ZFIN Glossary

This glossary provides definitions for terms that are useful in understanding zebrafish development, anatomy, genetics and bioinformatics. Terms are defined in a general sense as they apply to eukaryotic genetics, particularly zebrafish genetics; some terms are also defined as they are specifically used in ZFIN (e.g., gene). This list will grow as time goes on. If there is a term you think should be included in this list, please contact ZFIN User Support.

Anatomical terms were adapted from Kimmel et al., 1995. Bioinformatic terms were adapted from the MGI mouse glossary and we thank MGI for its generous help.

There are a number of other useful online glossaries:

The Zebrafish Anatomy Ontology displays anatomical terms of the zebrafish in a hierarchical manner for a series of developmental stages, using standard anatomical nomenclature.
The Zebrafish Developmental Staging Series describes the standard criteria used for identifying the developmental age of zebrafish.
The GO Term Definitions provides current definitions of all terms used in the Gene Ontology Project.
The Glossary of Genetic Terms at the National Human Genome Research Institute defines basic genetic terms most relevant to human genetics. This glossary includes audio explanations and illustrations.
The Genome Glossary for the Human Genome Project defines many basic genetic terms.
The MeSH Browser at NCBI contains useful definitions of many terms, organized as a hierarchical controlled vocabulary.
The On-line Medical Dictionary provides definitions for hundreds of medical terms used in describing human phenotypes.
The Hypermedia Glossary of Genetic Terms by Birgid Schlindwein contains over 600 genetic terms.
The Zebrafish Behavior Catalog includes close to 200 zebrafish behavior terms covering both larval and adult behaviors.

If you find an online glossary that you think should be included here, please contact ZFIN User Support.

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3' (3-prime)

A term that identifies one end of a single-stranded nucleic acid molecule. The 3' end is the end of the molecule that terminates in a 3' hydroxyl 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. See the Figure at NHGRI. See also 5' (5-prime), central dogma.

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.

5' (5-prime)

A term that identifies one end of a single-stranded nucleic acid molecule. The 5' end is the end of the molecule that 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. See the Figure at NHGRI. See also 3' (3-prime), central dogma.

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.

accession ID

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

allele

Any of the alternative forms of a gene occupying a given locus; any one of several mutational forms of a gene. In ZFIN, allelic variants are associated with mutants and mutant phenotypes.

allele designation

In ZFIN, an "allele disignation" is a set of letters and numbers that uniquely identifies an allele of a given gene. The allele designation is added as a superscript to the gene symbol. For details see the Zebrafish Nomenclature Guidelines for alleles. See also gene name.

alternative splicing

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

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 the Figure at NHGRI. For Figures showing the strucutre of each of the twenty primary animo acids, see Figure1 and Figure2 from "Molecular Biology of the Cell" by Alberts et al.

amino terminus

A term that identifies one end of a protein molecule. The amino terminus is that end of the molecule that terminates in a free amino group. See the Figure at NHGRI. See also amino acid, central dogma.

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.
See also:

ancestor

In bioinformatics, this term refers to terms in a hierarchical controlled vocabulary like ones containing Gene Ontology (GO) 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]. See also: children, parent. sibling.

aneuploid

Not euploid.

annotation

Note added to a document or image to provide additional needed information. See also sequence annotation.

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. See also STS.

antibody

A protein produced by cells of the immune system that binds to an antigen. See the Figure at NHGRI. See also monoclonal antibody.

antigen

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

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.
See also:

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.

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).

approved

With respect to a gene symbol, gene name, or allele designation within ZFIN, an "approved" symbol or name is one that has been assigned by the Zebrafish Nomenclature Committee.

ATCC

American Type Culture Collection. A large collection of microbial stocks, including microbes containing DNA segments. See the ATCC home page for further information.

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.

autosome

Any chromosome that is not a sex chromosome.

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.

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.

backcross

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

bacteriophage

A virus that infects bacteria.

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), whereas the pyrimidine bases are cytosine (C) and thymine (T). In RNA, the purine bases are adenine (A) and guanine (G), whereas the pyrimidine bases are cytosine (C) and uracil (U). See the Figure at NHGRI.

base pair (bp)

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 the Figure at NHGRI.

bioinformatics

The acquisition, storage, arrangement, analysis, display and communication of information related to the biology of living things, generally assisted by the use of computers.

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.

biosynthesis

Synthesis of chemical compounds by enzymatic processes in living organisms.

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.

BLAST

Basic Local Alignment and Searching Tool. A sequence comparison algorithm optimized for speed, which is used to search sequence databases for optimal local alignments to a query sequence. More information is available at NCBI.

cAMP

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

carboxyl terminus

A term that identifies one end of a protein molecule. The carboxyl terminus is the end of the molecule that terminates in a free carboxyl group. See the Figure at NHGRI. See also amino acid, central dogma.

catabolism

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

cDNA

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

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.

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.

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. See the Figure at Access Excellence or the Figure at NHGRI.

centromere

In zebrafish 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. See the Figure at NHGRI.

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.

children

In bioinformatics, 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]. See also: ancestor, sibling.

chimera

1. An animal formed from two different animals, that is from two different embryonic sources. See also mosaic.
2. A clone containing genomic DNA from nonadjacent genomic segments or cDNA from two different mRNAs (see cloning artifact).

chlorambucil

A chemical mutagen, also called nitrogen mustard.

chromatin

The nuclear material that makes up chromosomes, consisting of DNA and protein. See also euchromatin, heterochromatin.

chromogenic

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

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 the Figure at NHGRI.

chromosome aberration

1. A chromosome rearrangement.
2. Less commonly, a numerical aberration in the number of chromosomes.

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:

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.

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.

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.

cM

See centimorgan.

coding region

That part of a gene whose sequence is read as codons during translation. See also central dogma, transcription, translation, intron, Exon.

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. See also dominant, recessive, Semidominant.

codon

Three bases in a DNA or RNA sequence that specify an amino acid or a termination signal (stop codon). See the Figure at NHGRI. See also central dogma.

coisogenic

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.

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.

complementary sequence

A single-stranded nucleic acid that would bind to a given single-stranded nucleic acid by base pairing.

complementation

The appearance of only wild-type phenotypes in hybrid offspring from two mutant individuals homozygous or heterozygous for recessive mutations. Complementation shows that the two parental mutant individuals have mutant alleles of different genes, even if they are phenotypically similar.

complex/cluster/region

In ZFIN, the marker type "Complex/Cluster/Region" is used to refer to any of the following:

Gene complex; a group of genes linked closely together that are related evolutionarily or functionally. Interspersed unrelated genes located within the group are included.
A segment of the zebrafish genome defined by comparison to an orthologous segment in the genome of another species, or by some specific characteristic, such as loss of heterozygosity.
A marker repository for information pertaining to a specific gene family, where such information lacks precise family member resolution.

conserved synteny

The occurrence of synteny of orthologous genes in two different organisms. Conserved synteny between zebrafish and human or mouse does not extend over entire chromosomes.

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.

controlled vocabulary

A restricted set of defined terms allowing the representation of complex information in a database. See, for example, Gene Ontology.

cosmid

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

cre recombinase

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

cross

An experimental mating of two genetically distinct sexually reproducing organisms.
See also:

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.

crossover

A reciprocal recombination event.

Cy5

A fluorescent dye used to label DNA probes for FISH or antibodies for immunofluorescence or Western blots. Also used to label nucleic acid probes for microarray analysis.

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.

cytogenetic band

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

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.

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.

cytoplasm

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

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.

deficiency

A type of mutation caused by loss of one or more nucleotides from a DNA segment. Deficiencies can be very large, encompassing many genes and megabases of DNA, to the point of producing a visible cytological abnormality in a chromosome. Small deficiencies within a gene can alter the reading frame, and thus the amino acid sequence of the encoded protein. See the Figure at NHGRI.

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.

dimorphic

Having two forms.

diploid

Having twice the chromosome number normally found in a gamete. Normal zebrafish are diploid, having a chromosome set from the maternal gamete (the egg) and a chromosome set from the paternal gamete (the sperm). See also haploid.

DNA

Deoxyribonucleic acid. The nucleic acid of which genes are made. See the Figure at NHGRI. See also central dogma, nucleic acid, and RNA.

DNA construct

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

DNA mapping panel

A data set obtained by DNA typing of polymorphic markers in hybrid crosses of zebrafish. See a list of zebrafish Mapping Panels at ZFIN.

DNA polymerase

An enzyme that carries out replication.

DNA segment

1. A length of DNA.
2. In ZFIN, 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.

dNTP

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

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. See also codominant, recessive, semidominant.

duplication

An additional copy of a DNA segment present in the genome. Gene duplication is the source of paralogous genes. See the Figure at NHGRI.

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.

early pressure (EP)

Early pressure method to produce homozygous diploid offspring.

electroporation

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

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.

EMS

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

endogenous

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

endonuclease

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

enhancer

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

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. 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. See also gene trap.

ENU

Ethylnitrosourea. A chemical mutagen. In zebrafish, the mutation rate caused by ENU can be as high as one mutation/ locus/500-1000 gametes.

enzyme

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

EP

See early pressure.

epigenetic

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

epistasis

Masking of a phenotypic trait through the action of a mutant allele. For example, albino (absence of pigment) is epistatic to melanin pigment genes that determine the dark color of zebrafish eyes and stripes.

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 to identify transcribed regions in genomic sequence, to characterize patterns of gene expression in the tissue that was the source of the cDNA and as markers for genetic mapping.

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.

euchromatin

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

euploid

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

evolution

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

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.

exon

Part of a gene whose sequence is present in a mature mRNA after splicing. See also Intron.

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. See also penetrance.

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 fluorescence microscopy. See the Figure at NHGRI. See also in situ hybridization.

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.

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.

FTP

File Transfer Protocol. A method for transferring files to and from remote computer systems.

frameshift

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

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. See also:

gamete

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

GenBank

The database of nucleic acid sequences at NCBI.

gene

The basic unit of heredity; a portion of DNA that (usually) codes for a protein product. See also central dogma.
In ZFIN, "gene" may be used to refer to any of the following:

A locus in the nuclear genome characterized by an altered phenotype or by an effect on an inserted reporter gene, such as a gene trap or enhancer trap.
A locus in the nuclear genome that is necessary and sufficient to express the complete complement of functional products derived from a unit of transcription.
A locus in the zebrafish nuclear genome identified by hybridization to a nucleic acid segment derived from a non-zebrafish species, where the segment used as probe represents some portion of a functional unit of transcription in the nuclear genome of the non-zebrafish species.
An exon-encoding segment of the germ-line nuclear genome located within a region that undergoes somatic rearrangement.
A locus in the nuclear genome that is within an intron of (but not, itself, an exon of) a unit of transcription, which gives rise to a functional product upon transcript processing of the host unit.

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.

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.

gene duplication

See Duplication.

gene expression

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

gene family

A group of paralogous genes.

gene name

In ZFIN, a "gene name" is a word or phrase that uniquely identifies a gene. The gene name has an abbreviation that is the gene symbol. See also Allele Designation, Gene Symbol.

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.

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, especially those cases in which the RNA molecule is not translated (see tRNA, rRNA).

gene symbol

As used in ZFIN, a "gene symbol" is a unique abbreviation for the gene name. See also allele designation, gene name.

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. 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 thus expressed in the same cells and developmental stages as the gene into which the gene trap has inserted. See also enhancer trap

genetic code

The relationship of the sixty-four nucleic acid codons to the twenty primary amino acids. See the Figure for the standard genetic code. See also central dogma.

genetic map

A map showing the position of genes or markers on a chromosome. See physical map,linkage map, and cytogenetic map.

genome

The total genetic information of a cell or organelle. In eukaryotes, "genome" usually refers to nuclear DNA rather than to mitochondrial or chloroplast DNA.

genotype

A description of the genetic information carried by an organism. In the simplest case, "genotype" may refer to the information carried at a single locus, as in A/A, A/a, or a/a.

GFP

Green Fluorescent Protein. A fluorescent marker used to label cells expressing transgenes.

germ line

Cells of an animal that give rise to gametes.

haploid

Having the chromosome number normally found in a gamete. See also diploid.

haploinsufficient

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

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.

heat shock (HS)

1. Method to produce homozygous diploid offspring.
2. Method to induce expression of transgenes under the control of a heat shock promoter.

hemizygous

The state of a gene present in only one copy in a diploid cell, such as a gene on the X chromosome in a male mammal, or a gene whose homologue has been deleted.

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.
See also euchromatin.

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. See also Homogametic, X chromosome, Y chromosome.

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.

heterozygote

An individual that is heterozygous.

heterozygous

Producing two gamete types with respect to at least one gene (A/a).

heterozygosity

The state of being heterozygous.

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. See also heterogametic, X chromosome, Y chromosome.

homologue

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, homologue, 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.

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.

homology

1. 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.
2. In ZFIN, assertions of mammalian homology imply presumed orthology even though there may be duplicates of the homologous gene in zebrafish. See also: homologue, orthology, paralogy.

homozygote

An individual that is homozygous.

homozygous

Producing only a single gamete type with respect to one or more genes (A/A).

homozygosity

The state of being homozygous.

horseradish peroxidase

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

HTML

Hypertext Markup Language. An authoring language for creating and sharing electronic documents over the Internet. This document is written in HTML.
You can view the HTML source code for this document by:

selecting Page Source from the View menu in Netscape Navigator
selecting Source from the View menu in Microsoft Internet Explorer.

hybrid

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

hybridization

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

hydrophilic

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

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.

hypertext

Text displayed electronically with embedded links to other text or to images, sounds, movies or other multimedia content. This document is an example of hypertext.

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 an increased level.
See also:

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.
See also:

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. See also similarity.

idiogram

An idealized drawing.

I.M.A.G.E. Consortium

Integrated Molecular Analysis of Genome Expression Consortium. A collection of a large number of partially sequenced ESTs or cDNAs. See the homepage of the I.M.A.G.E. Consortium for further information.

immunofluorescence

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

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. Alternatively, the secondary antibody can be directly coupled to a fluorofluor. Microscopic examination reveals the presence of labeling, and hence of the specific protein to be detected.

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.

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.

in silico

Computationally, as opposed to in vitro or in vivo.

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). See also FISH.

in vitro

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

in vivo

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

inbred strain

A strain that is essentially homozygous at all loci due to brother-sister matings for at least 20 sequential generations.

incross

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

inhibitor

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

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.

intercross

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

intergenic

Between genes.

intron

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

inversion

A type of mutation in which a length of DNA is broken at 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.

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.

kb

Kilobase.

kilobase

Unit of DNA or RNA sequence equal to 1000 nucleotides.

kinetochore

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

knock-down

A casual term for the reduction of gene function by injection of morpholinos.

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. See also knock-out.

knock-out

A casual term for a type of targeted mutation in which an amorphic ( loss-of-function) allele is produced. See also knock-in.

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).

ligate

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

ligand

A molecule that binds to a receptor protein.

linkage

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

linkage analysis

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

linkage map

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

locus

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

LOH

See loss of heterozygosity.

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.
See also:

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, deficiency, or gene conversion. "Loss of heterozygosity (LOH)" events are often important steps in tumor progression.

loxP Sequence

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

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 ZFIN, a Marker is an object for which unique official nomenclature must be assigned. Markers in ZFIN can be of type: gene, mutant, BAC/YAC, cDNA, EST, SSLP, SSR, STS, RAPD, RFLP.

Mb

megabase.

megabase (Mb)

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

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.

meiotic map

See linkage map.

meiotic maping panel

A set of DNAs used to generate a linkage map.

membrane

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

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.

MGI

Mouse Genome Informatics. The collection of bioinformatics projects at The Jackson Laboratory.

microarray

An array of DNA or protein samples that can be hybridized with probes to study patterns of gene expression.

microsatellite marker

See SSLP.

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.

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.

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).

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 the Figure at NHGRI.

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. See also Retrotransposon.

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.

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.

monosomy

The condition of having a single chromosome of a particular type; lacking a homologous chromosome. See also Trisomy.

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.

mosaic

An individual consisting of cells of two or more genotypes. One example is a wild-type host into which mutant cells have been transplanted.

mRNA

Messenger RNA. An RNA molecule that is the product of transcription of a gene, after that molecule has been spliced and polyadenylated, that can be translated into a protein product. See the Figure at NHGRI. See also central dogma.

mutagen

An agent that causes mutations.

mutant

1. A term applied to a gene or phenotype altered by mutation.
2. An individual carrying a mutation.

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:

name

1. As used in ZFIN, a gene "name" is a word or phrase that uniquely identifies a gene. The gene name has an abbreviation that is the gene symbol.
2. As used in ZFIN, an allele "name" is a set of letters and numbers that uniquely identifies a particular allele of a gene. The allele name is the allele designation.

NCBI

National Center for Biotechnology Information.

neomorphic mutation

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

NHGRI

National Human Genome Research Institute.

noncoding RNA

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

non-Mendelian

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

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 Southern blot and Western blot.

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 the Figure at NHGRI.

nucleotide

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

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. See also microsatellite.

nucleotide substitution

A point mutation.

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 the Figure at NHGRI.

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. See also:

numerical aberrationn

A change in the number of chromosomes from the wild-type number in the absence of any chromosome rearrangement. See also monosomy, trisomy.

offset

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

oligonucleotide

A short length of nucleic acid.

OMIM

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

ontology

As used by 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.

open reading frame (ORF)

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

organelle

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

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. Some mammalian genes have two orthologs in zebrafish due to gene duplication. See also homologue, paralog, orthology.

orthology

The relationship of any two homologous characters whose common ancestor lies in the most recent common ancestor of the taxa being considered. In ZFIN, assertions of mammalian homology imply presumed orthology. See also: homology, ortholog, paralogy.

other genome feature

In ZFIN, "other genome feature" refers to any feature of the genome that is considered to have biological significance but 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.

outcross

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

P1

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

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.

paralog

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

paralogy

The relationship of any two homologous characters that arose by a genetic duplication. See also homology, orthology, and paralog.

parent

1. Mother or father of an individual or a set of progeny.
2. In ZFIN, this term refers to terms in a hierarchical controlled vocabulary such as those containing Gene Ontology (GO) terms. A "parent" of a term is a 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]. See also: children, ancestor, sibling.

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 the Figure at Access Excellence.

penetrance

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

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.

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.

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, morpholino injection.

phenotype

A description of the observable state of an individual with respect to some inherited characteristic. Often, individuals with different genotypes display the same phenotype. See dominant and recessive.

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.

phycoerythrin

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

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.

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.

pleiotropy

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

point mutation

A type of mutation in which a single nucleotide is changed to one of the other three possible nucleotides. See also nucleotide substitution transition, transversion.

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.

polygenic

A trait determined by multiple genes.

polymorphic strains

In zebrafish, polymorphic strains have differences in DNA sequence at many loci. A panel of recombinant offspring derived from a cross between two polymorphic 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.

polymorphism

An instance of genotypic variation within a population.

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, adding nucleotides to the growing strand by base complementarity to the template. See also PCR.

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 ZFIN, the term "probe" applies not only to nucleic acid probes detected as described above, but also to antibody probes used to detect proteins by immunohistochemistry.

promoter

One of the necessary regulatory elements of a gene. The promoter is the DNA sequence to which RNA polymerase binds and initiates transcription. See also enhancer.

protein

A polymer of amino acids. See the Figure at NHGRI.

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.

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.

proteome

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

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.

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.

purine

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

pyrimidine

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

quantitative trait locus (QTL)

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.

query

A request for information submitted to a computerized database.

query form

As used in ZFIN, a Query Form is a web page allowing users to retrieve information from the ZFIN database.

query sequence

A DNA or protein sequence submitted to a computerized database for comparison, e.g., a BLAST search.

radiation

1. Electromagnetic energy: gamma rays, X rays, ultraviolet light, visible light, infrared light, microwaves and radio waves. In zebrafish 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.

radiation hybrid (RH) 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 zebrafish are available a at ZFIN.

radiation hybrid (RH) panel

A set of DNAs used to generate a radiation hybrid map.

RAPD

Random Amplified Polymorphic DNA. Segments of DNA amplified by PCR using short primers with sequences chosen at random that are used as polymorphic markers for mapping.

reading frame

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

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. See also Codominant, Dominant, Semidomint.

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.

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). See also enhancer, promoter.

regulatory gene

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

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. See the Figure at NHGRI.

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. See also enhancer trap, gene trap.

restriction enzyme

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

restriction fragment

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

retrotransposon

A type of mobile genetic element that utilizes an RNA intermediate and reverse transcriptase to transpose.

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 group of viruses includes HIV (AIDS virus).

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. See also cDNA.

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.

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.

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, deficiencies, or microsatellite expansions.

ribosome

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

ribozyme

An RNA molecule with catalytic activity.

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 the Figure at NHGRI. See also central dogma and DNA.

RNA editing

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

RNA polymerase

An enzyme that carries out transcription.

RNA processing

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

RNAse

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

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.

rRNA

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

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.

segregation

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

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. See also codominant, dominant, recessive.

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).

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.

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.

sex linked

Located on the X chromosome or the Y chromosome.

sibling

1. A brother or sister sharing the same parents.
2. In ZFIN, this term refers to terms in a hierarchical controlled vocabulary like ones 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]. See also: ancestor, children.

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. See also Identity.

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.

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.

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 the Figure from Alberts, et al., Molecular Biology of the Cell. See also Northern blot and Western blot.

somatic

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

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 zebrafish 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 zebrafish chromosome allows that marker to be assigned to that chromosome. See also: Radiation Hybrid Mapping.

spindle

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

splice acceptor site

In the splicing of RNA, the site at the 3' end of an intron. See also splice donor site.

splice donor site

In the splicing of RNA, the site at the 5' end of an intron. See also splice acceptor site.

splice junction

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

splicing

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

spontaneous

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

SQL

Structured Query Language. A programming language for extracting information from relational databases. The query forms at ZFIN operate by generating instructions in SQL.

SSLP

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. SSLPs 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 zebrafish strains. SSLPs are also sometimes called microsatellite markers.

SSR

See SSLP.

stop codon

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

structural gene

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

structural protein

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

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.

substrate

A molecule acted upon by an enzyme.

symbol

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

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. See also conserved synteny

synonym

In ZFIN, a synonym is a gene symbol or name that has appeared in the scientific literature, is not pending approval, and has never been an approved symbol or name.

tab-delimited

A text file with data fields separated by "tab" characters. Such files can be converted to spreadsheet files, such as those used by Microsoft Excel.

targeted mutation

A type of mutation in which a chromosomal gene is altered by the substitution of a DNA construct assembled in vitro. 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.

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 the Figure at NHGRI.

template

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

termination codon

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

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 or heterozygous 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.
See also:

Texas red

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

thermostable

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

trait

A particular aspect of the phenotype that can be measured or observed directly, e.g. blood flow or body color.

transcript

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

transcription

The enzymatic synthesis of an RNA molecule directed by information in a DNA molecule. See the Figure at NHGRI. See also central dogma.

transgene

A gene in a living organism that is derived from another organism and introduced experimentally.

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. See also transversion.

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 the Figure at NHGRI. See also central dogma.

translocation

A type of mutation in which two nonhomologous chromosomes are each broken and then repaired in such a way that:

the resulting chromosomes each contain material from the other chromosome (a reciprocal translocation; see the Figure at NHGRI),
one of the chromosomes contains an insertion of material from the other chromosome, with the other chromosome containing a deficiency (an insertional translocation; see the Figure at NHGRI), or
the two chromosomes, each with breaks near the centromere, fuse to form a single chromosome with a single centromere (a Robertsonian translocation).

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.

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).

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. See also transition.

trisomy

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

tRNA

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

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.

unknown

In ZFIN, a map location of "unknown" means that the marker has not yet been assigned to a chromosome.

URL

Uniform Resource Locator. An Internet address giving the protocol to be used for obtaining resources on the Internet such as "ftp:" for an FTP site or "http:" for a World Wide Web page. It also includes the server name and sometimes the path to the resource. The URL for ZFIN is "http://zfin.org".

Vector

See cloning vector.

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.

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 electrophorectic transfer. Specific proteins are then detected on the membrane using antibody staining. See Southern blot and Northern blot.

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.

withdrawn

With respect to gene nomenclature, a withdrawn symbol or name was once the approved symbol or name for a marker; there is currently a different approved symbol or name for that marker.

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.

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.

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.

YAC

Yeast Artificial Chromosome. A type of cloning vector containing a yeast centromere and telomeres that allows large DNA segments to be cloned in yeast. A YAC can carry 200 - 1000 kb of foreign DNA.

ZFIN

The Zebrafish Information Network. The on-line zebrafish information network.

ZIRC

The Zebrafish International Resource Center. The resource that provides strains of wild-type and mutant zebrafish and research materials used for their study.

Z marker

One of a large series of SSLP markers in the zebrafish, developed at the Massachusetts General Hospital. These markers have been used to map many markers and to align the physical and linkage maps in zebrafish.