI

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Amplification

An increase in the number of copies of a specific DNA fragment; can be in vivo or in vitro.

Reference: MGI

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Ancestor

This term refers to terms in a hierarchical controlled vocabulary such as those containing Gene Ontology (GO), Mammalian Phenotype Ontology, and Adult Mouse Anatomical Dictionary terms. An "ancestor" of a term is a term any number of levels above it in the hierarchy from which it is descended. For example, the GO term enzyme [GO:0003824] is an ancestor to the GO term alcohol dehydrogenase [GO:0004022].

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Aneuploid

Not euploid.

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Angiogenesis

Development of new blood vessels.

Reference: NCI-Thesaurus

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Animal Husbandry

The science of breeding, feeding and care of domestic animals; includes housing and nutrition.

Reference: NCI-Thesaurus

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Anonymous DNA segment

A segment of DNA not known to correspond to a named gene that can be used as a marker in the construction of genetic maps.

Reference: MGI

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Antibody

A type of protein made by B lymphocytes in response to a foreign substance (antigen). Each antibody only binds to a specific antigen, helping to destroy the antigen directly or by assisting white blood cells to destroy the antigen.

Reference: NCI-Thesaurus

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Antigen

A protein or other molecule that can elicit an immune response; the antibody protein that is produced binds to the antigen.

Reference: MGI

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Antimorphic Mutation

A type of mutation in which the altered gene product possesses an altered molecular function that acts antagonistically to the wild-type allele. Antimorphic mutations are always dominant or semidominant.

Reference: MGI

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Antisense

1. In molecular biology, that strand of a DNA molecule whose sequence is complementary to the strand represented in mRNA. 2. In molecular biology, an RNA molecule complementary to the strand normally processed into mRNA and translated.

Reference: MGI

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Apoptosis

Programmed cell death, that is, the death of cells by a specific sequence of events triggered in the course of normal development (e.g., cells between digits in the limb bud) or as a means of preserving normal function (e.g., in response to viral infection).

Reference: MGI

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Arrayed Library

Individual primary recombinant clones (hosted in phage, cosmid, YAC, or other vector) that are placed in two-dimensional arrays in microtiter dishes. Each primary clone can be identified by the identity of the plate and the clone location (row and column) on that plate. Information gathered on individual clones from various experimental techniques is entered into a relational database and used to construct physical and genetic linkage maps simultaneously; clone identifiers serve to interrelate the multilevel maps.

Reference: MGI

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Assay

In general, the qualitative or quantitative analysis of a substance. An assay is a type of experiment that is designed to detect the level of gene expression of a particular gene, or to determine the pattern of expression of a gene among different tissue types, anatomical structures, or developmental stages. The assay may detect one or more of the RNA transcripts of a gene or one or more of its protein products. Assay types include: Immunohistochemistry, Northern blot, Protein histochemistry, RNA In situ hybridization, In situ reporter, RNAse protection, RT-PCR, Western blot

Reference: MGI

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Assembly Coordinates

Numerical values defining a sequence interval along a chromosome in the mouse genome assembly. In MGI, gene sequences are defined as the interval between the start position of the first exon and the end position of the last exon of a gene as annotated by NCBI Gene or Ensembl. See NCBI Gene Model and Ensembl Gene Model for further information.

Reference: MGI

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Assembly Sequence

The sequence defined by an interval along a chromosome in the genome assembly. Assembly sequences are defined as the interval between the start position of the first exon and the end position of the last exon of a gene as annotated by the NCBI or Ensembl gene models.

Reference: MGI

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ATCC

American Type Culture Collection. A large collection of microbial stocks, including microbes containing mammalian DNA segments.

Reference: MGI

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Autoradiography

The detection of a unstable isotope that emits radiation by a photographic emulsion. In the case of in situ hybridization, this involves dipping microscope slides in liquid emulsion. In the case of Southern blots, Northern blots, or Western blots, the membrane is placed next to a sheet of X-ray film.

Reference: MGI

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Autosome

Any chromosome that is not a sex chromosome.

Reference: MGI

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B-Lymphocyte

Immunologically important lymphocyte that is not thymus-dependent, is either short-lived and naive or long-lived and of memory phenotype, and resembles the bursa-derived lymphocyte of birds in that it is responsible for the production of immunoglobulins.

Reference: NCI-Thesaurus

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BAC

Bacterial Artificial Chromosome. A type of cloning vector derived from the naturally-occurring F factor episome. A BAC can carry 100 - 200 kb of foreign DNA.

Reference: MGI

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BAC/YAC End

BAC/YAC end refers to sequences at the end of foreign DNA inserts in a BAC or YAC. These sequences are a source of STSs to determine the extent of overlap between BACs or YACs and to aid in the alignment of sequence contigs.

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Backcross

A type of genetic cross in which a hybrid strain is crossed to one of the two parental strains.

Reference: MGI

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Bacteriophage

A virus that infects bacteria.

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Base

One of a set of nitrogenous compounds attached to the sugar-phosphate backbone in a nucleic acid. In DNA, the purine bases are adenine (A) and guanine (G), while the pyrimidine bases are cytosine (C) and thymine (T). In RNA, the purine bases are adenine (A) and guanine (G), while the pyrimidine bases are cytosine (C) and uracil (U).

Reference: MGI

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Base Pair

In double-stranded nucleic acids, a "base pair" is the structure formed between two complementary nucleotides by hydrogen bonding. In DNA, adenine(A) pairs with thymine (T) and cytosine (C) pairs with guanine (G). In RNA, adenine (A) pairs with uracil (U) and cytosine (C) pairs with guanine (G). See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Base Sequence

The order of nucleotide bases in a DNA or RNA molecule.

Reference: MGI

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BIND

Biomolecular Interaction Network Database. A collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature.

Reference: MGI

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Bioassay

A laboratory test or analysis of the biological activity of a substance performed by studying its effect on an organism or in a test tube under controlled conditions.

Reference: NCI-Thesaurus

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Biochemical

Of or relating to biochemistry; involving chemical processes in living organisms.

Reference: NCI-Thesaurus

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Bioinformatics

The application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research, particularly in genomics.

Reference: MGI

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Biological Process

Refers to a broad category of biological tasks accomplished via one or more ordered assemblies of molecular functions. Usually there is some temporal aspect to it, although a process event may be essentially instantaneous. It often involves transformation, in the sense that something goes into a process and something different comes out of it. Examples of biological processes included in this category are cell growth and maintenance, signal transduction, pyrimidine metabolism, and cAMP biosynthesis. In the GO Project vocabularies, Biological Process is a primary class of terms. See the GO Consortium site for further information.

Reference: MGI

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Biomarker

A variation in cellular or biochemical components or processes, structures, or functions that is objectively measurable in a biological system and that characterizes normal biologic processes, pathogenic processes, an organism's state of health or disease, likelihood of developing a disease, prognosis, or response to a particular therapeutic intervention. Biomarkers include but not limited to such phenotypic parameters as specific enzyme or hormone concentration, specific gene phenotype, presence or absence of biological substances.

Reference: NCI-Thesaurus

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Biosynthesis

Synthesis of chemical compounds by enzymatic processes in living organisms.

Reference: MGI

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Biotechnology

The field devoted to applying the techniques of biochemistry, cellular biology, biophysics, and molecular biology to addressing issues related to human beings and the environment.

Reference: NCI-Thesaurus

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Biotin

One of the water-soluble B vitamins. It is useful in molecular biology as a chemical tag on nucleic acid probes or antibodies, because the biotin-scavenging proteins avidin and streptavidin bind biotin with high affinity. These biotin-binding proteins can be coupled to fluorescent dyes, enzymes that can be detected using chromogenic reactions, or colloidal gold, allowing detection of biotin-labeled probes or antibodies on Southern blots, Northern blots, Western blots, or cytological preparations.

Reference: MGI

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BLAST

Basic Local Alignment and Searching Tool. A sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query sequence. There is a description of the specific algorithm used, and additional information, at NCBI.

Reference: MGI

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Blastocyst

An embryo made up of two groups of cells. One group will develop into the fetus and the other will become the placenta.

Reference: NCI-Thesaurus

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Blood-Brain Barrier

A network of blood vessels with closely spaced cells that makes it difficult for potentially toxic substances (such as anticancer drugs) to penetrate the blood vessel walls and enter the brain.

Reference: NCI-Thesaurus

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cAMP

Cyclic AMP. A form of the nucleotide adenosine monophosphate that serves as a signaling molecule within and between cells.

Reference: MGI

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Carboxyl Terminus

A term that identifies one end of a protein molecule. The carboxyl terminus is that end of the molecule which terminates in a free carboxyl group.

Reference: MGI

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Carcinogen

Any chemical, biological or physical agents that increase the risk of neoplasms in humans or animals. Carcinogens include natural or synthesized compounds, certain viruses, and various sources of radiation. A carcinogen may directly alter the genetic material of cells (genotoxic), thereby initiating or promoting the process of malignant transformation; it also may induce cancers by mechanisms that do not involve a direct alteration of cellular genetic material (non-genotoxic). (NCI04)

Reference: NCI-Thesaurus

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Carcinogenesis

A pathological process in which normal cells are transformed into malignant cancer cells within a primary tumor. Metastasis occurs in advanced stage cancers, whereby cancer cells are released into the bloodstream and attach to sites distinct from the primary tumor, resulting in the formation of secondary tumors.

Reference: NCI-Thesaurus

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Carcinoma

A malignant tumor arising from epithelial cells. Carcinomas that arise from glandular epithelium are called adenocarcinomas, those that arise from squamous epithelium are called squamous cell carcinomas, and those that arise from transitional epithelium are called transitional cell carcinomas. Morphologically, the malignant epithelial cells may display abnormal mitotic figures, anaplasia, and necrosis. Carcinomas are graded by the degree of cellular differentiation as well, moderately, or poorly differentiated. Carcinomas invade the surrounding tissues and tend to metastasize to other anatomic sites. Lung carcinoma, skin carcinoma, breast carcinoma, colon carcinoma, and prostate carcinoma are the most frequently seen carcinomas.

Reference: NCI-Thesaurus

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Cardiovascular

Pertaining to the heart or blood vessels.

Reference: NCI-Thesaurus

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Catabolism

Degradation of chemical compounds into compounds having a lower molecular weight by enzymatic processes in living organisms.

Reference: MGI

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cDNA

Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase.

Reference: MGI

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Cell Microenvironment

 The complex relationships between tumor cells and the neighboring cells in the host environment. Cellular signaling within the microenvironment can promote the continuing survival and growth of tumor cells, or apoptosis (cell death). Research is currently underway to manipulate this relationship by altering the host environment in ways that silence or inhibit pro-survival signals concurrent with standard therapies.

Reference: NCI-Thesaurus

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Cellular Component

Refers to subcellular structures, locations, and macromolecular complexes. Some examples are nucleus, telomere and origin recognition complex. In the GO Project vocabularies, Cellular Component is a primary class of terms. See the GO Consortium site for further information.

Reference: MGI

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Centimorgan

A unit of length in a genetic map. Two loci are 1 cM apart if recombination is detected between them in 1% of meioses.

Reference: MGI

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Central Dogma

The principal statement of the molecular basis of inheritance. In its simplest form: "DNA makes RNA makes protein." This means that (generally) genetic information is stored in and transmitted as DNA. Genes are expressed by being copied as RNA (transcription), which is processed into mRNA via splicing and polyadenylation. The information in mRNA is translated into a protein sequence using a genetic code to interpret three-base codons as instructions to add one of twenty amino acids or to stop translation.

Reference: MGI

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Centromere

In mammalian genetics, the primary constriction of a chromosome separating it into the short arm (p) and the long arm (q). The centromere is the chromosomal region over which the kinetochore is organized. Mouse chromosomes have centromeres close to one end and have essentially no short arm. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Chemical

A substance with a defined atomic or molecular structure that results from, or takes part in, reactions involving changes in its structure, composition, or properties.

Reference: NCI-Thesaurus

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Chemically Induced Mutation

A mutation induced by treatment with a chemical mutagen, for example, ENU (ethyl nitrosourea) or chlorambucil.

Reference: MGI

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Chemoprevention

The use of natural or synthetic substances (e.g., drugs, vitamins, hormones, plant products) or food supplements to reduce the risk of developing a disease, to reduce the chance that disease will recur, or to delay the recurrence.

Reference: NCI-Thesaurus

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Chemotherapy

The use of synthetic or naturally-occurring chemicals for the treatment of diseases. Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity.

Reference: NCI-Thesaurus

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Chiasma

The cytologically visible consequence of a reciprocal recombination event in meiosis, observable in the later stage of meiotic prophase. Chiasmata hold homologous chromosomes together prior to anaphase of the first meiotic division.

Reference: MGI

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Children

In MGI, this term refers to terms in a hierarchical controlled vocabulary like ones containing Gene Ontology (GO) terms. A "child" of a term is a term any number of levels below it in the hierarchy that is a descendant of the term. For example, the GO term alcohol dehydrogenase [GO:0004022] is a child of the GO term enzyme [GO:0003824].

Reference: MGI

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Chimera

1. An animal formed from two different animals, that is from two different embryonic sources. In mouse genetics, targeted mutations produced in embryonic stem cells are recovered by breeding chimeric mice resulting from the mixture of ES cells with a genetically-distinct blastocyst.2. A clone containing genomic DNA from nonadjacent genomic segments or cDNA from two different mRNAs.

Reference: MGI

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Chlorambucil

A chemical mutagen, also called nitrogen mustard.

Reference: MGI

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Cholangiocarcinoma

An malignant tumor composed of cells resembling those of bile ducts. Cholangiocarcinoma is a relatively rare tumor in most populations. It can arise from any portion of the intrahepatic bile duct epithelium or the hepatic ducts. Grossly, the lesions are nodular, grayish-white firm and solid. Microscopically, the vast majority of cholangiocarcinomas are adenocarcinomas showing tubular and/or papillary structures. Early detection of cholangiocarcinomas is difficult, and the overall prognosis after resection is poor (adapted from WHO, 2000).

Reference: NCI-Thesaurus

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Chromatin

The nuclear material that makes up chromosomes, consisting of DNA and protein.

Reference: MGI

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Chromogenic

Color-generating. A chromogenic substrate is colorless until acted upon by an enzyme; it then becomes an insoluble pigment.

Reference: MGI

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Chromosome

A structural unit within a eukaryotic nucleus that carries genes. A chromosome consists of a long, continuous strand of DNA and associated proteins. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Chromosome Aberration

1. A chromosome rearrangement. 2. Less commonly, a numerical aberration.

Reference: MGI

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Chromosome Rearrangement

A kind of mutation in which there is a change in the arrangement of the genome into chromosomes; this term usually applies to those changes that are visible cytogenetically. Classes of chromosome rearrangements include: Deletion, Duplication, Insertion, Inversion, Translocation, Transposition

Reference: MGI

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Clone

1. A segment of DNA contained within a cloning vector. 2. An organism derived from a founding individual by asexual means that is genetically identical to the founding individual.

Reference: MGI

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Clone Collection

Clone collections in MGI refer to designated sets of clones from specific clone libraries. In some cases, the designated set of clones includes all clones from the specified libraries (for example, the IMAGE clone collection is the group of clones from all IMAGE. consortium clone libraries). In other cases, the designated set of clones includes a well-defined subset of clones from the specified libraries (for example, the NIA 15K clone set is a subset of clones derived from NIA libraries). Clone data in MGI include sequence associations and clone library molecular source information. For all MGI clone collections, molecular source information is mapped to MGI controlled vocabularies.

Reference: MGI

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Cloning Artifact

A DNA clone whose structure does not accurately represent genomic or mRNA sequence, due to errors in the cloning process. For example, two noncontiguous genomic fragments may be joined by ligation prior to being incorporated into the cloning vector.

Reference: MGI

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Cloning Vector

A DNA construct capable of replication within a bacterial or yeast host that can harbor foreign DNA, facilitating experimental manipulation of that DNA segment.

Reference: MGI

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cM

See centimorgan.

Reference: MGI

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Co-clinical Trial

In a co-clinical trial, drug combinations are tested contemporaneously in mouse models that closely mimic human diseases, and in small numbers of molecularly matched patients who have failed initial or follow-up standard-of-care therapy. Clinical, biological, and pharmacological information are accrued, analyzed in parallel, and integrated to facilitate response biomarker discovery and to advise selection of imaging biomarkers to distinguish responders from non-responders.

Reference: Emice

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Coding Region

That part of a gene whose sequence is read as codons during translation.

Reference: MGI

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Codominant

One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "a" is said to be codominant with respect to the wild-type allele "A" if the A/a heterozygote fully expresses both of the phenotypes associated with the a/a and A/A homozygotes. An example of codominance is the ABO blood type antigens in humans, where AA individuals are type A, BB individuals are type B, and AB individuals are type AB.

Reference: MGI

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Codon

Three bases in a DNA or RNA sequence that specify an amino acid or a termination signal (stop codon).

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Cohort

A group of individuals, identified by a common characteristic.

Reference: NCI-Thesaurus

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Coisogenic Strain

A strain that differs from a particular inbred strain at only one locus. A coisogenic strain arises when a mutation occurs in an inbred strain. The coisogenic strain can be propagated by intercrossing heterozygotes to produce homozygotes; if these are nonviable, the strain can be maintained by backcrossing heterozygotes to the original inbred strain. See also the Rules for Nomenclature of Mouse and Rat Strains.

Reference: MGI

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Colloidal Gold

Fine particles of gold (on the order of 5-20 nm diameter) that can be coupled to antibodies or other proteins, allowing the detection of the binding of the labeled proteins by electron microscopy.

Reference: MGI

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Complementary DNA

See cDNA.

Reference: MGI

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Complementary Sequence

A single-stranded nucleic acid that would bind to a given single-stranded nucleic acid by following base pairing rules (A pairs with T and C with G). The complementary sequence to GTAC for example, is CATG.

Reference: MGI

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Complementation

The appearance of a wild-type phenotype in an individual that is the hybrid offspring of two mutant individuals homozygous for recessive mutations. Complementation shows that the two parental mutant individuals have mutant alleles of different genes, even if they are phenotypically similar. For example, a cross between two light gray mice(ash/ash and d/d) would produce a black mouse.

Reference: MGI

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Complex/Cluster/Region

In MGI, the marker type "Complex/Cluster/Region" refers to any of the following: 1. Gene complex; a group of genes closely linked together that are related evolutionarily or functionally. Interspersed unrelated genes located within the group are included. 2. A segment of the mouse genome defined by comparison to an orthologous segment in the genome of another species, or by some specific characteristic, such as loss of heterozygosity. 3. A marker repository for information pertaining to a specific gene family, where such information lacks precise family member resolution.

Reference: MGI

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Compound Heterozygote

A heterozygote where different mutant alleles are present at the two copies of a given locus. In MGI, a compound heterozygote occurs when the two opposing alleles are associated with different MGI markers.

Reference: MGI

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Conditional Genotype

A genotype that is dependent on the presence of some other factor (often a DNA sequence that expresses a protein functioning in specific recombination events). In MGI, conditional is most commonly used to represent Cre-mediated excision of genomic sequences flanked by loxP sites. In most instances, excision of the endogenous genomic sequence flanked by loxP sites is accompanied by simultaneous insertion of some selectable marker (e.g. neomycin). The excised genotype, which is often associated with a phenotype, is dependent (or conditional) on the presence of the Cre-expressing construct.

Reference: MGI

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Congenic Strain

Congenic strains are produced by transferring a mutation from one genetic background to a specific inbred strain through repeated backcrossing. The congenic strain and the inbred partner are expected to be identical at all loci except for the transferred locus and a linked segment of chromosome. The size of the segment and the possibility of transferred alleles on other chromosomes depend on the number of backcross generations. A strain is considered fully congenic after ten generations of backcrossing (N10). (from JAX Strain Information)

Reference: NCI-Thesaurus

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Conplastic Strain

Conplastic strains are developed by backcrossing the nuclear genome from one inbred strain into the cytoplasm of another, i.e. the mitochondrial parent is always the female parent during the backcrossing program. The strain designation is NUCLEAR GENOME-mtCYTOPLASMIC GENOME. For example, C57BL/6J-mtBALB/c is a strain with the nuclear genome of C57BL/6J and the cytoplasmic genome of BALB/c. It was developed by crossing male C57BL/6J mice with BALB/c females, followed by repeated backcrossing of female offspring to male C57BL/6J. As with congenic strains, a minimum of 10 backcross generations is required, counting the F1 generation as generation 1. See also the Rules for Nomenclature of Mouse and Rat Strains.

Reference: MGI

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Conserved Sequence

A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained relatively unchanged throughout evolution.

Reference: MGI

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Conserved Synteny

The occurrence of synteny of orthologous genes in two different organisms. Conserved synteny between mouse and human does not usually extend over entire chromosomes, with the exception of the X chromosome. See the Orthology Map for a graphical display of conserved synteny.

Reference: MGI

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Consomic Strain

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.

Reference: IMSR

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Constitutively active

In cell biology, a constitutively active protein is a protein whose activity is constant and active

Reference: Wikipedia

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Contig

1. A physical map of contiguous genomic DNA assembled using overlapping cloned segments (see STS). 2. A contiguous DNA sequence assembled using overlapping DNA sequences.

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Controlled Vocabulary

A restricted set of defined terms allowing the representation of complex information in a database.

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Copy Number

The number of molecules of a particular type on or in a cell or part of a cell. Usually applied to specific genes or to plasmids within a bacterium.

Reference: NCI-Thesaurus

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Copy Number Polymorphism

Variation in the number of copies of a particular sequence within the genetic material of an individual. Large-scale copy number polymorphisms are common and widely distributed in the human genome.

Reference: NCI-Thesaurus

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Copy Number Variation

A copy number variant (CNV) is a segment of DNA in which copy-number differences have been found by comparison of two or more genomes. The segment may range from one kilobase to several megabases in size. Humans (being diploid) ordinarily have two copies of each autosomal region, one per chromosome. This may vary for particular genetic regions due to deletion or duplication.

Reference: Wikipedia

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Cosmid

A type of cloning vector derived from bacteriophage lambda. A cosmid can carry about 40 kb of foreign DNA.

Reference: MGI

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Cre Recombinase

A site-specific recombination enzyme that recognizes the 34 base pair loxP sequence.

Reference: MGI

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Cross

An experimental mating of two genetically distinct sexually reproducing organisms.

Reference: MGI

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Cross-hybridization

With respect to nucleic acids, "cross-hybridization" refers to the formation of double-stranded DNA, RNA, or DNA/RNA hybrids by complementary base pairing between two molecules that are not identical in sequence. Cross-hybridization may be observed between nucleic acids derived from orthologous or paralogous genes.

Reference: MGI

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Crossover

A reciprocal recombination event.

Reference: MGI

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Cryopreservation

Preservation of cells, tissues, organs, or embryos by storage at low temperatures.

Reference: NCI-Thesaurus

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Cy5

A fluorescent dye used to label DNA probes for FISH or antibodies for immunofluorescence or Western blots.

Reference: MGI

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Cyclosporine

A natural cyclic polypeptide immunosuppressant isolated from the fungus Beauveria nivea. The exact mechanism of action of cyclosporine is not known but may involve binding to the cellular protein cytophilin, resulting in inhibition of the enzyme calcineurin. This agent appears to specifically and reversibly inhibit immunocompetent lymphocytes in the G0-or G1-phase of the cell cycle. T-lymphocytes are preferentially inhibited with T-helper cells as the primary target. Cyclosporine also inhibits lymphokine production and release.

Reference: NCI-Thesaurus

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Cytoband

One of the subregions of a chromosome visible microscopically after special staining.

Reference: MGI

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Cytogenetic

Refers to the correlation of genetic and cytological information through the microscopic analysis of stained preparations of chromosomes, including those from individuals carrying mutations.

Reference: MGI

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Cytogenetic Band

One of the subregions of a chromosome visible microscopically after special staining.

Reference: MGI

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Cytogenetic Map

A type of genetic map relating gene positions to chromosomal banding patterns. The maps are built from relating the positions of genes to cytogenetic markers or by in situ hybridization.

Reference: MGI

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Cytogenetic Marker

1. A structure within a chromosome that is visible by microscopic examination, possibly after special staining methods are used. 2. A chromosome rearrangement that is visible by microscopic examination.

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Cytogenetics

The branch of biology that studies the cellular aspects of heredity, especially the chromosomes. Includes the study of disease states caused by numerical and structural chromosome abnormalities.

Reference: NCI-Thesaurus

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Cytoplasm

That part of a eukaryotic cell that is not the nucleus.

Reference: MGI

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Cytosine (C)

A pyrimidine base that is a component of nucleotides and thus a normal component of DNA and RNA. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Degenerate

A term describing one of the qualities of the genetic code, specifically, that some amino acids may be specified by more than one codon.

Reference: MGI

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Deletion

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. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Denaturation

1. The separation of the two strands of a double-stranded nucleic acid caused by treatments that overcome hydrogen bonding, e.g., heat. 2. A usually irreversible change in the conformation of a protein caused by treatments that overcome hydrogen bonding, hydrophobic interactions, or other chemical forces that maintain the structure of proteins, e.g., heat.

Reference: MGI

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Deoxyribonucleotide

A monomer unit of DNA, consisting of a purine or pyrimidine base, a deoxyribose sugar molecule, and phosphate group(s).

Reference: MGI

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Dephosphorylation

The catalyzed removal of phosphate groups from biological molecules, by phosphatases.

Reference: NCI-Thesaurus

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Dimorphic

Having two forms.

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Diploid

Having twice the chromosome number normally found in a gamete. Normal mice are diploid, having a chromosome set from the maternal gamete (the egg) and a chromosome set from the paternal gamete (the sperm). See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Direct detection

Indicates that the expression of the reporter gene was detected using a direct method, such as fluorescence or using an enzymatic substrate.

Reference: MGI

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Directed Sequencing

The sequencing of a large DNA segment through the sequencing of subsegments known to be adjacent.

Reference: MGI

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Disease

In MGI, any human disease, condition, or syndrome listed in the OMIM database.

Reference: MGI

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DNA

A long linear double-stranded polymer formed from nucleotides attached to a deoxyribose backbone and found in the nucleus of a cell; associated with the transmission of genetic information.

Reference: NCI-Thesaurus

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DNA Construct

An assembly of DNA sequences made in vitro to serve an experimental purpose.

Reference: MGI

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DNA Methylation

Attachment of methyl groups (-CH3) to DNA, most commonly at the cytosine bases.

Reference: MGI

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DNA Polymerase

An enzyme that carries out replication.

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DNA Replication

The use of existing DNA as a template for the synthesis of new DNA strands. In mouse and other eukaryotes, replication occurs in the cell nucleus.

Reference: MGI

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DNA Segment

1. A length of DNA. 2. In MGI, a DNA segment is a genomic feature recognized by anonymous DNA probes. Symbols for such segments most commonly represent intergenic markers used in genetic mapping.

Reference: MGI

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DNA Sequence

The relative order of base pairs, whether in a fragment of DNA, a gene, a chromosome, or an entire genome.

Reference: MGI

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DNA Sequence Rearrangement

Any process affecting a DNA sequence that results in the gain, loss or exchange of DNA between chromosomes and/or autonomous replicons.

Reference: NCI-Thesaurus

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dNTP

Deoxyribonucleotide triphosphate. A generic term referring to the four deoxyribonucleotides: dATP, dCTP, dGTP and dTTP.

Reference: MGI

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Dominant

One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "A" is said to be dominant with respect to the allele "a" if the A/A homozygote and the A/a heterozygote are phenotypically identical and different from the a/a homozygote. An example is the Pmp22(Tr) mutation in mouse, which causes a myelination defect associated with a "trembler" phenotype. Pmp22(Tr)/Pmp22(Tr) and Pmp22(Tr)/Pmp22(+) animals are phenotypically identical, displaying the mutant phenotype, while Pmp22(+)/Pmp22(+) animals are wild-type. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Double Helix

The shape that two linear strands of DNA assume when hydrogen-bonded together.

Reference: MGI

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Draft Genome Sequence

Sequence of genomic DNA having lower accuracy than finished sequence; some segments are missing or in the wrong order or orientation.

Reference: MGI

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Duplication

An additional copy of a DNA segment present in the genome. Gene duplication is the source of paralogous genes. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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E. coli

Common bacterium that geneticists have studied intensively because of its small genome size, normal lack of pathogenicity, and ease of growth in the laboratory.

Reference: MGI

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EC Number

A number assigned to a type of enzyme according to a scheme of standardized enzyme nomenclature developed by the Enzyme Commission of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). EC numbers may be found in ENZYME, the Enzyme nomenclature database, maintained at the ExPASy molecular biology server of the Geneva University Hospital and the University of Geneva, Switzerland.

Reference: MGI

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Electrophoresis

The separation of charged molecules (DNA, RNA or protein) in an electrical field, usually in a supporting medium such as an agarose or polyacrylamide gel.

Reference: MGI

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Electroporation

The use of strong, brief pulses of electric current to create temporary holes in cell membranes, allowing the introduction of DNA.

Reference: MGI

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EMBL

European Molecular Biology Laboratory Nucleotide Sequence Database.

Reference: MGI

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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: they can differentiate into any cell type in the mouse.

Reference: MGI

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EMS

Ethyl methanesulfonate (methanesulfonic acid ethyl ester). A chemical mutagen.

Reference: MGI

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Endogenous

Contained within. In mouse genetics, endogenous viruses are those that are integrated into the mouse genome and transmitted to progeny as chromosomal elements.

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Endonuclease

A protein that cleaves the phosphodiester backbone of a nucleic acid enzymatically, for example a restriction enzyme.

Reference: MGI

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Enhancer

One of the necessary regulatory elements of a gene. An enhancer is a site on DNA to which a complex of transcription factors binds to affect the availability of the promoter to RNA polymerase. A gene may have multiple enhancers.

Reference: MGI

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Enhancer Trap

A type of DNA construct containing a reporter gene sequence downstream of a promoter that is capable of integrating into random chromosomal locations in mouse. Integration of the enhancer trap near an enhancer allows the expression of a new mRNA encoding the reporter gene. The reporter gene is therefore expressed in the cells and developmental stages where the enhancer is active.

Reference: MGI

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Ensembl Gene Model

A description of a gene associated with the mouse genome assembly from the Mouse Genome Sequencing Consortium (MGSC). The gene model includes the coordinates of each intron and exon, as well as the beginning and end of the transcript.

Reference: MGI

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ENU

A nitrosourea with potential antineoplastic activity. Used experimentally as a mutagen and carcinogen, ethylnitrosourea alkylates DNA and proteins, thereby damaging DNA and inducing point mutations. (NCI04)

Reference: NCI-Thesaurus

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Enzyme

A protein (or rarely, RNA) that catalyzes a chemical reaction.

Reference: MGI

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Epigenetic

Refers to factors affecting the development or function of an organism other than the primary sequence of the target genes.

Reference: MGI

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Epigenome

The term epigenome is derived from the Greek word epi which literally means "above" the genome. The epigenome consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it, and when to do it. Different cells have different epigenetic marks. These epigenetic marks, which are not part of the DNA itself, can be passed on from cell to cell as cells divide, and from one generation to the next.

Reference: NHGRI

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Episome

A plasmid able to integrate into bacterial DNA.

Reference: MGI

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Epistasis

Masking of a phenotypic trait through the action of a mutant allele. For example, albinism (absence of pigment) is epistatic to coat color genes that determine black vs. brown fur.

Reference: MGI

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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: they can differentiate into any cell type in the mouse.

Reference: MGI

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EST

Expressed Sequence Tag. A partial sequence of a randomly chosen cDNA, obtained from the results of a single DNA sequencing reaction. ESTs are used both to identify transcribed regions in genomic sequence and to characterize patterns of gene expression in the tissue that was the source of the cDNA.

Reference: MGI

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Ethidium Bromide

A fluorescent dye that intercalates between base pairs in double-stranded nucleic acids or between bases in single-stranded nucleic acids. Ethidium bromide is commonly used to visualize DNA on agarose gels.

Reference: MGI

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Ethylnitrosourea

A nitrosourea with potential antineoplastic activity. Used experimentally as a mutagen and carcinogen, ethylnitrosourea alkylates DNA and proteins, thereby damaging DNA and inducing point mutations. (NCI04)

Reference: NCI-Thesaurus

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Etiology

1. The cause of a disease. 2. In MGI, the genes identified as involved in causing a disease.

Reference: MGI

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Euchromatin

The part of the genome characterized by relatively high gene density and relative absence of highly repetitive sequences.

Reference: MGI

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Eukaryote

A cell or organism with membrane-bound, structurally discrete nucleus and other well-developed subcellular compartments. Eukaryotes include all organisms except viruses, bacteria, and blue-green algae.

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Euploid

Having a chromosome number that is an integral multiple of the haploid number without segmental duplications or deletions.

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Evolution

Change of the genes of a population over time, resulting in new species.

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Evolutionary Conservation

The presence of similar genes, portions of genes, or chromosome segments in different species, reflecting both the common origin of species and an important functional property of the conserved element.

Reference: MGI

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Exome

The exome is the part of the genome formed by exons, coding portions of genes in the genome that are expressed, that is, provide the genetic blueprint used in the synthesis of proteins and other functional gene products. It is the functionally most relevant part of the genome and most likely to contribute to the phenotypes of an organism. For the human genome, the exome is estimated to comprise 1.5% of the total genome.

Reference: Wikipedia

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Exon

The sequences of a gene that are present in the final, mature, spliced messenger RNA molecule from that gene.

Reference: NCI-Thesaurus

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Expressivity

The relative constancy of the phenotype of individuals of a given genotype. Mutations said to have variable expressivity show a relatively large amount of phenotypic variation among individuals having the same genotype.

Reference: MGI

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FASTA format

A data format for nucleic acid or protein sequences.

Reference: MGI

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Field

In a relational database, an item of information, such as a chromosome number, or the centimorgan length on a genetic map. Some fields are numeric, while others are textual; some are long, while others are short. In addition, every field has a name, called the field name. In database management systems, a field can be required, optional, or calculated. A required field is one in which you must enter data, while an optional field is one you may leave blank. A calculated field is one whose value is derived from some formula involving other fields. You do not enter data into a calculated field; the system automatically determines the correct value. A collection of fields is called a record.

Reference: MGI

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Finished sequence

Sequence of genomic DNA in which: a) bases are identified to an accuracy of no more than one error in 10,000 bases, b) there is no ambiguity about the order or orientation of any segment, and c) there are few if any gaps.

Reference: MGI

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FISH

Fluorescent in situ hybridization. A method for determining the cytogenetic location of a cloned segment of DNA. The DNA is labeled with a fluorescent dye and hybridized to a cytological preparation of chromosomes that has been denatured to allow nucleic acid hybridization between chromosomal DNA and the probe. The site of hybridization is determined by fluorescent microscopy. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Floxed

Refers to a DNA construct in which a gene or gene segment is flanked by loxP sites in the same orientation; Cre recombinase excises the segment between the loxP sites.

Reference: MGI

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Fluorescence

Emission of secondary light generated by excitation by ultraviolet light, a beta particle or a gamma ray.

Reference: MGI

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Fluorography

The detection of radiation or of a fluorescent compound by secondary light that was generated by the excitation of a "fluor" or a screen by light, a beta particle or a gamma ray.

Reference: MGI

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Frameshift

A type of mutation in which there is an insertion or deletion that changes the reading frame.

Reference: MGI

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Gain-of-function Mutation

A type of mutation in which the altered gene product possesses a new molecular function or a new pattern of gene expression. Gain-of-function mutations are almost always Dominant or Semidominant.

Reference: MGI

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Gamete

One of the differentiated cells that is a product of meiosis. In animals, sperm or egg cells.

Reference: MGI

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GCG Format

A data format for nucleic acid or protein sequences.

Reference: MGI

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GenBank

The database of nucleic acid sequences at NCBI.

Reference: MGI

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Gene

A functional unit of heredity which occupies a specific position (locus) on a particular chromosome, is capable of reproducing itself exactly at each cell division, and directs the formation of a protein or other product.

Reference: NCI-Thesaurus

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Gene Complex

A number of apparently functionally or evolutionarily related loci that are genetically closely linked. Alternative states of complexes are referred to as haplotypes rather than alleles.

Reference: MGI

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Gene Conversion

A type of nonreciprocal recombination event in which a recipient strand of DNA receives information from another strand having an allelic difference. The recipient strand has its original allele "converted" to the new allele as a consequence of the event.

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Gene Expression

Transcriptional activity of a gene resulting in one or more RNA products and, usually, following translation, one or more protein products.

Reference: MGI

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Gene Family

A group of paralogous genes.

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Gene Model

A representation of an mRNA transcript of a gene that contains information about features of the transcript such as exon- intron boundaries, splice sites, UTRs, etc. Due to alternative splicing of mRNA transcripts, there may be more than one gene model for any given gene.

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Gene Name

In MGI, a "gene name" is a word or phrase that uniquely identifies a gene. The gene name has an abbreviation that is the gene symbol.

Reference: MGI

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Gene Ontology (GO)

A set of controlled vocabularies used to describe biological features within a specified domain of biological knowledge. See the GO Consortium site for further information.

Reference: MGI

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Gene Product

1. A protein molecule that is the product of the expression of a gene, through which the gene influences development or metabolism. 2. An RNA molecule that is the product of the expression of a gene, specially those cases in which the RNA molecule is not translated.

Reference: MGI

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Gene Regulation Process

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene expression at the level of transcription or translation.

Reference: NCI-Thesaurus

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Gene Symbol

As used in MGI, a "gene symbol" is a unique abbreviation for the gene name.

Reference: MGI

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Gene Trap

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.

Reference: MGI

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Genetic

Having to do with information that is passed from parents to offspring through genes in sperm and egg cells.

Reference: NCI-Thesaurus

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Genetic Code

The relationship of the sixty-four nucleic acid codons to the twenty primary amino acids. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Genetic Map

A map showing the position of genes or markers on a chromosome. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Genetically Engineered Mouse

A mouse that has been genetically modified by introducing new genetic characteristics to it. It often involves the isolation, manipulation and reintroduction of DNA, usually to express a protein. Serves as an animal model for research purpose.

Reference: NCI-Thesaurus

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Genetics

The branch of biology that deals with heredity, especially the mechanisms of hereditary transmission and the variation of inherited characteristics among similar or related organisms

Reference: NCI-Thesaurus

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Genome

The complete genomic content of an organism, and possibly the full DNA sequence of that organism. It is contained in a set of chromosomes in eukaryotes, a single chromosome in bacteria, or a DNA or RNA molecule in viruses.

Reference: NCI-Thesaurus

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Genome-wide association study

In genetic epidemiology, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study), is an examination of all or most of the genes (the genome) of different individuals of a particular species to see how much the genes vary from individual to individual. Different variations are then associated with different traits, such as diseases.

Reference: Wikipedia

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Genomics

The comprehensive study of whole sets of genes and their interactions rather than single genes or proteins.

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Genotype

The genetic constitution of an organism or cell, as distinct from its expressed features or phenotype.

Reference: NCI-Thesaurus

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Genotyping

The process of assessing genetic variation present in an individual.

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Germ Line

Cells of an animal that give rise to gametes.

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Graft

Tissue or organ transplanted from a donor to a recipient.

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Guanine (G)

A purine base that is a component of nucleotides and thus a normal component of DNA and RNA. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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GWAS

In genetic epidemiology, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study), is an examination of all or most of the genes (the genome) of different

Reference: Wikipedia

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Haploid

Having the chromosome number normally found in a gamete.

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Haploinsufficient

A description applied to a gene that produces a mutant phenotype when present in a diploid individual heterozygous for an amorphic allele.

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Haplotype

One of the alternative forms of the genotype of a gene complex. This term is applied to gene complexes rather than the term allele, which refers to one of the forms of a single gene.

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Hemizygous

The state of a locus in a diploid organism, where only one copy of the locus is present. Examples are sex-linked genes in normal mammalian males, insertions such as transgenic insertions, and autosomal alleles in combination with deletions that remove entire gene regions.

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Hepatoblastoma

A malignant liver neoplasm that occurs almost exclusively in infants, although isolated cases in older children and adults have been reported. Grossly, hepatoblastoma is solid, well circumscribed, and more often solitary than multiple. Microscopically, most of the tumors are composed exclusively of immature hepatocytic elements. About a fourth of hepatoblastomas contain a stromal component that may be undifferentiated or develop into bone or cartilage. The treatment of choice for hepatoblastoma is surgical excision with adjuvant therapy. Liver transplantation is being increasingly used as well.

Reference: NCI-Thesaurus

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Hepatocellular

Pertaining to or affecting liver cells.

Reference: NCI-Thesaurus

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Heredity

The transmission of traits encoded in GENES from parent to offspring.

Reference: NCI-Metathesaurus

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Heritability

Heritability is the proportion of phenotypic variation in a population that is attributable to genetic variation among individuals. Phenotypic variation among individuals may be due to genetic and/or environmental factors. Heritability analyses estimate the relative contributions of differences in genetic and non-genetic factors to the total phenotypic variance in a population.

Reference: Wikipedia

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Heterochromatin

1. The part of the genome characterized by relatively low gene density and the presence of highly repetitive sequences. Heterochromatin is more highly condensed than euchromatin. 2. The X chromosome that is highly condensed in a mammalian cell that has undergone X inactivation. The inactive X chromosome resembles heterochromatin as defined above with respect to their state of condensation and genetic inactivity, although there is no change in the DNA sequence as a consequence of inactivation.

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Heterogametic

Producing two types of euploid gametes with respect to chromosomal content. This term is applied to one of the sexes in species with chromosomal sex determination; in mammals, males are heterogametic.

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Heterogeneity

The quality or state of consisting of elements that are not of the same kind or nature.

Reference: NCI-Thesaurus

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Heteropolymer

A polymer composed of different subunits. Some multimeric proteins are normally heteropolymers. Heteropolymers can also be made experimentally, using subunits derived from different species, as a test of homology. Formation of a functional multimeric protein product using subunits from different species is a demonstration of homology.

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Heterozygosity

Having two different allelic forms of a gene, one inherited from each parent, on each of the two homologous chromosomes.

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Heterozygote

An individual that is heterozygous.

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Heterozygous

The state of a diploid locus in which different alleles are present at the two copies of that locus (usually one is normal and the other is abnormal).

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Hierarchical

A description of a structure in which things are organized into a hierarchy.

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Hierarchy

An organization with few things, or one thing, at the top and with several things below each other thing. An inverted tree structure. An example in computing is a directory hierarchy where each directory may contain files or other directories. In MGI, it refers to terms in a controlled vocabulary such as ones containing Gene Ontology (GO) terms or to the Mouse Anatomical Dictionary.

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Histologic

Pertaining to the combined microscopic physical features of cells and their surrounding extracellular environment in tissues.

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Histology

The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains.

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Homogametic

Producing a single type of euploid gametes with respect to chromosomal content. This term is applied to one of the sexes in species with chromosomal sex determination; in mammals, females are homogametic.

Reference: MGI

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Homogeneity

The quality or state of being similar or comparable in kind or nature or of being uniform throughout in composition or structure.

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Homolog

1. One of a pair of chromosomes that segregate from one another during the first meiotic division. 2. A gene related to a second gene by descent from a common ancestral DNA sequence. The term, homolog, may apply to the relationship between genes separated by the event of speciation (see ortholog) or to the relationship betwen genes separated by the event of genetic duplication (see paralog). 3. A morphological structure in one species related to that in a second species by descent from a common ancestral structure.

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Homologous recombination

1. Reciprocal recombination between DNA sequences that have a high degree of similarity. 2. Reciprocal recombination between DNA sequences that have a high degree of similarity and that are located at corresponding positions on homologous chromosomes.

Reference: MGI

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Homology

The relationship of any two characters that have descended from a common ancestor. This term can apply to a morphological structure, a chromosome or an individual gene or DNA segment.

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Homozygosity

Having two identical allelic forms of a gene, one inherited from each parent, on each of the two homologous chromosomes.

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Homozygote

An individual that is homozygous.

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Homozygous

The state of a diploid locus in which identical alleles are present at both copies of that locus.

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Hormone

Chemicals produced by glands in the body and circulated in the bloodstream. Hormones control the actions of certain cells or organs.

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Horseradish Peroxidase

An enzyme for which a chromogenic substrate exists, commonly used as a label for antibodies.

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Hybrid

1. The offspring of two sexually-reproducing homozygous individuals of different genotypes. 2. As an MGI Mapping Data type, a somatic cell hybrid experiment.

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Hybridization

With respect to nucleic acids, "hybridization" refers to the formation of double-stranded DNA, RNA, or DNA/RNA hybrids by complementary base pairing.

Reference: MGI

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Hydrocarbon

A group of organic compounds that consist of only hydrogen (H) and carbon (C) atoms and are involved in energy production. They may be cyclic or non-cyclic compounds. They may have double bonds, single bonds or both with carbon forming the backbone.

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Hydrophilic

Literally, "water-loving"; polar or charged compounds that are soluble in water.

Reference: MGI

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Hydrophobic

Literally, "water-fearing"; nonpolar compounds that are immiscible with water. The side chains of some amino acids are nonpolar, and hence protein sequences rich in these amino acids tend to locate to the interior of the protein in its native state, away from the solvent.

Reference: MGI

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Hypermorphic Mutation

A type of mutation in which the altered gene product possesses an increased level of activity, or in which the wild-type gene product is expressed at a increased level.

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Hypomorphic Mutation

A type of mutation in which the altered gene product possesses a reduced level of activity, or in which the wild-type gene product is expressed at a reduced level.

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Identity

In comparison of nucleic acid or protein sequences, the extent to which two sequences have the same nucleotide or amino acid at equivalent positions, usually expressed as a percentage.

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IMAGE Consortium

Integrated Molecular Analysis of Genome Expression Consortium. A collection of a large number of partially sequenced cDNAs. See the homepage of the IMAGE Consortium for further information.

Reference: MGI

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Immunocompetent

Having the ability to produce a normal immune response.

Reference: NCI-Thesaurus

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Immunodeficiency

Immunodeficiency (or immune deficiency) is a state in which the immune system's ability to fight infectious disease is compromised or entirely absent

Reference: Wikipedia

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Immunofluorescence

The detection of an antigen in cytological preparations by using a fluorescent-labeled antibody.

Reference: MGI

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Immunohistochemistry

A method of detecting the presence of specific proteins in cells or tissues. Fixed cells or tissue on a microscope slide, made permeable if necessary with a detergent, are reacted with a primary antibody to the specific protein to be assayed. The preparation is then treated with a secondary antibody that has been coupled to an enzyme and which is directed against the primary antibody (e.g., goat anti-rabbit antibody). The preparation is then treated with a chromogenic substrate. Microscopic examination reveals the presence of staining, and hence of the specific protein to be detected.

Reference: MGI

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Immunological Cross-reaction

The binding of an antibody to a protein that is different from the protein against which the antibody was raised. This result demonstrates sequence or structural similarity between the two proteins and can be evidence of homology.

Reference: MGI

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Immunology

The study of the immune system and its reaction to pathogens, as well as its malfunctions (autoimmune diseases, allergies, rejection of organ transplants).

Reference: NCI-Thesaurus

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Immunotherapy

Therapy designed to induce changes in a patient's immune status in order to treat disease.

Reference: NCI-Thesaurus

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Imprinting

An epigenetic modification of genes that identifies a given gene as having been inherited from the maternal or paternal parent. In mammals, some genes are expressed primarily from the maternally-inherited or paternally-inherited alleles as a consequence of imprinting.

Reference: MGI

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IMSR

International Mouse Strain Resources. A resource of mouse strain information contributed by a number of participating institutions world wide and hosted by MGI and The Jackson Laboratory. IMSR offers web-based strain detail pages with information about the biology, stock, and availability of strains.

Reference: MGI

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In silico

Computationally, as opposed to in vitro or in vivo.

Reference: MGI

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in situ

in the natural or normal place, confined to the site of origin without invasion of neighboring tissues.

Reference: NCI-Thesaurus

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In situ Hybridization

A method of detecting the presence of specific nucleic acid sequences within a cytological preparation. A DNA or RNA probe is labeled radioactively or chemically and hybridized to a cytological preparation to detect RNA or to a denatured cytological preparation to detect DNA. The hybridization is detected by autoradiography (for radioactive probes) or by chromogenic reactions or fluorescence (for chemically-labeled probes).

Reference: MGI

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In situ Reporter (Knock in)

An assay type that uses mice containing a targeted mutation in which a reporter gene has replaced an endogenous gene. The two most common reporter genes are lacZ and green fluorescent protein.

Reference: MGI

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In utero

A reaction, process or experiment on an embryo in a living mammal rather than in vitro.

Reference: MGI

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In vitro

Literally, "in glass", meaning a reaction, process or experiment in a metaphorical test tube rather than in a living organism. In MGI this term also applies to cDNA clones originating from tissue culture cells rather than from tissues from whole organisms.

Reference: MGI

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In vivo

Literally, "in life", meaning a reaction, process or experiment in a living organism rather than in a metaphorical test tube.

Reference: MGI

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Inbred Strain

A strain that has been maintained by sibling (sister x brother) matings for 20 or more consecutive generations. (from JAX Strain Information)

Reference: NCI-Thesaurus

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Incross

A cross between two identically homozygous individuals (A/A X A/A).

Reference: MGI

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Inflammatory

Relating to inflammation.

Reference: NCI-Thesaurus

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Inheritance Mode

The manner in which a particular genetic trait is expressed when passed from one generation to another (for example, dominant, recessive, semidominant, etc.).

Reference: MGI

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Inhibitor

A chemical compound that has the effect of blocking or slowing an enzymatic reaction.

Reference: MGI

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Insertion

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.

Reference: MGI

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Intercross

A cross between two identically hybrid individuals (A/a X A/a).

Reference: MGI

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Intergenic

Between genes.

Reference: MGI

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Interim

In MGI, a term appended to a gene symbol that is under review.

Reference: MGI

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InterPro domain

One of a collection of amino acid sequences of identifiable features in known proteins that can be compared to unknown protein sequences. See InterPro at EMBL/EBI.

Reference: MGI

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Intestine

The portion of the gastrointestinal tract between the stomach and the anus. It includes the small intestine and large intestine.

Reference: NCI-Thesaurus

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Introgression

Introgression, also known as introgressive hybridization, in genetics (particularly plant genetics), is the movement of a gene (gene flow) from one species into the gene pool of another by repeated backcrossing an interspecific hybrid with one of its parent species. Introgression is a long-term process; it may take many hybrid generations before the backcrossing occurs.

Reference: Wikipedia

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Intron

Part of a gene whose sequence is transcribed but not present in a mature mRNA after splicing.

Reference: MGI

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Invasive

Marked by a tendency to spread, especially into healthy surrounding tissue.

Reference: NCI-Thesaurus

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Inversion

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.

Reference: MGI

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Ionization

Any process by which a neutral atom gains or loses electrons, thus acquiring a net charge, as the dissociation of a substance in solution into ions or ion production by the passage of radioactive particles.

Reference: NCI-Thesaurus

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Irradiation

Treatment with radiation, generally meaning exposure to ionizing radiation or radiation of wavelengths shorter than those of visible light.

Reference: NCI-Thesaurus

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Isogenic

Characterized by essentially identical genes. Identical twins are isogenic.

Reference: MGI

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Karyotype

A description of the condensed chromosomes of a eukaryote as they are seen at metaphase. Additional details are revealed by a variety of staining techniques that produce banded chromosomes. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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kb

Kilobase. Unit of DNA or RNA sequence equal to 1000 nucleotides.

Reference: MGI

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Kinetochore

A structure formed adjacent to the centromere of a condensed chromosome that allows the chromosome to attach to microtubules of the meiotic or mitotic spindle.

Reference: MGI

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Knock in

A casual term for a type of targeted mutation in which an alteration in gene function other than a loss-of-function allele is produced.

Reference: MGI

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Knock-out

A casual term for a type of targeted mutation in which an amorphic (loss-of-function) allele is produced by homologous recombination. Knockouts are often created in laboratory organisms such as yeast or mice so that scientists can study the knockout organism as a model for a particular disease.

Reference: NCI-Thesaurus

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Lentivirus

A genus of the family Retroviridae consisting of non-oncogenic retroviruses that produce multi-organ diseases characterized by long incubation periods and persistent infection. Lentiviruses are unique in that they contain open reading frames (ORFs) between the pol and env genes and in the 3' env region. Five serogroups are recognized, reflecting the mammalian hosts with which they are associated. HIV-1 is the type species.

Reference: NCI-Thesaurus

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Leukemia

A malignant (clonal) hematologic disorder, involving hematopoietic stem cells and characterized by the presence of primitive or atypical myeloid or lymphoid cells in the bone marrow and the blood. Leukemias are classified as acute or chronic based on the degree of cellular differentiation and the predominant cell type present. Leukemia is usually associated with anemia, fever, hemorrhagic episodes, and splenomegaly. Common leukemias include acute myeloid leukemia, chronic myelogenous leukemia, acute lymphoblastic or precursor lymphoblastic leukemia, and chronic lymphocytic leukemia. Treatment is vital to patient survival; untreated, the natural course of acute leukemias is normally measured in weeks or months, while that of chronic leukemias is more often measured in months or years.

Reference: NCI-Thesaurus

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Library

In molecular biology, a "library" is a complex mixture of recombinant DNA molecules in a suitable cloning vector representing either the entire genome of an organism (a genomic library) or the messenger RNA population of a whole organism, cell type, or tissue type (a cDNA library).

Reference: MGI

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Ligand

A molecule that binds to a receptor protein.

Reference: MGI

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Ligate

In molecular biology, to join two separate DNA or RNA segments to form a single DNA or RNA molecule enzymatically.

Reference: MGI

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Linkage

The property displayed by two genes that do not segregate independently of each other. Genes that are linked are on the same chromosome.

Reference: MGI

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Linkage Analysis

The construction of a linkage map through the analysis of meiotic recombination frequencies between pairs of genes.

Reference: MGI

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Linkage Map

A type of genetic map showing relative gene positions based on meiotic recombination frequencies. The unit of measurement is the centimorgan.

Reference: MGI

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Locus

Literally, "place". The location of a gene or set of genes on a chromosome.

Reference: MGI

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LOD score

A statistical estimate of whether two loci are likely to lie near each other on a chromosome and are therefore likely to be inherited together. Lod stands for "log of the odds ratio." In this case, the odds ratio is the likelihood that two markers are linked divided by the likelihood that they are not linked. A LOD score of three or more is generally taken to indicate that the two loci are close.

Reference: MGI

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LOH

Loss of heterozygosity.

Reference: MGI

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Loss of Heterozygosity

A genetic event that can occur in the dividing cells of a diploid organism heterozygous for one or more markers, in which a daughter cell becomes homozygous or hemizygous for one or more alleles through mitotic recombination, deletion, or gene conversion. "Loss of heterozygosity (LOH)" events are often important steps in tumor progression.

Reference: MGI

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Loss-of-function Mutation

A type of mutation in which the altered gene product lacks the molecular function of the wild-type gene. Synonyms: Amorphic Mutation, Null Mutation.

Reference: MGI

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loxP Sequence

A 34 base pair DNA sequence recognized by the site-specific recombination enzyme Cre.

Reference: MGI

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Lymph

A clear, transparent, sometimes faintly yellow and slightly opalescent fluid that is collected from the tissues throughout the body, flows in the lymphatic vessels (through the lymph nodes), and is eventually added to the venous blood circulation. Lymph consists of a clear liquid portion, varying numbers of white blood cells (chiefly lymphocytes), and a few red blood cells.

Reference: NCI-Thesaurus

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Lymphoma

A malignant (clonal) proliferation of B- lymphocytes or T- lymphocytes which involves the lymph nodes, bone marrow and/or extranodal sites. This category includes Non-Hodgkin lymphomas and Hodgkin lymphomas.

Reference: NCI-Thesaurus

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Magnetic Resonance Imaging

Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders.

Reference: NCI-Thesaurus

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Major Histocompatibility Congenic

A congenic strain in which the donor allele transferred to the host strain background is a major histocompatibility gene.

Reference: MGI

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Malignant

 Refers to abnormal cell activity manifested by decreased control over growth and function, causing tumor growth or spread into surrounding tissue and adverse effects to the host.

Reference: NCI-Thesaurus

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Malignant Neoplasm

A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas.

Reference: NCI-Thesaurus

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Mammalian Phenotype Ontology

A controlled vocabulary that provides standardized terms for describing phenotypic characteristics of mammalian systems. See the Mammalian Phenotype Browser for more information, and see the Open Biological Ontologies (OBO) site for further information about other structured, shared vocabularies for use within biological domains.

Reference: MGI

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Marker

1. 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. 2. A feature that distinguishes a particular biological state. For example, an expression profile of natural or engineered genes, or a characteristic morphology. 3. In MGI, a Marker is an object for which unique official nomenclature must be assigned. Markers in MGI can be of type: Gene, DNA Segment, Cytogenetic Marker, QTL, Transgene, Pseudogene, BAC/YAC end, Other Genome Feature, Complex/Cluster/Region

Reference: MGI

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Mass Spectrometry

An analytical technique wherein ions are separate according to their ratio of charge to mass. From the mass spectrum produced, the atomic weight of the particle can be deduced.

Reference: NCI-Thesaurus

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Megabase

Unit of DNA or RNA sequence equal to one million nucleotides.

Reference: MGI

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Meiosis

A pair of nuclear divisions forming gametes wherein the number of chromosomes is reduced from the diploid to the haploid number; resulting cells normally contain one member of each pair of homologous chromosomes.

Reference: MGI

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Melanoma

A malignant, usually aggressive tumor composed of atypical, neoplastic melanocytes. Most often, melanomas arise in the skin (cutaneous melanomas) and include the following histologic subtypes: superficial spreading melanoma, nodular melanoma, acral lentiginous melanoma, and lentigo maligna melanoma. Cutaneous melanomas may arise from acquired or congenital melanocytic or dysplastic nevi. Melanomas may also arise in other anatomic sites including the gastrointestinal system, eye, urinary tract, and reproductive system. Melanomas frequently metastasize to lymph nodes, liver, lungs, and brain.

Reference: NCI-Thesaurus

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Membrane

1. A phospholipid bilayer that forms a hydrophobic barrier around and within cells. 2. A sheet of nylon, nitrocellulose, or similar material used to create a replica of a gel for Southern blots, Northern blots, or Western blots.

Reference: MGI

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Mendelian

1. That type of inheritance in which a specific trait is affected by a set of alleles of a single gene. 2. That type of inheritance in which genetic information is transmitted by one or more nuclear genes, as opposed to cytoplasmic or epigenetic mechanisms.

Reference: MGI

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Messenger RNA

A class of RNA molecule containing protein-coding information in its nucleotide sequence that can be translated into the amino acid sequence of a protein.

Reference: NCI-Thesaurus

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Metabolic Process

Organic processes in a cell or organism that are necessary to sustain life. Cellular metabolism can be divided into two categories. Anabolism entails the construction of complex organic molecules from simpler precursors, while catabolism involves the breakdown of complex substances into simpler molecules.

Reference: NCI-Thesaurus

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Metadata

Data about data. In data processing, metadata is definitional data providing information about or documentation of other data managed within an application or environment, for example, data about: data elements or attributes (name, size, data type, etc.), records or data structures (length, fields, columns, etc.) and data (where located, how associated, what ownership, and so on). Metadata may include descriptive information about the context, quality and condition, or characteristics of the data.

Reference: MGI

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Metastasis

The spread or migration of cancer cells from one part of the body (the organ in which it first appeared) to another. The secondary tumor contains cells that are like those in the original (primary) tumor. For example, breast cancer cells may spread (metastasize) to the lungs and cause the growth of a new tumor. When this happens, the disease is called metastatic breast cancer.

Reference: NCI-Thesaurus

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MGD

Mouse Genome Database. One of several databases integrated into MGI, containing data on the genes of the mouse.

Reference: MGI

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MGI

Mouse Genome Informatics. The collection of bioinformatics projects at The Jackson Laboratory including MGD, GXD, and MTB.

Reference: MGI

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Micelles

A micelle is an aggregate of surfactant molecules dispersed in a liquid colloid. A typical micelle in aqueous solution forms an aggregate with the hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single tail regions in the micelle centre. This phase is caused by the insufficient packing issues of single tailed lipids in a bilayer. Micelle formation is essential for the absorption of fat-soluble vitamins and complicated lipids within the body.

Reference: Wikipedia

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Microarray

A piece of glass or plastic on which different samples have been affixed at separate locations in an ordered manner thus forming a microscopic array. The samples are usually DNA fragments but may also be antibodies, other proteins, or tissues.

Reference: NCI-Thesaurus

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MicroRNA

MicroRNAs (miRNAs) are a group of noncoding RNA molecules, generally 21 to 24 nucleotides in length, which are usually cleaved from a larger hairpin-containing RNA (itself often processed from some portion of mRNA). miRNAs are conserved through evolution, and their abundance and expression patterns are suggestive of diverse regulatory roles.

Reference: MGI

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Microsatellite Marker

A short (up to several hundred base pairs) segment of DNA that consists of multiple tandem repeats of a two or three base-pair sequence. Microsatellites expand and contract (that is, add or remove repeat units) with a frequency much higher than other types of mutations, making them useful as polymorphic markers in closely related mouse strains.

Reference: MGI

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Microtubule

A cytoskeletal element of eukaryotic cells that is a long, generally straight, hollow tube with an external diameter of 24 nm, consisting of polymerized monomers of tubulin. Microtubules make up the bulk of the spindle.

Reference: MGI

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Minor Histocompatibility Congenic

A congenic strain in which the donor allele transferred to the host strain background is a minor histocompatibility gene.

Reference: MGI

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MIT marker

One of a large series of microsatellite markers in the mouse, developed at the Massachusetts Institute of Technology. These markers have been used to align the physical and linkage maps in mouse.

Reference: MGI

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Mitochondria

The organelles that generate energy in eukaryotic cells. Mitochondria have their own genome encoding a subset of the proteins found in mitochondria; the mitochondrial genome uses an alternate genetic code.

Reference: MGI

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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).

Reference: MGI

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Mitosis

The division of the replicated chromosomes of a eukaryotic cell into two daughter nuclei that are genetically identical to that of the original cell. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Mobile Genetic Element

A DNA segment carried within the chromosomes that is capable of moving to new sites in the genome other than by mutation.

Reference: MGI

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Molecular Function

Refers to the tasks or activities characteristic of particular gene products. For example, transcription factor refers to one of a number of proteins performing similar tasks. In the GO Project vocabularies, Molecular Function is a primary class of terms. See the GO Consortium site for further information.

Reference: MGI

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Molecular Mutation

A description of the type of molecular event giving rise to a specific mutation, for example, deletion, inversion, point mutation, and so on.

Reference: MGI

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Monoclonal Antibody

An antibody produced by cultured cells that have their origin in a single antibody-producing cell and which is therefore of a single molecular type, in contrast to the polyclonal antibodies normally found in the serum of an immunized animal.

Reference: MGI

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Monosomy

The condition of having a single chromosome of a particular type; lacking a homologous chromosome. Normal male mice are monosomic for the X chromosome.

Reference: MGI

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Morphants

An organism which has been treated with a Morpholino antisense oligo to temporarily knock down expression of a targeted gene is called a Morphant.

Reference: Wikipedia

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Morpholino

An antisense oligonucleotide modified to make them more stable than RNA. Morpholinos are used to inhibit translation or splicing of particular mRNAs. The resulting reduction in gene function is sometimes casually referred to as a knock-down.

Reference: ZFIN

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Mosaic

An individual consisting of cells of two or more genotypes. One example is that of a normal female mammal heterozygous for different alleles of X-chromosome genes; because of the process of X-inactivation, such females consist of two cell types, each with a different X chromosome inactivated. This is an unusual example because there is no actual difference in genotype between the two cell types, but rather there is an epigenetic difference.

Reference: MGI

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Mouse Mammary Tumor Virus

Type B retrovirus. Etiologic agent of mouse mammary tumors. Transmitted horizontally through the lactating mammary gland and vertically through the germline. Mechanism of tumorigenesis involves the activation of cellular int genes by promoter/enhancer insertion.

Reference: NCI-Thesaurus

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MP

Mammalian Phenotype Ontology. An extensive ontology of mammalian phenotype classification terms with definitions.

Reference: MGI

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MTB

Mouse Tumor Biology Database. One of several databases at MGI, containing data on the mouse tumor biology.

Reference: MGI

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Mutagen

An agent that causes mutations.

Reference: MGI

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Mutagenesis

Production of genetic alterations by any technique, including chemicals, radiation, recombination, or other molecular biology methods.

Reference: NCI-Thesaurus

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Mutant

An altered form of an individual, organism, population, or genetic character that differs from the corresponding wild type due to one or more alterations (mutations).

Reference: NCI-Thesaurus

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Mutant ES Cell Line

A specific sub-line of embryonic stem (ES) cells containing an introduced mutation.

Reference: MGI

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Mutation

1. The process through which genes undergo a structural change. 2. Any permanent change in DNA, i.e., in its nucleotide sequence. Examples include chromosome rearrangements and point mutations. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Myeloproliferation

Myeloproliferation involves both medullary and extramedullary proliferation of bone marrow constituents, such as erythroblasts, granulocytes, megakaryocytes, and fibroblasts.

Reference: NCI-Thesaurus

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Myxoma

A benign soft tissue neoplasm characterized by the presence of spindle and stellate cells, lobulated growth pattern, and myxoid stroma formation.

Reference: NCI-Thesaurus

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Nanoparticle

A small, stable particle whose size is measured in nanometers. These particles are used in various biomedical applications in which they can be utilized as drug carriers or imaging agents. Various targeting agents, such as antibodies, drugs, imaging agents, and reporters can be attached to the surface of a nanoparticle.

Reference: NCI-Thesaurus

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NCBI

National Center for Biotechnology Information.

Reference: MGI

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NCBI Gene Model

A description of a gene associated with the mouse genome assembly from NCBI. The NCBI gene model includes the coordinates of each intron and exon, as well as the beginning and end of the transcript.

Reference: MGI

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Neomorphic Mutation

A type of mutation in which the altered gene product possesses a novel molecular function or a novel pattern of gene expression. Neomorphic mutations are usually dominant or semidominant.

Reference: MGI

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Neonatal

Newborn.

Reference: MGI

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Neoplasm

A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.

Reference: NCI-Thesaurus

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Neovascularization

Growth of new blood vessels feeding a tissue, as with a tumor.

Reference: NCI-Thesaurus

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Neuroglial Tumor

A benign or malignant brain and spinal cord tumor that arises from glial cells (astrocytes, oligodendrocytes, ependymal cells). Tumors that arise from astrocytes are called astrocytic tumors or astrocytomas. Tumors that arise from oligodendrocytes are called oligodendroglial tumors. Tumors that arise from ependymal cells are called ependymomas.

Reference: NCI-Thesaurus

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NHGRI

National Human Genome Research Institute.

Reference: MGI

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Non-Hodgkin Lymphoma

Distinct from Hodgkin lymphoma both morphologically and biologically, Non-Hodgkin lymphoma (NHL) is characterized by the absence of Reed-Sternberg cells, can occur at any age, and usually presents as a localized or generalized lymphadenopathy associated with fever and weight loss. The clinical course varies according to the morphologic type. NHL is clinically classified as indolent, aggressive, or having a variable clinical course. NHL can be of B-or T-/NK-cell lineage.

Reference: NCI-Thesaurus

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Non-Mendelian

1. That type of inheritance in which a specific trait is affected by a set of alleles of a multiple genes. Synonym: Polygenic 2. That type of inheritance in which genetic information is transmitted other than by nuclear genes.

Reference: MGI

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Noncoding RNA

An RNA molecule that functions structurally or catalytically (see ribozyme) without being translated. Noncoding RNAs lack conserved open reading frames. One example is Xist.

Reference: MGI

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Noninbred Stock

A stock that is known to be not inbred, or intentionally kept to prevent it from becoming inbred.

Reference: MGI

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Northern Blot

An assay that detects specific RNA molecules using a DNA or RNA probe with sequence similarity. Samples are subjected to electrophoresis on a slab gel. A replica of the gel is then made on a membrane by capillary transfer. Specific RNA sequences are then detected on the membrane with a radioactively- or chemically-labeled probe. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Nucleic Acid

DNA or RNA. Each of these compounds consists of a backbone of sugar molecules ribose for RNA and deoxyribose for DNA linked by single phosphate groups. Attached to the sugars of the backbone are any of four nitrogenous bases, A, T, C or G for DNA and A, U, C or G for RNA. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Nucleotide

A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA).

Reference: NCI-Thesaurus

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Nucleotide Repeat Expansion

A type of mutation in which a set of tandemly repeated sequences replicates inaccurately to increase the number of repeats. An example of this kind of mutation in humans is the FMR1 gene.

Reference: MGI

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Nucleotide Substitution

A point mutation.

Reference: MGI

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Nucleus

The organelle in a eukaryotic cell that contains the chromosomes. In most types of eukaryotic cells, the nucleus breaks down as chromosomes condense during cell division. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Nude Mouse

A hairless mutant mouse with thymic hypoplasia, lacking T-cells. They are unable to reject transplants.

Reference: NCI-Thesaurus

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Null Mutation

A type of mutation in which the altered gene product lacks the molecular function of the wild-type gene. Synonyms: Amorphic Mutation, Loss-of-function Mutation.

Reference: MGI

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Numerical Aberration

A change in the number of chromosomes from the wild-type number in the absence of any chromosome rearrangement.

Reference: MGI

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Offset

In MGI, the limits of the position of a gene on a chromosome on the cytogenetic map or the linkage map.

Reference: MGI

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Oligonucleotide

A short length of nucleic acid.

Reference: MGI

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OMIM

Online Mendelian Inheritance in Man. A database of human inherited diseases and genes.

Reference: MGI

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Oncogene

A gene that normally directs cell growth. If mutated or overexpressed in a dominant fashion, it can release the cell from normal restraints on growth. It alone or in concert with other changes, converts the cell into a tumor cell. Alterations can be inherited or caused by an environmental exposure to carcinogens.

Reference: NCI-Thesaurus

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Oncogenesis

The causation or production of tumors.

Reference: NCI-Thesaurus

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Oncology

The study of tumors encompassing the physical, chemical, and biologic properties.

Reference: NCI-Thesaurus

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Ontology

To researchers interested in the representation of biological knowledge by computer programs and databases, "ontology" refers to a controlled vocabulary, or set of such vocabularies, used to describe biological features within a specified domain of biological knowledge.

Reference: MGI

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Open Reading Frame (ORF)

A length of nucleotide sequence that lacks termination codons in a given reading frame.

Reference: MGI

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Organelle

One of a number of different kinds of membrane-bound substructures within a eukaryotic cell. Examples include the nucleus, mitochondria, and chloroplasts.

Reference: MGI

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Organism Strain

A population or type of organisms that is genetically different from others of the same species and possessing a set of defined characteristics.

Reference: NCI-Thesaurus

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Ortholog

One of a set of homologous genes that have diverged from each other as a consequence of speciation. For example, the alpha globin genes of mouse and chick are orthologs.

Reference: MGI

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Orthologous

Occurring in one species but corresponding to one in another species that is related via a common ancestral species.

Reference: NCI-Thesaurus

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Orthology

The relationship of any two homologous characters whose common ancestor lies in the most recent common ancestor of the taxa being considered. In MGI, assertions of Mammalian Homology imply presumed orthology.

Reference: MGI

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Orthotopic Transplant

Transplantation of a donor organ graft into the same site as that occupied by the original organ that failed

Reference: Emice

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Osteosarcoma

 A usually aggressive malignant bone-forming mesenchymal tumor, predominantly affecting adolescents and young adults. It usually involves bones and less frequently extraosseous sites. It often involves the long bones (particularly distal femur, proximal tibia, and proximal humerus). Pain with or without a palpable mass is the most frequent clinical symptom. It may spread to other anatomic sites, particularly the lungs.

Reference: NCI-Thesaurus

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Other Genome Feature

In MGI, "Other Genome Feature" refers to any feature of the genome that is considered to have biological significance but that cannot be classified with defined marker types. Major classes of other genome features include Endogenous Viruses and Retrotransposons, Integration Sites, and Repetitive Elements. An additional class of such features includes genomic segments that function or are biologically significant as DNA elements.

Reference: MGI

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Outbred Strain

Animals that are generated from breeding two genetically dissimilar strains of the same species.

Reference: NCI-Metathesaurus

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Outcross

A type of genetic cross in which an organism is crossed to a strain from which it was not recently derived.

Reference: MGI

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P1

A bacteriophage with a genome size of over 100 kb that has been used as a cloning vector.

Reference: MGI

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PAC

P1 Artificial Chromosome. A type of cloning vector derived from bacteriophage P1 that allows foreign DNA segments to be cloned in bacteria. The capacity of a PAC is up to 100 kb of foreign DNA.

Reference: MGI

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Papilloma

A benign epithelial neoplasm that projects above the surrounding epithelial surface and consists of villous or arborescent outgrowths of fibrovascular stroma.

Reference: NCI-Thesaurus

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Paralog

One of a set of homologous genes that have diverged from each other as a consequence of genetic duplication. For example, the mouse alpha globin and beta globin genes are paralogs. The relationship between mouse alpha globin and chick beta globin is also considered paralogous.

Reference: MGI

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Paralogy

The relationship of any two homologous characters that arose by a genetic duplication.

Reference: MGI

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Parent

In MGI, this term refers to terms in a hierarchical controlled vocabulary such as those containing Gene Ontology (GO) terms. A "parent" of a term is one any number of levels above it in the hierarchy from which it is descended. For example, the GO term enzyme [GO:0003824] is a parent to the GO term alcohol dehydrogenase [GO:0004022].

Reference: MGI

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Pathogen

An agent of disease; a disease producer.

Reference: NCI-Thesaurus

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Pathology

The medical science, and specialty practice, concerned with all aspects of disease, but with special reference to the essential nature, causes, and development of abnormal conditions, as well as the structural and functional changes that result from the disease processes. Informally used to mean the result of such an examination.

Reference: NCI-Thesaurus

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PCR

Polymerase Chain Reaction. A method of amplifying specific DNA segments based on hybridization to a primer pair. A DNA sample is denatured by heating in the presence of a vast molar excess of short single-stranded DNA primers (around 20 nucleotides) whose sequence is chosen based on the target sequence. The reaction mixture also contains a thermostable DNA polymerase, dNTPs, and buffer. The primer sequences are selected so that they: 1. are derived from opposite strands of the target sequence, 2. have their 3' ends facing each other, and 3. are separated by a length of DNA that can be reliably synthesized in vitro. The sample is then cooled to a temperature that allows primer annealing and in vitro replication. The sample is subjected to multiple cycles of denaturation and cooling to allow multiple rounds of replication. The quantity of the target sequence doubles during each cycle, causing the target sequence to be amplified, while other DNA sequences in the sample remain unamplified. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Pedigree

A record of descent or ancestry, particularly of a specific condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.

Reference: NCI-Thesaurus

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Penetrance

The fraction of individuals of a given genotype that show a particular phenotype, usually expressed as a percentage.

Reference: MGI

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Perinatal

Around the time of birth.

Reference: MGI

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Phage

1. A bacteriophage, a virus capable of infecting bacteria. 2. A type of cloning vector derived from a bacteriophage, usually capable of carrying an amount of foreign DNA that is at the upper range of that carried by a plasmid.

Reference: MGI

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Phagemid

A type of cloning vector derived from a phage and a plasmid. Phagemids are capable of carrying an amount of foreign DNA comparable to a plasmid, but have some special feature such as the ability to produce single-stranded DNA.

Reference: MGI

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Pharmacokinetics

The characteristic movements of drugs within biological systems, as affected by absorption, distribution, binding, elimination, biotransformation, and excretion; particularly the rates of such movements.

Reference: NCI-Thesaurus

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Pharmacology

The study of pharmacologic agents. This includes the preparation, compounding, and dispensing of drugs, as well as the characteristics and properties of drugs, their effects on the body, and how they are metabolized and eliminated from the body.

Reference: NCI-Thesaurus

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Phenocopy

The condition of an individual resembling that of a phenotype produced by a particular mutation by some experimental treatment other than the presence of that mutation, e.g., drug treatment.

Reference: MGI

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Phenome

A phenome is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species. Just as the genome and proteome signify all of an organism's genes and proteins, the phenome represents the sum total of its phenotypic traits.

Reference: Wikipedia

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Phenotype

The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment.

Reference: NCI-Thesaurus

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Phosphorimaging

The detection of radioactivity using "phosphor" compounds that emit visible light when exposed to radiation. Phosphorimaging instruments produce images of, for example, Southern blots and Northern blots, that are comparable to those produced by autoradiography, with superior quantitation.

Reference: MGI

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Phosphorylation

The creation of a phosphate derivative of an organic molecule. This is usually achieved by transferring a phosphate group from ATP via the action of a kinase.

Reference: NCI-Thesaurus

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Phycoerythrin

A fluorescent dye that can be coupled to antibodies for the detection of proteins on Western blots using fluorography.

Reference: MGI

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Physical Map

A map of DNA showing distances between and within genes or specified markers measured in base pairs of DNA. It is based on the direct measurement of DNA.

Reference: MGI

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Plasmid

A type of cloning vector derived from autonomously-replicating extrachromosomal circular DNAs in bacteria. The amount of foreign DNA that can be carried in a plasmid is small, ranging up to about 20 kb.

Reference: MGI

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Pleiotropy

The production of a phenotype affecting multiple traits by a single mutation.

Reference: MGI

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Pluripotent

Able to mature or develop in any of several ways.

Reference: NCI-Thesaurus

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Point Mutation

A type of mutation in which a single nucleotide is changed to one of the other three possible nucleotides.

Reference: MGI

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Polyadenylation

The process by which a series of adenosine (A) ribonucleotides is added to the 3' end of a spliced RNA to make a mature mRNA. This addition to the RNA is sometimes referred to as a poly-A tail, and commonly contains several hundred bases.

Reference: MGI

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Polygenic

A trait determined by multiple genes.

Reference: MGI

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Polymorphism

An instance of genotypic variation within a population.

Reference: MGI

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Postnatal

After birth.

Reference: MGI

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Precancerous Condition

A pathological process with signs indicating it may become cancerous. Representative examples include leukoplakia, dysplastic nevus, actinic keratosis, xeroderma pigmentosum, and intraepithelial neoplasia.

Reference: NCI-Thesaurus

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Preclinical

Refers to in vitro testing or in vivo animal testing before clinical trials in humans are to be carried out.

Reference: NCI-Thesaurus

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Premalignant

Descriptive of a condition that may or is likely to become cancerous.

Reference: NCI-Thesaurus

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Prenatal

The time period after impregnation and before birth.

Reference: NCI-Thesaurus

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Primer

A single-stranded nucleic acid that can "prime" replication of a template. More specifically, a single-stranded nucleic acid capable of hybridizing to a template single-stranded nucleic acid in such a way as to leave part of the template to the 3' end of the primer single-stranded. DNA polymerase can then synthesize a new strand starting from the 3' end of the primer and adding nucleotides to the growing strand by base complementarity to the template. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Probe

1. In molecular biology, a nucleic acid that has been labeled either radioactively or chemically that allows the detection of nucleic acids with sequence similarity in a sample by hybridization. Probes are used to detect DNA on membranes in Southern blots, to detect RNA on membranes in Northern blots, and either DNA or RNA in cytological preparations for in situ hybridization. 2. In MGI, the term "probe" applies not only to nucleic acid probes detected as described above, but also to primers for PCR. This usage is not common outside of MGI.

Reference: MGI

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Prokaryote

Cell or organism lacking a membrane-bound, structurally discrete nucleus and other subcellular compartments. Bacteria are prokaryotes.

Reference: MGI

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Promoter

One of the necessary regulatory elements of a gene. The promoter is the site on DNA to which RNA polymerase binds and initiates transcription. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Pronucleus

The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents. [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]

Reference: NCI-Metathesaurus

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Protein Domain

A region of a protein responsible for a particular function, as recognized experimentally and by the occurrence of similar segments in other proteins sharing that function, e.g., a DNA binding domain.

Reference: MGI

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Protein Histochemistry

1. A method of detecting a particular enzyme in a cell or tissue sample. A sample of cells or tissue is fixed, then treated with a chromogenic substrate for the enzyme to be detected. Microscopic examination reveals the presence of staining, and hence of the specific protein to be detected. 2. Immunohistochemistry.

Reference: MGI

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Proteome

The complete collection of all proteins encoded by the genome of an organism.

Reference: MGI

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Proteomics

Systematic analysis of protein expression of normal and diseased tissues that involves the separation, identification and characterization of all of the proteins in an organism.

Reference: MGI

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Proto-Oncogene

Oncogenes are altered forms of normal cellular genes called proto-oncogene. Many proto-oncogenes are homologous to viral oncogenes and involved in the control of cell proliferation or differentiation. Mutations, amplifications or rearrangements of proto-oncogenes lead to upregulated or deregulated cell growth and allow them to function as oncogenes.

Reference: NCI-Thesaurus

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Pseudoautosomal

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.

Reference: MGI

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Pseudogene

A non-functional locus derived from a functional locus either by 1. replicative transfer, such as transposition, retrotransposition or duplication or by 2. mutation, where the non-functional locus is not considered an allele of an existing functional locus in the mouse.

Reference: MGI

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Purine

One of the bases of nucleic acids, either adenine (A) or guanine (G).

Reference: MGI

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Pyrimidine

One of the bases of nucleic acids, cytosine (C), thymine (T) or uracil (U).

Reference: MGI

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QTL

See Quantitative Trait Locus.

Reference: MGI

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Quantitative Trait Locus (QTL)

1. A heritable genetic region that affects a measurable characteristic of the animal (e.g., body weight or blood pressure). 2. The type of marker described by statistical association to quantitative variation in a particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.

Reference: MGI

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Radiation

1. Electromagnetic energy: gamma rays, X rays, ultraviolet light, visible light, infrared light, microwaves and radio waves. In mouse genetics, this term generally refers to gamma rays and X rays. 2. Subatomic particles emitted by the decay of unstable isotopes: electrons (beta particles) and helium nuclei (alpha particles). Common unstable isotopes in molecular biology are tritium (3H),which emits low-energy beta particles, 35S, which emits beta particles of moderate energy, and 32P, which emits high-energy beta particles. 3. Subatomic particles from a particle accelerator, such as protons, neutrons, and electrons.

Reference: MGI

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Radiation Hybrid Mapping

A type of genetic mapping providing resolution between relatively low-resolution linkage analysis and high-resolution physical mapping by the assembly of contiguous cloned DNA segments. The method consists of fusing irradiated cultured cells of one species with cultured cells of a different species. A panel of hybrid cells is then tested for the occurrence of pairs of markers. The closer two markers are to each other, the more likely that both are present in an individual hybrid cell. Radiation hybrid mapping data for the mouse are available at The Jackson Laboratory Mouse Radiation Hybrid Database and at MGI.

Reference: MGI

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Radiation Induced Mutation

A mutation induced by irradiation, in mouse usually gamma-ray or X-ray.

Reference: MGI

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Reading Frame

One of three ways of reading a single strand of nucleic acid sequence as codons.

Reference: MGI

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Reagent

Any natural or synthetic substance used in a chemical or biological reaction in order to produce, identify, or measure another substance.

Reference: NCI-Thesaurus

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Recessive

One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "a" is said to be recessive with respect to the allele "A" if the A/A homozygote and the A/a heterozygote are phenotypically identical and different from the a/a homozygote. An example is the nonagouti (a) allele of the mouse. A(+)/A(+) and (+)/a mice have identical agouti banding of individual hairs in the coat, while a/a mice have hairs of uniform color.

Reference: MGI

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Recombinant Congenic Strain

Strains formed by crossing two inbred strains, followed by a few backcrosses to one of the parental strains, with subsequent inbreeding without selection.

Reference: MGI

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Recombinant Inbred Strain

In mouse, an inbred strain of animals started from a cross between two different inbred strains followed by inbreeding for at least 20 generations. A panel of recombinant inbred strains derived from a cross between two 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. See also the Rules for Nomenclature of Mouse and Rat Strains.

Reference: MGI

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Recombination

Transfer of information from one DNA molecule to another. Recombination may be reciprocal, in which case the products are equivalent to breakage of the two DNA molecules and rejoining of the broken ends to form new molecules. Recombination may also be nonreciprocal, in which case the product is equivalent to transfer of information from the donor DNA molecule to the recipient DNA molecule, with no change in the donor DNA molecule. Reciprocal recombination events are also called crossovers.

Reference: MGI

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RefSeq

The collection of integrated, non-redundant sequences including genomic DNA, transcript (RNA), and protein products at NCBI.

Reference: MGI

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Regression

Return to a former state; a subsidence of the symptoms of a disease process; in cancer, a decrease in the size of a tumor or in the extent of cancer in the body.

Reference: NCI-Thesaurus

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Regulatory Element

A DNA sequence that is required for a gene on the same DNA molecule to be transcribed, or to be transcribed in the proper cell type(s) and developmental stage(s).

Reference: MGI

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Regulatory Gene

A gene whose function is to regulate the expression of a structural gene.

Reference: MGI

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Replication

The process of synthesizing a copy of a DNA molecule from nucleotides using information contained within one strand of a template DNA molecule. The new strand of DNA is synthesized from the 5' end to the 3' end.

Reference: MGI

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Reporter Gene

A gene whose product is easily detected and not ordinarily present in an organism or cell type under study that is expressed as part of a DNA construct introduced experimentally. Bacterial beta-galactosidase, whose activity can be detected using a staining reaction, is a commonly used reporter gene, as is green fluorescent protein.

Reference: MGI

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Restriction Enzyme

A protein that recognizes specific, short nucleotide sequences and cuts DNA at those sites.

Reference: MGI

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Restriction Fragment

A length of DNA whose ends are the result of cutting by a restriction enzyme.

Reference: MGI

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Retrotransposon

Retrotransposons are transposable DNA elements (transposons) that employ retroviral-like reverse transcription during the process of transposition: retrotransposon DNA is first transcribed into an RNA template, then reverse transcribed into DNA, and then inserted into a new genomic site.

Reference: NCI-Thesaurus

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Retrovirus

A virus whose primary genetic material is RNA instead of DNA. Replication of the genome of such a virus requires the RNA to be copied into DNA using reverse transcriptase. This RNA serves as a template for the synthesis of a complementary DNA, which may be integrated into the host DNA. This group of viruses includes HIV (AIDS virus).

Reference: MGI

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Reverse Transcriptase

An enzyme that is able to synthesize DNA from information in RNA. It requires an RNA template and a DNA or RNA primer.

Reference: MGI

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Reversion

A mutation event that alters an allele conferring a mutant phenotype into one conferring a wild-type phenotype. The mutation need not restore the gene to its original nucleotide sequence to be considered a reversion event.

Reference: MGI

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Revertant

An individual carrying an allele of a given gene that at one time produced a mutant phenotype, but which since has undergone a subsequent mutation that restored a wild-type phenotype. The mutation need not restore the gene to its original nucleotide sequence to be considered a reversion event.

Reference: MGI

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RFLP

Restriction Fragment Length Polymorphism. A genetic polymorphism with respect to the observed length of a restriction fragment. RFLPs can result from single nucleotide polymorphisms as well as from insertions, deletions, or microsatellite expansions.

Reference: MGI

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Ribosome

A complex of proteins and RNA within which translation is carried out.

Reference: MGI

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Ribozyme

An RNA molecule with catalytic activity.

Reference: MGI

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RNA

Ribonucleic acid. A nucleic acid that is the primary product of gene expression. Chemically, it differs from DNA by the substitution of ribose for deoxyribose in the sugar-phosphate backbone and by the substitution of the base uracil for thymine. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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RNA Editing

The alteration of the sequence of an RNA molecule by enyzmatic modification of individual bases without normal splicing.

Reference: MGI

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RNA Interference

Sequence-specific posttranscriptional gene silencing. It is mediated by 21- and 22-nucleotide small interfering RNAs (siRNAs) generated by ribonuclease III cleavage from longer dsRNAs.

Reference: NCI-Thesaurus

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RNA Polymerase

An enzyme that carries out transcription.

Reference: MGI

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RNA Processing

Modifications to an RNA molecule after transcription, including splicing, polyadenylation, and editing.

Reference: MGI

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RNAse

Ribonuclease. A protein that cleaves the phosphodiester backbone of RNA enzymatically.

Reference: MGI

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RNAse Protection

A method of detecting the presence of a specific RNA in a sample. A radioactively-labeled RNA probe is prepared by transcribing the antisense strand of a DNA construct. The labeled probe is hybridized to the sample. The sample is then treated with RNAse, which is specific to single-stranded RNA. The sample is then subjected to electrophoresis and autoradiography. The presence of full-length probe that has not been cleaved by RNAse indicates the presence of the sense strand, and hence gene expression, in the sample.

Reference: MGI

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Robertsonian Translocation

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.

Reference: MGI

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rRNA

Ribosomal RNA. The RNA molecules that are a structural and catalytic component of the ribosome.

Reference: MGI

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RT-PCR

Reverse-Transcription PCR. A method of amplifying mRNA by first synthesizing cDNA with reverse transcriptase, then amplifying the cDNA using PCR. A positive result is evidence of a particular mRNA, and hence of gene expression, in a sample.

Reference: MGI

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Schema

1. An underlying organizational pattern or structure; conceptual framework. 2. A collection of items that model part or all of a real world object, particularly in the context of a database, i.e., a database schema. 3. The structure of a database system, described in a formal language supported by the database management system (DBMS). In a relational database, the schema defines the tables, the fields in each table, and the relationships between fields and tables. Schemas are generally stored in a data dictionary. Although a schema is defined in text database language, the term is often used to refer to a graphical depiction of the database structure. 4. In computer science, a description of the logical organization, structure, and content of a database.

Reference: MGI

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SCID Mouse

Severe combined immunodeficient (SCID) mice like their human counterparts with immunodeficiency diseases are helpless not only to fight infection but also to reject transplanted tissue. These animals lack both T and B-cells and are used extensively in researches of immune disease or tissue transplantation.

Reference: NCI-Thesaurus

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Segregating Inbred Strain

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.

Reference: MGI

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Segregation

1. The separation of homologous chromosomes during meiosis. 2. The separation of different alleles of the same gene during meiosis.

Reference: MGI

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Semidominant

One of a series of terms applied to the phenotypic effect of a particular allele in reference to another allele (usually the standard wild-type allele) with respect to a given trait. An allele "A" is said to be semidominant with respect to the allele "a" if the A/A homozygote has a mutant phenotype, the A/a heterozygote has a less severe phenotype, while the a/a homozygote is wild-type. An example is Pmp22(Tr-J) in mouse. Pmp22(Tr-J)/Pmp22(Tr-J) animals display a myelination defect associated with a "trembler" phenotype, while Pmp22(Tr-J)/Pmp22(+) animals are less severely affected, and Pmp22(+)/Pmp22(+) animals are wild-type.

Reference: MGI

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Sense

1. In molecular biology, that strand of a DNA molecule whose sequence is represented in mRNA. 2. In molecular biology, an RNA molecule normally processed into mRNA and translated (rather than the complementary sequence).

Reference: MGI

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Sequence

In MGI, a series of nucleotides in RNA or DNA molecules or of amino acids in a protein.

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Sequence Annotation

Additional information added to genomic sequence to identify genes, delimit the intron and exon structures of those genes, identify regulatory elements, note the positions of allelic variation, etc.

Reference: MGI

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Sequence ID (SeqID)

Sequence accession identifier. A unique alphanumeric character string that unambiguously identifies a sequence record in a database. Examples of MGI genomic sequence providers are NCBI and Ensembl; examples of sequence IDs from these providers are 16590 and ENSMUSG00000053869, respectively.

Reference: MGI

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Sequence Provider

Whole genome sequencing data from large-scale genome projects. MGI genomic sequence providers are NCBI and Ensembl; examples of sequence IDs from these providers are 16590 and ENSMUSG00000053869, respectively.

Reference: MGI

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Sequencing

Determination of the order of nucleotides (base sequences) in a DNA or RNA molecule or the order of amino acids in a protein.

Reference: MGI

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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.

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Sex Linked

Located on the X chromosome or the Y chromosome.

Reference: MGI

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Shotgun Sequencing

The sequencing of a large DNA segment through the sequencing of randomly-derived subsegments whose order and orientation within the large segment is unknown until the assembly of overlapping sequences. The method works if all positions in the large segment are covered by multiple overlapping subsegments. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Sibling

In MGI, this term refers to terms in a hierarchical controlled vocabulary such as those containing Gene Ontology (GO) terms. A "sibling" of a term is a term at the same level of the hierarchy sharing at least one ancestor. For example, the GO term alcohol dehydrogenase GO:0004022] is a sibling to the GO term aldehyde oxidase [GO:0004031]; they share the ancestor term enzyme [GO:0003824].

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Similarity

1. In comparison of nucleic acid sequences, the extent to which two nucleic acid sequences have identical bases at equivalent positions, usually expressed as a percentage. 2. In comparison of protein sequences, the extent to which the amino acid sequences of two proteins have identical or functionally similar amino acids at equivalent positions, usually expressed as a percentage.

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Simple Genotype

A genotype involving a single allele pair.

Reference: MGI

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Simple Sequence Repeat (SSR)

A sequence consisting largely of a tandem repeat of a specific k-mer (such as (CA)15). Many SSRs are polymorphic and have been widely used in genetic mapping.

Reference: MGI

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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.

Reference: MGI

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Small Interfering RNA

21- and 22-nucleotide double-stranded RNAs. These are the mediators of a sequence-specific messenger RNA degradation process known as RNA interference. They are generated by ribonuclease III cleavage from longer dsRNAs.

Reference: NCI-Thesaurus

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SNP

Single Nucleotide Polymorphism. A type of polymorphism in which two chromosomes differ in a given segment by the identity of a single base pair.

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Somatic

Cells in an animal other than those that constitute the germ line.

Reference: MGI

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Somatic Cell Hybrid

A type of mapping experiment permitting the assignment of markers to chromosomes. The method consists of fusing cultured cells of one species with cultured cells of a different species. The hybrid cells are unstable in karyotype during growth, with most chromosomes from one species typically being lost. Among clonal populations of hybrid cells following growth, different chromosomes are retained from one species. A panel of hybrid cell cultures can be assayed for which mouse chromosomes (for example) are retained, and simultaneously assayed for the presence of particular markers. The correlation of the presence of a particular marker across the panel with the presence of a particular mouse chromosome allows that marker to be assigned to that chromosome.

Reference: MGI

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Southern Blot

An assay that detects specific DNA molecules using a DNA or RNA probe with sequence similarity. Samples are subjected to electrophoresis on a slab gel. A replica of the gel is then made on a membrane by capillary transfer following denaturation. Specific DNA sequences are then detected on the membrane with a radioactively- or chemically-labeled probe. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

Reference: MGI

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Spindle

The cellular apparatus that directs chromosome movement during cell division in mitosis or meiosis. The spindle is largely composed of microtubules.

Reference: MGI

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Splice Acceptor Site

In the splicing of RNA, the site at the 3' end of an intron.

Reference: MGI

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Splice Donor Site

In the splicing of RNA, the site at the 5' end of an intron.

Reference: MGI

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Splice Junction

In the splicing of RNA, the site of a former intron in a mature mRNA.

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Splicing

Part of the processing of an RNA transcript into mRNA, in which introns are removed enzymatically.

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Spontaneous

As a type of mutation, one that has occurred in the absence of any experimental mutagenic treatment, such as irradiation or treatment with chemical mutagens.

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SSLP

Simple Sequence Length Polymorphism, a type of polymorphism that results from variation in the length of an SSR.

Reference: MGI

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SSR

Simple Sequence Repeat, a DNA sequence consisting largely of a tandem repeat of a specific k-mer (such as (CA)15). Many SSRs are polymorphic and have been widely used in genetic mapping.

Reference: MGI

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Stop Codon

One of three codons that signal that translation of an RNA sequence should cease.

Reference: MGI

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Strain of Origin

The strain on which a given allele combination arose.

Reference: MGI

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Structural Gene

A gene that encodes an enzyme or structural protein, in contrast to a regulatory gene.

Reference: MGI

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Structural Protein

A protein that functions as a structural element of cells rather than as an enzyme, for example, collagen.

Reference: MGI

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STS

Sequence Tagged Site. A short segment of unique sequence derived from genomic DNA. A large collection of STSs can be used to assemble a physical map of the genome from a collection of genomic clones (e.g., BACs or YACs) by testing each clone for the presence of each STS. Two clones that contain one or more STSs in common must overlap. For examples, see the physical maps of the mouse genome at MGI.

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Subcutaneous

Beneath the skin.

Reference: NCI-Thesaurus

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Substrate

A molecule acted upon by an enzyme.

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SV40

A small (40 to 45 nm) DNA virus of the genus Polyomavirus, family Papovaviridae; the cause of seemingly inapparent infections in monkeys, especially rhesus, and a common contaminant of monkey cell cultures; the virus may cause inapparent infection in humans and may be excreted in stools of children for several weeks; it can produce fibrosarcoma in suckling hamsters, and transformation may occur in human diploid cells; it may also form "hybrid" virus in cells also infected with certain adenoviruses.

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SWISS-PROT

A curated protein sequence database. See the SWISS-PROT site for more details.

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Symbol

As used in MGI, a gene symbol is a unique abbreviation for the gene name or the allele name.

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Syngeneic

Denoting individuals or tissues that are genetically identical.

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Synonym

In MGI, a synonym is either an unofficial symbol that has appeared in the scientific literature or in public databases such as GenBank, or a formerly official symbol, withdrawn due to gene family revisions or to conform to the human ortholog symbol.

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Synteny

The state of being on the same chromosome. A gene is also said to be syntenic to a particular chromosome if it is known to be located on that chromosome but is otherwise unmapped.

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System Catalog

The data dictionary of a DBMS. The system catalog stores metadata including the schemas of the databases. It is a mini-database, and is usually stored using the DBMS itself in special tables called system tables. It maybe referred to as being "on line", as it is active, and users can query it like any other table.

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T-Antigen

Proteins encoded by the genomes of specific DNA tumor viruses that are associated with the neoplastic transformation of infected cells. T-antigens stimulate the production of antibodies and are immunogenic.

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Targeted Mutation

A type of mutation in which a chromosomal gene is altered by the substitution of a DNA construct assembled in vitro. In mouse, the constructs are usually designed to eliminate gene function; such targeted mutations are often casually referred to as knock outs. Some DNA constructs are designed to alter gene function; such targeted mutations are often casually referred to as knock ins.

Reference: MGI

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Telomere

A specialized structure at the ends of linear chromosomes in eukaryotes. Telomeres confer stability on chromosome ends. Chromosome ends lacking telomeres, such as those generated from interstitial sites by chromosome breaks, are reactive, often fusing with other broken ends to generate chromosome rearrangements. Telomeres also permit the ends of linear chromosomes to replicate fully. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

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Template

In the process of replication or transcription, the strand of DNA that serves as the source of information.

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Termination Codon

One of three codons that signal that translation of an RNA sequence should cease.

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Testcross

A type of cross in which individuals whose genotype with respect to one or more genes is unknown are crossed to a test strain homozygous for a recessive allele at the genes under study. For example, a cross of an individual that was A/A or A/a (identical in phenotype) to a/a would reveal the genotype of the individual being tested, because if the individual being tested were A/A, all of the progeny would show the dominant phenotype, while if the individual being tested were A/a, half of the progeny would show the dominant phenotype and half would show the recessive phenotype.

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Texas Red

A fluorescent dye used to label antibodies for immunofluorescence or Western blots.

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Theiler Stage

One of a standard set of stages describing mouse development. See the Table of Theiler stages and the summary Images at Edinburgh.

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Thermostable

Used to describe an enzyme or other protein that is not denatured at temperatures that denature most other proteins.

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Thymine (T)

A pyrimidine base that is a component of nucleotides and thus a normal component of DNA. Uracil replaces thymine in RNA. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

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Toxic

Having to do with poison or something harmful to the body. Toxic substances usually cause unwanted side effects.

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Toxicity

The finding of bodily harm due to the poisonous effects of something.

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Toxicology

Toxicology is the branch of pharmacology that deals with the nature and effects and treatments of poisons.

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Trait

A trait is a distinct variant of a phenotypic character of an organism that may be inherited, environmentally determined or somewhere in between.

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Transcript

An RNA molecule (or species of RNA molecule) that is the product of transcription.

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Transcription

The enzymatic synthesis of an RNA molecule directed by information in a DNA molecule. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

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Transcriptional Activation

The process by which an unexpressed gene is activated to serve as a transcription template for synthesis of RNA.

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Transgene

Any DNA sequence or combination of sequences that has been introduced via a construct into the germ line of the animal by random integration.

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Transition

A type of point mutation in which a purine is substituted for another purine or a pyrimidine for another pyrimidine. These substitutions include A for G, G for A, C for T, or T for C.

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Translation

The enzymatic synthesis of a protein molecule directed by the information in an mRNA molecule. The mRNA is read from the 5' end to the 3' end, with the protein being synthesized from the amino terminus to the carboxyl terminus. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

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Translocation

A type of mutation in which two nonhomologous chromosomes are each broken and then repaired in such a way that: 1. the resulting chromosomes each contain material from the other chromosome (areciprocal translocation) 2. one of the chromosomes contains an insertion of material from the other chromosome, with the other chromosome containing a deletion (an insertional translocation,) or 3. the two chromosomes, each with breaks near the centromere, fuse to form a single chromosome with a single centromere (a Robertsonian translocation). See also the entry at NHGRI's Talking Glossary of Genetic Terms.

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Transplantation

Transference of a tissue or organ within an individual, between individuals of the same species, or between individuals of different species.

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Transposition

1. A type of chromosome rearrangement in which a segment of a chromosome is moved to a different location on the same chromosome, resembling an insertional translocation involving a single chromosome. 2. The movement of a mobile genetic element to a new location.

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Transposon

A type of mobile genetic element consisting of DNA that moves to new genomic locations conservatively (without replicating itself) or replicatively (moving a copy of itself).

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Transversion

A type of point mutation in which a purine is substituted for a pyrimidine or a pyrimidine for a purine. These substitutions include C or T for A, C or T for G, A or G for C, and A or G for T.

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TrEMBL

A protein sequence database that contains all the translations of EMBL nucleotide sequences. See the TrEMBL site for more details.

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Trisomy

The condition of having three chromosomes of a particular type. Down Syndrome in humans is a trisomy for chromosome 21.

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tRNA

Transfer RNA. Small RNA molecules that bind to the codons of mRNA in the ribosome after being "charged" with amino acids.

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Tumor

A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.

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Tumor suppressor gene

A tumor suppressor gene, or anti-oncogene, is a gene that protects a cell from one step on the path to cancer. When this gene is mutated to cause a loss or reduction in its function, the cell can progress to cancer, usually in combination with other genetic changes.

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Tumorigenesis

The origin or production, or development of cancer, including carcinomas and other malignant neoplasms.

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UCSC Genome Browser

The genome browser at the University of California at Santa Cruz.

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UniGene

An experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location. See the UniGene page at NCBI.

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Uniparental Disomy

The inheritance, in a diploid organism, of both copies of a single chromosome from one parent. This may result from the union of a gamete bearing two copies of one chromosome with a gamete bearing no copy of that chromosome, or from the union of a gamete bearing two copies of one chromosome with a normal gamete, followed by the loss of one chromosome through an error in mitosis. Because of imprinting, uniparental disomy can have phenotypic consequences in mammals. See, for example, Prader-Willi Syndrome.

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Uracil (U)

A pyrimidine base that is a componentof nucleotides and thus a normal component of RNA. Thymine replaces uracil in DNA. See also the entry at NHGRI's Talking Glossary of Genetic Terms.

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Vaccination

Administration of vaccines to stimulate the host's immune response. This includes any preparation intended for active immunological prophylaxis or treatment.

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Vaccine

Preparations containing substances with antigenic properties administered to activate the immune system, inducing an immune response. Vaccine ranges from inactivated or attenuated microorganisms (bacteria and viruses), enhanced autologous tumor cells, tumor antigens or epitopes, to peptide cojugated immunotoxins that are used to elicit host immune responses. Vaccines are used for the prevention, amelioration, or treatment of infectious diseases and cancer.

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Vector

See Cloning Vector.

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VEGA

Vertebrate Genome Annotation. The VEGA database is a central repository for high quality, frequently updated, manual annotation of vertebrate finished genome sequence. VEGA developed within Ensembl as a joint project between EMBL-EBI and the Sanger Institute.

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Virology

The science that deals with the study of viruses.

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Virus

A noncellular biological entity that requires a host cell for reproduction. Viruses consist of a nucleic acid genome that is either DNA or, in the case of retroviruses, RNA. The viral genome is covered with a protein coat; some viruses have a host-derived membrane over the protein coat.

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VISTA

A suite of programs and databases for comparative analysis of genomic sequences. Users can either submit sequences and alignments for analysis or examine precomputed whole-genome alignments of different species. See the VISTA website.

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Western Blot

An assay that detects specific proteins within a protein mixture. Samples are subjected to electrophoresis on a slab gel. A replica of the gel is then made on a membrane by electrophoretic transfer. Specific proteins are then detected on the membrane using antibody staining.

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Whole-genome Shotgun Sequencing

The sequencing of the entire genome of an organism through the sequencing of randomly-derived subsegments whose order and orientation is unknown until the assembly of overlapping sequences is performed computationally. The method works if all positions in the genome are covered by multiple overlapping subsegments.

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Wild Type

1. The phenotype with respect to a given inherited characteristic that is considered to be the "normal" type commonly found in natural populations. 2. The allele of a particular gene that confers the phenotype considered to be the "normal" type commonly found in natural populations. N.B.: Because some DNA sequence polymorphisms do not produce different phenotypes, there can be multiple "wild-type" alleles of a gene.

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Wild Type Allele

One of many possible versions of a gene that functions normally, as opposed to versions of a gene that are functionally abnormal (i.e., mutant alleles).

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X Chromosome

One of pair of chromosomes that is sexually dimorphic in mammals. Normal female mammals have two X chromosomes, while normal male mammals have an X chromosome and a Y chromosome.

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X Inactivation

The condensation of all but one of the X chromosomes of a mammal into a heterochromatic state, eliminating gene expression from all but the active X chromosome. This process ensures that male and female mammals have the same level of gene activity of X-chromosome genes.

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Xenograft

A graft transferred from a donor of one species to a recipient of another species.

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Xenograft Model

Describes to xenografts (implanting tissue or cell lines from a different species) and allografts (implanting tissue or cell lines form the same species). The grafts are transplanted in immuno-compromised animals where they grow and, depending on the graft material, form tumors.

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Y Chromosome

One of pair of chromosomes that is sexually dimorphic in mammals. Normal female mammals have two X chromosomes, while normal male mammals have an X chromosome and a Y chromosome.

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YAC

Yeast Artificial Chromosome.

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Zinc Finger Domain

The Zinc Finger Domain is found in many proteins that bind nucleic acids, typically DNA binding transcription factors. There are several classes of Zn finger proteins. Some bind Zn with only Cys residues (e.g., nuclear receptor superfamily) while others coordinate Zn with Cys and His residues. In the 25-amino acid C2H2 type motif, Zn2+ is held between a pair of anti-parallel beta strands and a single alpha helix by a pair of invariant Cys and His residues. The Cys/His type proteins generally contain repeated units and bind DNA as a monomer, while Cys/Cys proteins contain two units that bind inverted DNA repeats as homo- or heterodimers. In some Cys/Cys types the Zn ion folds the involved region into a globular structure that binds DNA.

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Zinc Finger Nuclease

Zinc-finger nucleases (ZFNs) are artificial restriction enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger domains can be engineered to target desired DNA sequences which enables zinc-finger nucleases to target unique sequence within a complex genome. By taking advantage of endogenous DNA repair machinery, these reagents can be used to precisely alter the genomes of higher organisms.

Reference: Wikipedia

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