Glossary of genetics (0–L) Information

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https://en.wikipedia.org/wiki/Glossary_of_genetics_(0–L)

This glossary of genetics is a list of definitions of terms and concepts commonly used in the study of genetics and related disciplines in biology, including molecular biology, cell biology, and evolutionary biology. [1] It is split across two articles:

  • This page, Glossary of genetics (0–L), lists terms beginning with numbers and those beginning with the letters A through L.
  • Glossary of genetics (M−Z) lists terms beginning with the letters M through Z.


The glossary is intended as introductory material for novices; for more specific and technical detail, see the article corresponding to each term. For related terms, see Glossary of evolutionary biology and Glossary of chemistry.


0–9

3' untranslated region (3'-UTR)

Also three-prime untranslated region and trailer sequence.

3'-end

Also three-prime end.

One of two ends of a single linear strand of DNA or RNA, specifically the end at which the chain of nucleotides terminates at the third carbon atom in the furanose ring of deoxyribose or ribose (i.e. the terminus at which the 3' carbon is not attached to another nucleotide via a phosphodiester bond; in vivo, the 3' carbon is often still bonded to a hydroxyl group). By convention, sequences and structures positioned nearer to the 3'-end relative to others are referred to as downstream. Contrast 5'-end.
A ribose ring with the carbon atoms numbered 1' through 5' according to chemical convention. The 5' carbon is said to be upstream; the 3' carbon is said to be downstream. Bonds to a generic base and a phosphate group are also shown.
5' cap

Also five-prime cap.

A specially altered nucleotide attached to the 5'-end of some primary RNA transcripts as part of the set of post-transcriptional modifications which convert raw transcripts into mature RNA products. The precise structure of the 5' cap varies widely by organism; in eukaryotes, the most basic cap consists of a methylated guanine nucleoside bonded to the triphosphate group that terminates the 5'-end of an RNA sequence. Among other functions, capping helps to regulate the export of mature RNAs from the nucleus, prevent their degradation by exonucleases, and promote translation in the cytoplasm. Mature mRNAs can also be decapped.
5' untranslated region (5'-UTR)

Also five-prime untranslated region and leader sequence.

5'-end

Also five-prime end.

One of two ends of a single linear strand of DNA or RNA, specifically the end at which the chain of nucleotides terminates at the fifth carbon atom in the furanose ring of deoxyribose or ribose (i.e. the terminus at which the 5' carbon is not attached to another nucleotide via a phosphodiester bond; in vivo, the 5' carbon is often still bonded to a phosphate group). By convention, sequences and structures positioned nearer to the 5'-end relative to others are referred to as upstream. Contrast 3'-end.
5-bromodeoxyuridine
See bromodeoxyuridine.
5-methyluracil
See thymine.


A

A-DNA
One of three main biologically active structural conformations of the DNA double helix, along with B-DNA and Z-DNA. The A-form helix has a right-handed twist with 11 base pairs per full turn, only slightly more compact than B-DNA, but its bases are sharply tilted with respect to the helical axis. It is often favored in dehydrated conditions and within sequences of consecutive purine nucleotides (e.g. GAAGGGGA); it is also the primary conformation adopted by double-stranded RNA and RNA-DNA hybrids. [2]
acentric
(of a linear chromosome or chromosome fragment) Having no centromere. [3]
acrocentric
(of a linear chromosome or chromosome fragment) Having a centromere positioned very close to one end of the chromosome, as opposed to at the end or in the middle. [3]
activation
See upregulation.
activator
A type of transcription factor that increases the transcription of a gene or set of genes. Most activators work by binding to a specific sequence located within or near an enhancer or promoter and facilitating the binding of RNA polymerase and other transcription machinery in the same region. See also coactivator; contrast repressor.
adenine (A)
A purine nucleobase used as one of the four standard nucleobases in both DNA and RNA molecules. Adenine forms a base pair with thymine in DNA and with uracil in RNA.
adenosine (A)
One of the four standard nucleosides used in RNA molecules, consisting of an adenine base with its N9 nitrogen bonded to the C1 carbon of a ribose sugar. Adenine bonded to deoxyribose is known as deoxyadenosine, which is the version used in DNA.
affected relative pair
Any pair of organisms which are related genetically and both affected by the same trait. For example, two cousins who both have blue eyes are an affected relative pair since they are both affected by the allele that codes for blue eyes.
allele
One of multiple alternative versions of an individual gene, each of which is a viable DNA sequence occupying a given position, or locus, on a chromosome. For example, in humans, one allele of the eye-color gene produces blue eyes and another allele of the eye-color gene produces brown eyes.
allele frequency
The relative frequency with which a particular allele of a given gene (as opposed to other alleles of the same gene) occurs at a particular locus in the members of a population; more specifically, it is the proportion of all chromosomes within a population that carry a particular allele, expressed as a fraction or percentage. Allele frequency is distinct from genotype frequency, although they are related.
allosome

Also sex chromosome, heterochromosome, or idiochromosome.

Any chromosome that differs from an ordinary autosome in size, form, or behavior and which is responsible for determining the sex of an organism. In humans, the X chromosome and the Y chromosome are sex chromosomes.
alpha helix (α-helix)
A common structural motif in the secondary structures of proteins consisting of a right-handed helix conformation resulting from hydrogen bonding between amino acid residues which are not immediately adjacent to each other.
alternative splicing

Also differential splicing or simply splicing.

A regulated phenomenon of eukaryotic gene expression in which specific exons or parts of exons from the same primary transcript are variably included within or removed from the final, mature messenger RNA transcript. A class of post-transcriptional modification, alternative splicing allows a single gene to code for multiple protein isoforms and greatly increases the diversity of proteins that can be produced by an individual genome. See also RNA splicing.
amber
One of three stop codons used in the standard genetic code; in RNA, it is specified by the nucleotide triplet UAG. The other two stop codons are named ochre and opal.
amino acid
Any of a class of organic compounds whose basic structural formula includes a central carbon atom bonded to amine and carboxyl functional groups and to a variable side chain. Out of nearly 500 known amino acids, a set of 20 are coded for by the standard genetic code and incorporated into long polymeric chains as the building blocks of peptides and hence of polypeptides and proteins. The specific sequences of amino acids in the polypeptide chains that form a protein are ultimately responsible for determining the protein's structure and function.
Every amino acid has the same basic structural formula, a central "alpha" (α) carbon bonded to three major substituents: one amino group (blue), one carboxyl group (red), and one variable side chain (green). The side chain gives each particular amino acid its unique identity, and can range from a simple methyl group ( alanine) to more complex functional groups such as a double-ringed indole ( tryptophan). During translation, amino acids are joined into a linear chain by condensation reactions which create peptide bonds between the carboxyl group of one amino acid and the amino group of an adjacent amino acid. The first and last amino acids in the chain are said to be N-terminal and C-terminal, respectively, in reference to the unbonded amino group of the first amino acid and the unbonded carboxyl group of the last.
amino terminus
See N-terminus.
aminoacyl-tRNA (aa-tRNA)

Also aminoacylated tRNA.

aminoacyl-tRNA synthetase

Also tRNA-ligase.

Any of a set of enzymes which catalyze the transesterification reaction that results in the attachment of a specific cognate amino acid (or a precursor) to one of its cognate transfer RNA molecules, forming an aminoacyl-tRNA. Each of the 20 different amino acids used in the genetic code is recognized and attached by its own specific synthetase enzyme, and most synthetases are cognate to several different tRNAs according to their specific anticodons.
amplicon
Any DNA or RNA sequence or fragment that is the source and/or product of an amplification reaction. The term is most frequently used to describe the numerous copied fragments that are the products of the polymerase chain reaction or ligase chain reaction, though it may also refer to sequences that are amplified naturally within a genome, e.g. by gene duplication.
amplification
The replication of a biomolecule, in particular the production of one or more copies of a nucleic acid sequence, known as an amplicon, either naturally (e.g. by spontaneous duplications) or artificially (e.g. by PCR), and especially implying many repeated replication events resulting in thousands, millions, or billions of copies of the target sequence, which is then said to be amplified.
anaphase
The stage of mitosis and meiosis that occurs after metaphase and before telophase, when the replicated chromosomes are segregated and each of the sister chromatids are moved to opposite sides of the cell.
anaphase lag
The failure of one or more pairs of sister chromatids or homologous chromosomes to properly migrate to opposite sides of the cell during anaphase of mitosis or meiosis due to a defective spindle apparatus. Consequently, both daughter cells are aneuploid: one is missing one or more chromosomes (creating a monosomy) while the other has one or more extra copies of the same chromosomes (creating a polysomy).
aneuploidy
The condition of a cell or organism having an abnormal number of one or more particular chromosomes (but excluding abnormal numbers of complete sets of chromosomes, which instead is known as euploidy).
annealing
The hybridization of two single-stranded nucleic acid molecules containing complementary sequences, creating a double-stranded molecule with paired nucleobases. The term is used in particular to describe steps in certain laboratory techniques such as the polymerase chain reaction, where double-stranded DNA molecules are repeatedly denatured into single strands by heating and then exposed to cooler temperatures, causing the strands to reassociate with each other or with complementary primers. The exact temperature at which annealing occurs is strongly influenced by the length and specific sequence of the individual strands.
anticipation
A phenomenon by which the symptoms of a genetic disorder become apparent (and often more severe) at an earlier age in affected individuals with each generation that inherits the disorder.
anticodon
A series of three consecutive nucleotides within a transfer RNA which complement the three nucleotides of a codon within an mRNA transcript. During translation, each tRNA recruited to the ribosome contains a single anticodon triplet that pairs with one or more complementary codons from the mRNA sequence, allowing each codon to specify a particular amino acid to be added to the growing peptide chain. Anticodons containing inosine in the first position are capable of pairing with more than one codon due to a phenomenon known as wobble base pairing.
antioncogene
A gene which helps to regulate cell growth and suppress tumors when functioning correctly, such that its absence or malfunction can result in uncontrolled cell growth and possibly cancer. [4] Compare oncogene.
antiparallel
The orientation of two strands of a double-stranded nucleic acid (and more generally any pair of biopolymers) which are parallel to each other but with opposite directionality. For example, the two complementary strands of a DNA molecule run side-by-side but in opposite directions, with one strand oriented 5'-to- 3' and the other 3'-to-5'.
antisense
See template strand.
antisense RNA (asRNA)

Also antisense transcript and antisense oligonucleotide (ASO).

A single-stranded non-coding RNA molecule containing an antisense sequence that is complementary to a sense strand, such as a messenger RNA, with which it readily hybridizes, thereby inhibiting the sense strand's further activity (e.g. translation into protein). Many different classes of naturally occurring RNA such as siRNA function by this principle, making them potent gene silencers in various gene regulation mechanisms. Synthetic antisense RNA has also found widespread use in gene knockdown studies, and in practical applications such as antisense therapy.
artificial gene synthesis
A set of laboratory methods used to assemble a gene (or any other nucleic acid sequence) from free nucleotides de novo, i.e. without relying on an existing template strand, which makes it theoretically possible to construct completely synthetic molecules with no restrictions on size or sequence.
associative overdominance
The phenomenon by which the linkage of a neutral locus to a selectively maintained polymorphism causes the heterozygosity of the neutral locus to increase. [5]
asynapsis
The failure of homologous chromosomes to properly pair with each other during meiosis. [5] Contrast synapsis and desynapsis.
attached X

Also compound X.

A single monocentric chromosome containing two or more physically attached copies of the normal X chromosome as a result of either a natural internal duplication or any of a variety of genetic engineering methods. The resulting compound chromosome effectively carries two or more doses of all genes and sequences included on the X, yet functions in all other respects as a single chromosome, meaning that haploid 'XX' gametes (rather than the ordinary 'X' gametes) will be produced by meiosis and inherited by progeny. In mechanisms such as genic balance in which the sex of an organism is determined by the total dosage of X-linked genes, an abnormal 'XXY' zygote, fertilized by one XX gamete and one Y gamete, will develop into a female.
autosome
Any chromosome that is not an allosome and hence is not involved in the determination of the sex of an organism. Unlike the sex chromosomes, the autosomes in a diploid cell exist in pairs, with the members of each pair having the same structure, morphology, and genetic loci.
autozygote
A cell or organism that is homozygous for a locus at which the two homologous alleles are identical by descent, both having been derived from a single gene in a common ancestor. [5] Contrast allozygote.


B

B-DNA
The "standard" or classical structural conformation of the DNA double helix in vivo, thought to represent an average of the various distinct conformations assumed by very long DNA molecules under physiological conditions. [2] The B-form double helix has a right-handed twist with a diameter of 23.7 ångströms and a pitch of 35.7 ångströms or about 10.5 base pairs per full turn, such that each nucleotide pair is rotated 36° around the helical axis with respect to its neighboring pairs. See also A-DNA and Z-DNA.
The three principal biologically active conformations of DNA molecules: A-DNA, B-DNA, and Z-DNA (left to right), as viewed from the side and down the axis of the double helix.
back mutation
A mutation that reverses the effect of a previous mutation which had inactivated a gene, thus restoring wild-type function. [6] See also reverse mutation.
backcrossing

Also testcrossing.

The breeding of a hybrid organism with one of its parents or an individual genetically similar to one of its parents, often intentionally as a type of selective breeding, with the aim of producing offspring with a genetic identity which is closer to that of the parent. The reproductive event and the resulting progeny are both referred to as a backcross, often abbreviated in genetics shorthand with the symbol BC.
bacterial artificial chromosome (BAC)
base
An abbreviation of nitrogenous base and nucleobase.
base pair (bp)
A pair of two nucleobases on complementary DNA or RNA strands which are bonded to each other by hydrogen bonds. The ability of consecutive base pairs to stack one upon another contributes to the long-chain double helix structures observed in both double-stranded DNA and double-stranded RNA molecules.
baseline
A measure of the gene expression level of a gene or genes prior to a perturbation in an experiment, as in a negative control. Baseline expression may also refer to the expected or historical measure of expression for a gene.
bivalent
blunt end
bromodeoxyuridine (BUDR, BrdU)

Also 5-bromodeoxyuridine.


C

C-terminus

Also carboxyl terminus.

The end of a linear chain of amino acids (i.e. a peptide) that is terminated by the free carboxyl group (-COOH) of the last amino acid to be added to the chain during translation. This amino acid is said to be C-terminal. By convention, sequences, domains, active sites, or any other structure positioned nearer to the C-terminus of the polypeptide or its folded protein form relative to others are described as downstream. Contrast N-terminus.
C-value
The total amount of DNA contained within a haploid nucleus (e.g. a gamete) of a particular organism or species, expressed in number of base pairs or in units of mass (typically picograms); or, equivalently, one-half the amount in a diploid somatic cell. For simple diploid eukaryotes the term is often used interchangeably with genome size, but in certain cases, e.g. in hybrid polyploids descended from parents of different species, the C-value may actually represent two or more distinct genomes contained within the same nucleus. C-values apply only to genomic DNA, and notably exclude extranuclear DNA.
C-value enigma

Also C-value paradox.

A term used to describe a diverse variety of questions regarding the immense variation in nuclear C-value or genome size among eukaryotic species, in particular the observation that genome size does not correlate with the perceived complexity of organisms, nor necessarily with the number of genes they possess; for example, many single-celled protists have genomes containing thousands of times more DNA than the human genome. This was considered paradoxical until the discovery that eukaryotic genomes consist mostly of non-coding DNA, which lacks genes entirely. The focus of the enigma has since shifted to understanding why and how genomes came to be filled with so much non-coding DNA, and why some genomes have a higher gene content than others.
cadastral gene
A regulatory gene that restricts the expression of other genes to specific tissues or body parts in an organism, typically by producing gene products which variably inhibit or permit transcription of the other genes in different cell types. [5] The term is used most commonly in plant genetics.
canalisation
The ability of a population to consistently produce the same phenotype regardless of the variability of its environment or the genetic variation within its genome. The concept is most often used in developmental biology to interpret the observation that developmental pathways are frequently shaped by natural selection such that developing cell lineages are "guided" or "canalized" towards a single, definite fate, becoming progressively more resistant to any minor perturbations that may redirect development of the cells away from their initial course.
candidate gene
A gene whose location on a chromosome is associated with a particular phenotype (often a disease-related phenotype), and which is therefore suspected of causing or contributing to the phenotype. Candidate genes are often selected for study based on a priori knowledge or speculation about their functional relevance to the trait or disease being researched.
canonical sequence
See consensus sequence.
carboxyl terminus
See C-terminus.
carrier
An individual who has inherited a recessive allele for a genetic trait or mutation but in whom the trait is not usually expressed or observable in the phenotype. Carriers are usually heterozygous for the recessive allele and therefore still able to pass the allele onto their offspring, where the associated phenotype may reappear if the offspring inherits another copy of the allele. The term is commonly used in medical genetics in the context of a disease-causing recessive allele.
CCAAT box

Also CAAT box or CAT box.

A highly conserved regulatory DNA sequence located approximately 75 base pairs upstream (i.e. -75) of the site of the start of transcription for many eukaryotic genes. [3]
cDNA
See complementary DNA.
cell-free DNA (cfDNA)
Any DNA molecule that exists outside of a cell or nucleus, freely floating in an extracellular fluid such as blood plasma.
cellular reprogramming
The conversion of a cell from one tissue-specific cell type to another. This involves dedifferentiation to a pluripotent state; an example is the conversion of mouse somatic cells to an undifferentiated embryonic state, which relies on the transcription factors Oct4, Sox2, Myc, and Klf4. [7]
centimorgan (cM)

Also map unit (m.u.).

A unit for measuring genetic linkage defined as the distance between chromosomal loci for which the expected average number of intervening chromosomal crossovers in a single generation is 0.01. Though not an actual measure of physical distance, it is used to infer the actual distance between two loci based on the apparent likelihood of a crossover occurring between them.
central dogma of molecular biology
A generalized framework for understanding the flow of genetic information between macromolecules within biological systems. The central dogma outlines the fundamental principle that the sequence information encoded in the three major classes of biopolymerDNA, RNA, and protein—can only be transferred between these three classes in certain ways, and not in others: specifically, information transfer between the nucleic acids and from nucleic acid to protein is possible, but transfer from protein to protein, or from protein back to either type of nucleic acid, is impossible and does not occur naturally.
Possible types of information transfer according to the central dogma of molecular biology. Three general transfers, in red, occur routinely in all living cells: DNA-to-DNA ( DNA replication), DNA-to-RNA ( transcription), and RNA-to-protein ( translation). Three special transfers, in blue, are known to occur only in viruses or in the laboratory: RNA-to-RNA ( RNA replication), RNA-to-DNA ( reverse transcription), and DNA-to-protein (direct translation without an mRNA intermediate). An additional three transfers are believed not to be possible at all: protein-to-protein, protein-to-RNA, and protein-to-DNA—though it has been argued that there are exceptions by which all three can occur.
centriole
A cylindrical organelle composed of microtubules, present only in certain eukaryotes. A pair of centrioles migrate to and define the two opposite poles of a dividing cell where, as part of a centrosome, they initiate the growth of the spindle apparatus.
centromere
A specialized DNA sequence within a chromosome that links a pair of sister chromatids. The primary function of the centromere is to act as the site of assembly for kinetochores, protein complexes which direct the attachment of spindle fibers to the centromere and facilitate segregation of the chromatids during mitosis or meiosis.
centromeric index
The proportion of the total length of a chromosome encompassed by its short arm, typically expressed as a percentage; e.g. a chromosome with a centromeric index of 15 is acrocentric, with a short arm comprising only 15% of its overall length. [5]
cfDNA
See cell-free DNA.
Chargaff's rules
A set of axioms which state that, in the DNA of any chromosome, species, or organism, the total number of adenine (A) residues will be approximately equal to the total number of thymine (T) residues, and the number of guanine (G) residues will be equal to the number of cytosine (C) residues; accordingly, the total number of purines (A + G) will equal the total number of pyrimidines (T + C). These observations illustrate the highly specific nature of the complementary base-pairing that occurs in all duplex DNA molecules: even though non-standard pairings are technically possible, they are exceptionally rare because the standard ones are strongly favored in most conditions. Still, the 1:1 equivalence is seldom exact, since at any given time nucleobase ratios are inevitably distorted to some small degree by unrepaired mismatches, missing bases, and non-canonical bases. The presence of single-stranded DNA polymers also alters the proportions, as the sequence of an individual strand may contain any number of any of the bases.
charged tRNA
A transfer RNA to which an amino acid has been attached; i.e. an aminoacylated tRNA. Uncharged tRNAs lack amino acids. [5]
chDNA
See chloroplast DNA.
chiasma

Plural chiasmata.

A cross-shaped junction that forms the physical point of contact between two non-sister chromatids belonging to homologous chromosomes during synapsis. As well as ensuring proper segregation of the chromosomes, these junctions are also the breakpoints at which chromosomal crossover may occur during mitosis or meiosis, which results in the reciprocal exchange of DNA between the synapsed chromatids.
chimerism
The presence of two or more populations of cells with distinct genotypes in an individual organism, known as a chimera, which has developed from the fusion of cells originating from separate zygotes; each population of cells retains its own genome, such that the organism as a whole is a mixture of genetically non-identical tissues. Genetic chimerism may be inherited (e.g. by the fusion of multiple embryos during pregnancy) or acquired after birth (e.g. by allogeneic transplantation of cells, tissues, or organs from a genetically non-identical donor); in plants, it can result from grafting or errors in cell division. It is similar to but distinct from mosaicism.
chloroplast DNA (cpDNA, chDNA, ctDNA)
The set of DNA molecules contained within chloroplasts, a type of photosynthetic plastid organelle located within the cells of some eukaryotes such as plants and algae, representing a semi-autonomous genome separate from that within the cell's nucleus. Like other types of plastid DNA, cpDNA usually exists in the form of small circular plasmids.
chondriome
The complete set of mitochondria or of mitochondrial DNA within a cell, tissue, organism, or species.
chromatid
One copy of a newly copied chromosome, which is joined to the original chromosome by a centromere.
chromatin
A complex of DNA, RNA, and protein found in eukaryotic cells that is the primary substance comprising chromosomes. Chromatin functions as a means of packaging very long DNA molecules into highly organized and densely compacted shapes, which prevents the strands from becoming tangled, reinforces the DNA during cell division, helps to prevent DNA damage, and plays an important role in regulating gene expression and DNA replication.
chromatin immunoprecipitation (ChIP)
chromocenter
A central amorphous mass of polytene chromosomes found in the nuclei of cells of the salivary glands in Drosophila larvae and resulting from the fusion of heterochromatic regions surrounding the centromeres of the somatically paired chromosomes, with the distal euchromatic arms radiating outward. [5]
chromomere

Also idiomere.

A region of a chromosome that has been locally compacted or coiled into chromatin, conspicuous under a microscope as a "bead", node, or dark-staining band, especially when contrasted with nearby uncompacted strings of DNA.
chromosomal crossover

Also crossing over.

chromosomal duplication
The duplication of an entire chromosome, as opposed to a segment of a chromosome or an individual gene.
chromosome
A DNA molecule containing part or all of the genetic material of an organism. Chromosomes may be considered a sort of molecular "package" for carrying DNA within the nucleus of cells and, in most eukaryotes, are composed of long strands of DNA coiled with packaging proteins which bind to and condense the strands to prevent them from becoming an unmanageable tangle. Chromosomes are most easily distinguished and studied in their completely condensed forms, which only occur during cell division. Some simple organisms have only one chromosome made of circular DNA, while most eukaryotes have multiple chromosomes made of linear DNA.
chromosome condensation
The process by which eukaryotic chromosomes become shorter, thicker, denser, and more conspicuous under a microscope during prophase due to systemic coiling and supercoiling of chromatic strands of DNA in preparation for cell division.
chromosome segregation
The process by which sister chromatids or paired homologous chromosomes separate from each other and migrate to opposite sides of the dividing cell during mitosis or meiosis.
chromosome walking
See primer walking.
circulating tumor DNA (ctDNA)
Any extracellular DNA fragments derived from tumor cells which are circulating freely in the bloodstream.
cis
On the same side; adjacent to; acting from the same molecule. Contrast trans.
cis-acting
Affecting a gene or sequence on the same nucleic acid molecule. A locus or sequence within a particular DNA molecule such as a chromosome is said to be cis-acting if it influences or acts upon other sequences located within short distances (i.e. physically nearby, usually but not necessarily downstream) on the same molecule or chromosome; or, in the broadest sense, if it influences or acts upon other sequences located anywhere (not necessarily within a short distance) on the same chromosome of a homologous pair. Cis-acting factors are often involved in the regulation of gene expression by acting to inhibit or to facilitate transcription. Contrast trans-acting.
cis-dominant mutation
A mutation occurring within a cis-regulatory element (such as an operator) which alters the functioning of a nearby gene or genes on the same chromosome. Cis-dominant mutations affect the expression of genes because they occur at sites that control transcription rather than within the genes themselves.
cis-regulatory element (CRE)

Also cis-regulatory module (CRM).

Any sequence or region of non-coding DNA which regulates the transcription of nearby genes (e.g. a promoter, operator, silencer, or enhancer), typically by serving as a binding site for one or more transcription factors. Contrast trans-regulatory.
cisgenesis
cistron
classical genetics
The branch of genetics based solely on observation of the visible results of reproductive acts, as opposed to that made possible by the modern techniques and methodologies of molecular biology. Contrast molecular genetics.
cloning
The process of producing, either naturally or artificially, individual organisms or cells which are genetically identical to each other. Clones are the result of all forms of asexual reproduction, and cells that undergo mitosis produce daughter cells that are clones of the parent cell and of each other. Cloning may also refer to biotechnology methods which artificially create copies of organisms or cells, or, in molecular cloning, copies of DNA fragments or other molecules.
closed chromatin
See heterochromatin.
coactivator
A type of coregulator that increases the expression of one or more genes by binding to an activator.
coding strand

Also sense strand, positive (+) sense strand, and nontemplate strand.

The strand of a double-stranded DNA molecule whose nucleotide sequence corresponds directly to that of the RNA transcript produced during transcription (except that thymine bases are substituted with uracil bases in the RNA molecule). Though it is not itself transcribed, the coding strand is by convention the strand used when displaying a DNA sequence because of the direct analogy between its sequence and the codons of the RNA product. Contrast template strand; see also sense.
codominance
codon
A series of three consecutive nucleotides in a coding region of a nucleic acid sequence. Each of these triplets codes for a particular amino acid or stop signal during protein synthesis. DNA and RNA molecules are each written in a language using four "letters" (four different nucleobases), but the language used to construct proteins includes 20 "letters" (20 different amino acids). Codons provide the key that allows these two languages to be translated into each other. In general, each codon corresponds to a single amino acid (or stop signal). The full set of codons is called the genetic code.
codon usage bias
The preferential use of a particular codon to code for a particular amino acid rather than alternative codons that are synonymous for the same amino acid, as evidenced by differences between organisms in the frequencies of the synonymous codons occurring in their coding DNA. Because the genetic code is degenerate, most amino acids can be specified by multiple codons. Nevertheless, certain codons tend to be overrepresented (and others underrepresented) in different species.
cofactor
Any non-protein organic compound that is bound to an enzyme. Cofactors are required for the initiation of catalysis.
comparative genomic hybridization (CGH)
complementarity
A property of nucleic acid biopolymers whereby two polymeric chains or " strands" aligned antiparallel to each other will tend to form base pairs consisting of hydrogen bonds between the individual nucleobases comprising each chain, with each type of nucleobase pairing almost exclusively with one other type of nucleobase; e.g. in double-stranded DNA molecules, A pairs only with T and C pairs only with G. Strands that are paired in such a way, and the bases themselves, are said to be complementary. The degree of complementarity between two strands strongly influences the stability of the duplex molecule; certain sequences may also be internally complementary, which can result in a single strand binding to itself. Complementarity is fundamental to the mechanisms governing DNA replication, transcription, and DNA repair.
complementary DNA (cDNA)

Also copy DNA.

DNA that is synthesized from a single-stranded RNA template (typically mRNA or miRNA) in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is produced both naturally by retroviruses and artificially in certain laboratory techniques, particularly molecular cloning. In bioinformatics, the term may also be used to refer to the sequence of an mRNA transcript expressed as its DNA coding strand counterpart (i.e. with thymine replacing uracil).
complementation
complex trait
See quantitative trait.
compound X
See attached X.
conditional expression
The controlled, inducible expression of a transgene, either in vitro or in vivo.
congression
The movement of chromosomes to the spindle equator during the prometaphase and metaphase stages of mitosis. [5]
consanguineous
(of two or more individuals) Closely genetically related; sharing a recent common ancestor (usually no more than three or four generations distant). The effect of consanguineous mating, also known as inbreeding, is to increase the probability that the progeny will be homozygous at any given pair of genetic loci. [8]
consensus sequence

Also canonical sequence.

A calculated order of the most frequent residues (of either nucleotides or amino acids) found at each position in a common sequence alignment and obtained by comparing multiple closely related sequence alignments.
conservation genetics
An interdisciplinary branch of population genetics which applies genetic methods and concepts in an effort to understand the dynamics of genes in populations, with a principal aim of avoiding extinctions and preserving and restoring biodiversity.
conservative replication
conserved sequence
A nucleic acid or protein sequence that is highly similar or identical across many species or within a genome, indicating that it has remained relatively unchanged through a long period of evolutionary time.
conspecific
Belonging to the same species.
constitutive expression
1.  The continuous transcription of a gene, as opposed to facultative expression, in which a gene is only transcribed as needed. A gene that is transcribed continuously is called a constitutive gene.
2.  A gene whose expression depends only on the efficiency of its promoter in binding RNA polymerase, [5] and not on any transcription factors or other regulatory elements which might promote or inhibit its transcription.
contig
A continuous sequence of genomic DNA generated by assembling cloned fragments by means of their overlapping sequences. [6]
copy DNA (cDNA)
See complementary DNA.
copy error
A mutation resulting from a mistake made during DNA replication. [5]
copy-number variation (CNV)
A phenomenon in which sections of a genome are repeated and the number of repeats varies between individuals in the population, usually as a result of duplication or deletion events that affect entire genes or sections of chromosomes. Copy-number variations play an important role in generating genetic variation within a population.
coregulator
A protein that works together with one or more transcription factors to regulate gene expression.
corepressor
A type of coregulator that reduces (represses) the expression of one or more genes by binding to and activating a repressor.
cosmid
cpDNA
See chloroplast DNA.
CpG site

Also CG site and C-G site.

A sequence of DNA in which a cytosine nucleotide is immediately followed by a guanine nucleotide on the same strand in the 5'-to-3' direction; the "p" in CpG refers simply to the intervening phosphate group linking the two consecutive nucleotides.
CpG island

Also CG island and C-G island.

A region of a genome in which CpG sites occur repetitively or with high frequency.
crossbreeding

Also crossing and outbreeding.

The breeding of purebred parents belonging to two different breeds, varieties, or populations, often intentionally as a type of selective breeding, with the aim of producing offspring which share traits of both parent lineages or which show heterosis. In animal breeding, the progeny of a cross between breeds of the same species is called a crossbreed, whereas the progeny of a cross between different species is called a hybrid.
crossing over
See chromosomal crossover.
An abnormal chemical bond between two or more nucleobases on opposite strands of a double-stranded DNA molecule (interstrand), or between bases on the same strand (intrastrand), specifically via the formation of covalent bonds that are stronger than the hydrogen bonds of base pairing. Crosslinks can be generated by a variety of exogenous and endogenous agents, and tend to interfere with normal cellular processes such as DNA replication and transcription. They are common targets of DNA repair pathways.
CRISPR gene editing
ctDNA
1.  An abbreviation of circulating tumor DNA.
2.  An abbreviation of chloroplast DNA.
cryptic unstable transcript (CUT)
cytidine (C, Cyd)
One of the four standard nucleosides used in RNA molecules, consisting of a cytosine base with its N9 nitrogen bonded to the C1 carbon of a ribose sugar. Cytosine bonded to deoxyribose is known as deoxycytidine, which is the version used in DNA.
cytogenetics
The branch of genetics that studies how chromosomes influence and relate to cell behavior and function, particularly during mitosis and meiosis.
cytokinesis
The final stage of cell division in both mitosis and meiosis, during which the closing of the contractile ring causes the cytoplasm of the parent cell to be divided approximately evenly between the two daughter cells. Contrast karyokinesis.
cytosine (C)
A pyrimidine nucleobase used as one of the four standard nucleobases in both DNA and RNA molecules. Cytosine forms a base pair with guanine.


D

de novo mutation
A spontaneous mutation in the genome of an individual organism that is new to that organism's lineage, having first appeared in a germ cell of one of the organism's parents or in the fertilized egg that develops into the organism; i.e. a mutation that was not present in either parent's genome. [5]
degeneracy
The redundancy of the genetic code, exhibited as the multiplicity of different codons that specify the same amino acid. For example, in the standard genetic code, the amino acid serine is specified by six unique codons (UCA, UCG, UCC, UCU, AGU, and AGC). Codon degeneracy accounts for the existence of synonymous mutations.
deletion

Denoted in shorthand with the symbol Δ.

A type of mutation in which one or more nucleotides are removed from a nucleic acid sequence.
denaturation
The process by which nucleic acids or proteins lose their quaternary, tertiary, and/or secondary structures, either reversibly or irreversibly, through the application of some external chemical or mechanical stress, e.g. by heating, agitation, or exposure to a strong acid or base, all of which can disrupt intermolecular forces such as hydrogen bonding and thereby change or destroy chemical activity. Denatured proteins may be both a cause and a consequence of cell death. Denaturation may also be a normal process; the denaturation of double-stranded DNA molecules, for example, which breaks the hydrogen bonds between base pairs and causes the separation of the duplex molecule into two single strands, is a necessary step in DNA replication and transcription and hence is routinely performed by enzymes such as helicases. The same mechanism is also fundamental to laboratory methods such as PCR.
deoxyadenosine

Abbreviated in shorthand with dA.

One of the four standard deoxyribonucleosides used in DNA molecules, consisting of an adenine base with its N9 nitrogen bonded to the C1 carbon of a deoxyribose sugar. Adenine bonded to ribose forms an alternate compound known simply as adenosine, which is used in RNA.
deoxycytidine

Abbreviated in shorthand with dC.

One of the four standard deoxyribonucleosides used in DNA molecules, consisting of a cytosine base with its N9 nitrogen bonded to the C1 carbon of a deoxyribose sugar. Cytosine bonded to ribose forms an alternate compound known simply as cytidine, which is used in RNA.
deoxyguanosine

Abbreviated in shorthand with dG.

One of the four standard deoxyribonucleosides used in DNA molecules, consisting of a guanine base with its N9 nitrogen bonded to the C1 carbon of a deoxyribose sugar. Guanine bonded to ribose forms an alternate compound known simply as guanosine, which is used in RNA.
deoxythymidine
See thymidine.
deoxyribonuclease (DNase)
Any of a class of nuclease enzymes which catalyze the hydrolytic cleavage of phosphodiester bonds in DNA molecules, thereby severing strands of deoxyribonucleotides and causing the degradation of DNA polymers into smaller components. Compare ribonuclease.
deoxyribonucleic acid (DNA)
A polymeric nucleic acid molecule composed of a series of deoxyribonucleotides, each of which incorporates one of four canonical nucleobases: adenine (A), guanine (G), cytosine (C), and thymine (T). DNA is most often found in double-stranded form, which consists of two complementary antiparallel nucleotide chains in which each of the nucleobases on each individual strand is paired via hydrogen bonding with one on the opposite strand; this structure commonly occurs in the shape of a double helix. DNA can also exist in single-stranded form.
deoxyribonucleotide
A nucleotide containing deoxyribose as its pentose sugar component, and the monomeric subunit of deoxyribonucleic acid (DNA) molecules. Deoxyribonucleotides canonically incorporate any of four nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Compare ribonucleotide.
deoxyribose

Also 2-deoxyribose.

A monosaccharide sugar derived from ribose by the loss of a single oxygen atom. D-deoxyribose, in its pentose ring form, is one of three primary functional groups of deoxyribonucleotides and hence of deoxyribonucleic acid (DNA) molecules.
Deoxyribose differs from ribose only at the 2' carbon, where ribose has an oxygen atom that deoxyribose lacks (hence its name).
desynapsis
The failure of homologous chromosomes that have synapsed normally during pachynema to remain paired during diplonema. Desynapsis is usually caused by the improper formation of chiasmata. [5] Contrast asynapsis.
diakinesis
In meiosis, the fifth and final substage of prophase I, following diplonema and preceding metaphase I. During diakinesis, the chromosomes are further condensed, the two centrosomes reach opposite poles of the cell, and the spindle apparatus begins to extend from the poles to the equator. [5]
dicentric
(of a linear chromosome or chromosome fragment) Having two centromeres instead of the normal one. [3]
dinucleotide
Any two nucleotides which are immediately adjacent to each other on the same strand of a nucleic acid molecule.
diploid

Denoted in shorthand with the somatic number 2n.

(of a cell or organism) Having two homologous copies of each chromosome. Contrast haploid and polyploid.
diplonema

Also diplotene stage.

In meiosis, the fourth of the five substages of prophase I, following pachynema and preceding diakinesis. During diplonema, the synaptonemal complex disassembles and the paired homologous chromosomes begin to separate from one another, though they remain tightly bound at the chiasmata where crossover has occurred.
directionality
The end-to-end chemical orientation of a single linear strand or sequence of a nucleic acid polymer or a polypeptide. The nomenclature used to indicate nucleic acid directionality is based on the chemical convention of identifying individual carbon atoms in the ribose or deoxyribose sugars of nucleotides, specifically the 5' carbon and 3' carbon of the pentose ring. The sequence of nucleotides in a polymeric chain may be read or interpreted in the 5'-to-3' direction – i.e. starting from the terminal nucleotide in which the 5' carbon is not connected to another nucleotide, and proceeding to the other terminal nucleotide, in which the 3' carbon is not connected to another nucleotide – or in the opposite 3'-to-5' direction. Most types of nucleic acid synthesis, including DNA replication and transcription, work exclusively in the 5'-to-3' direction, because the enzymes involved can only catalyze the addition of free nucleotides to the 3'-end of the previous nucleotide in the chain, and not to the 5'-end. Because of this, the convention when writing any nucleic acid sequence is to present it in the 5'-to-3' direction from left to right. In double-stranded nucleic acids, the two paired strands must be oriented in opposite directions in order to base-pair with each other. Similarly, polypeptide directionality is based on the labeling of the functional groups in amino acids, specifically the amino group, which forms the N-terminus, and the carboxyl group, which forms the C-terminus; amino acid sequences are assembled in the N-to-C direction during translation, and are almost always read or interpreted in the same direction.
direct repeat
Any two or more repetitions of a specific sequence of nucleotides occurring in the same orientation (i.e. in precisely the same order and not inverted) and on the same strand, either separated by intervening nucleotides or not. An example is the sequence TACCGnnnnnnTACCG, in which TACCG occurs twice, though separated by six nucleotides that are not part of the repeated sequence. A direct repeat in which the repeats are immediately adjacent to each other is known as a tandem repeat.
dispersive replication
distance measure
Any quantity used to measure the dissimilarity between the gene expression levels of different genes. [9]
DNA
See deoxyribonucleic acid.
DNA barcoding
A method of taxonomic identification in which short DNA sequences from one or more specific genes are isolated from unidentified samples and then aligned with sequences from a reference library in order to uniquely identify the species or other taxon from which the samples originated. The sequences used in the comparison are chosen carefully from genes that are both widely conserved and that show greater variation between species than within species, e.g. the cytochrome c oxidase gene for eukaryotes or certain ribosomal RNA genes for prokaryotes. These genes are present in nearly all living organisms but tend to evolve different mutations in different species, such that a unique sequence variant can be linked to one particular species, effectively creating a unique identifier akin to a retail barcode. DNA barcoding allows unknown specimens to be identified from otherwise indistinct tissues or body parts, where identification by morphology would be difficult or impossible, and the library of organismal barcodes is now comprehensive enough that even organisms previously unknown to science can often be phylogenetically classified with confidence. The simultaneous identification of multiple different species from a mixed sample is known as metabarcoding.
DNA condensation
The process of compacting very long DNA molecules into densely packed, orderly configurations such as chromosomes, either in vivo or in vitro.
DNA fingerprinting
DNA microarray
A high-throughput technology used to measure expression levels of mRNA transcripts or to detect certain changes in nucleotide sequence. It consists of an array of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles of a specific DNA sequence. This can be a short section of a gene or any other DNA element, and is used as a probe to hybridize a cDNA, cRNA or genomic DNA sample (called a target) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by fluorescence-based detection of fluorophore-labeled targets.
DNA polymerase
Any of a class of enzymes that synthesizes DNA molecules from individual deoxyribonucleotides. DNA polymerases are essential for DNA replication and usually work in pairs to create identical copies of the two strands of an original double-stranded molecule. They build long chains of DNA by adding nucleotides one at a time to the 3'-end of a DNA strand, usually relying on the template provided by the complementary strand to copy the nucleotide sequence faithfully.
DNA repair
The set of processes by which a cell identifies and corrects structural damage or mutations in the DNA molecules that encode its genome. The ability of a cell to repair its DNA is vital to the integrity of the genome and the normal functionality of the organism.
DNA replication
The process by which a DNA molecule copies itself, producing two identical copies of one original DNA molecule.
A diagram of the many components of DNA replication
DNA sequencing
The process of determining, by any of a variety of different methods and technologies, the order of the bases in the long chain of nucleotides that constitutes a sequence of DNA.
DNA turnover
Any mechanism by which DNA sequences are exchanged non-reciprocally (e.g. via gene conversion, transposition, or unequal crossing-over) that causes continual fluctuations in the copy number of DNA motifs during an organism's lifetime. Such mechanisms are often major drivers of speciation between populations. [8]
DNA-binding domain (DBD)
DNA-binding protein (DBP)
Any polypeptide or protein containing one or more domains capable of interacting chemically with one or more parts of a DNA molecule, and consequently having a specific or general affinity for single- and/or double-stranded DNA. DNA-binding activity often depends on the presence and physical accessibility of a specific nucleobase sequence, and mostly occurs at the major groove, since it exposes more of the functional groups that uniquely identify the bases. Binding is also influenced by the spatial conformation of the DNA chain and the occupancy of other proteins near the binding site; many proteins cannot bind to DNA without first undergoing structural changes induced by interactions with other molecules.
DNase
See deoxyribonuclease.
dominance
A relationship between the alleles of a gene in which one allele produces an effect on phenotype that overpowers or "masks" the contribution of another allele at the same locus; the first allele and its associated phenotypic trait are said to be dominant, and the second allele and its associated trait are said to be recessive. Often, the dominant allele codes for a functional protein while its recessive counterpart does not. Dominance is not an inherent property of any allele or phenotype, but simply describes its relationship to one or more other alleles or phenotypes; it is possible for one allele to be simultaneously dominant over a second allele, recessive to a third, and codominant to a fourth. In genetics shorthand, dominant alleles are often represented by a single uppercase letter (e.g. "A", in contrast to the recessive "a").
dosage compensation
Any mechanism by which organisms neutralize the large difference in gene dosage caused by the presence of differing numbers of sex chromosomes in the different sexes, thereby equalizing the expression of sex-linked genes so that the members of each sex receive the same or similar amounts of the products of such genes. An example is X-inactivation in female mammals.
double helix
The shape most commonly assumed by double-stranded nucleic acid molecules, resembling a ladder that has been twisted upon its long axis, with the rungs of the ladder consisting of paired nucleobases. This secondary structure is the most energetically stable conformation of the double-stranded forms of both DNA and RNA under most naturally occurring conditions, arising as a consequence of the primary structure of the phosphodiester backbone and the stacking of the nucleotides bonded to it. In B-DNA, the most common DNA variant found in nature, the double helix has a right-handed twist with about 10 base pairs per full turn, and the molecular geometry results in an alternating pattern of "grooves" of differing widths (a major groove and a minor groove) between the parallel backbones.
Double-stranded DNA most commonly exists in the shape of a double helix.
double-strand break (DSB)
The loss of continuity of the phosphate-sugar backbone in both strands of a double-stranded DNA molecule, in particular when the two breaks occur at sites that are directly across from or very close to each other on the complementary strands. [8] Contrast single-strand break.
double-stranded
Composed of two antiparallel, complementary nucleic acid molecules or strands (either DNA–DNA, RNA–RNA, or a DNA–RNA hybrid) which are held together by hydrogen bonds between the complementary nucleobases of each strand, known as base pairing. Compare single-stranded.
double-stranded DNA (dsDNA)
Any DNA molecule that is composed of two antiparallel, complementary deoxyribonucleotide polymers, known as strands, which are bonded together by hydrogen bonds between the complementary nucleobases. Though it is possible for DNA to exist as a single strand, it is generally more stable and more common in double-stranded form. In most cases, the complementary base pairing causes the twin strands to coil around each other in the shape of a double helix.
double-stranded RNA (dsRNA)
Any RNA molecule that is composed of two antiparallel, complementary ribonucleotide polymers, known as strands, which are bonded together by hydrogen bonds between the complementary nucleobases. Though RNA usually occurs in single-stranded form, it is also capable of forming duplexes in the same way as DNA; an example is an mRNA transcript pairing with an antisense version of the same transcript, which effectively silences the gene from which the mRNA was transcribed by preventing translation. As in dsDNA, the base pairing in dsRNA usually causes the twin strands to coil around each other in the shape of a double helix.
downregulation

Also repression or suppression.

Any process, natural or artificial, which decreases the level of gene expression of a certain gene. A gene which is observed to be expressed at relatively low levels (such as by detecting lower levels of its mRNA transcripts) in one sample compared to another sample is said to be downregulated. Contrast upregulation.
downstream
Towards or closer to the 3'-end of a chain of nucleotides, or to the C-terminus of a peptide chain. Contrast upstream.
dsDNA
See double-stranded DNA.
dsRNA
See double-stranded RNA.
duplex
See double-stranded.
duplication
The production of a second copy of part or all of a nucleotide sequence or amino acid sequence, either naturally or artificially, and the retention of both copies; especially when both the copy and the original sequence are retained in situ within the same molecule, often but not necessarily adjacent to each other. See also gene duplication, chromosomal duplication, and repeat.
dyad
See sister chromatids.


E

ecological genetics
The study of genetics as it pertains to the ecology and fitness of natural populations of living organisms.
elongation

Also extension.

emergenesis
The quality of genetic traits that results from a specific configuration of interacting genes, rather than simply their combination.
endonuclease
Any enzyme whose activity is to cleave phosphodiester bonds within a chain of nucleotides, including those that cleave relatively nonspecifically (without regard to sequence) and those that cleave only at very specific sequences (so-called restriction endonucleases). When recognition of a specific sequence is required, endonucleases make their cuts in the middle of the sequence. Contrast exonuclease.
enhancer
A region of DNA near a gene that can be bound by an activator to increase gene expression or by a repressor to decrease expression.
enhancer RNA (eRNA)
A subclass of long non-coding RNAs transcribed from regions of DNA containing enhancer sequences. The expression of a given eRNA generally correlates with the activity of the corresponding enhancer in enhancing transcription of its target genes, suggesting that eRNAs play an active role in gene regulation in cis or in trans.
epigenetics
epigenome
episome
1.  Another name for a plasmid, especially one that is capable of integrating into a chromosome.
2.  In eukaryotes, any non-integrated extrachromosomal circular DNA molecule that is stably maintained and replicated in the nucleus simultaneously with the rest of the host cell. Such molecules may include viral genomes, bacterial plasmids, and aberrant chromosomal fragments.
epistasis
The collective action of multiple genes interacting during gene expression. A form of gene action, epistasis can be either additive or multiplicative in its effects on specific phenotypic traits.
ergosome
See polysome.
euchromatin

Also open chromatin.

A relatively open, lightly compacted form of chromatin in which DNA is only sporadically bound in nucleosomes and thus broadly accessible to binding and manipulation by proteins and other molecules. Euchromatic regions of a genome are often enriched in genes and actively undergoing transcription, in contrast to heterochromatin, which is relatively gene-poor, nucleosome-rich, and less accessible to transcription machinery.
euploidy
The condition of a cell or organism having an abnormal number of complete sets of chromosomes, possibly excluding the sex chromosomes. Euploidy differs from aneuploidy, in which a cell or organism has an abnormal number of one or more specific individual chromosomes.
evolution
The change in the heritable characteristics of biological populations over successive generations. In the most traditional sense, it occurs by changes in the frequencies of alleles in a population's gene pool.
exome
The entire set of exons within a particular genome, including untranslated regions of mature mRNAs as well as coding regions.
exon
Any part of a gene that encodes a part of the final mature messenger RNA produced by that gene after introns have been removed by alternative splicing. The term refers to both the sequence as it exists within a DNA molecule and to the corresponding sequence in RNA transcripts.
exon skipping
exonuclease
Any enzyme whose activity is to cleave phosphodiester bonds within a chain of nucleotides, including those that cleave only upon recognition of a specific sequence (so-called restriction exonucleases). Exonucleases make their cuts at either the 3' or 5'-end of the sequence (rather than in the middle, as with endonucleases).
exosome complex
An intracellular multi-protein complex which serves the function of degrading various types of RNA molecules.
expression vector

Also expression construct.

A type of vector, usually a plasmid or viral vector, designed specifically for the expression of a transgene insert in a target cell, rather than for some other purpose such as cloning.
Plasmid map of a 3,756- bp expression vector used in the expression of a transgene that makes green fluorescent protein (GFP). The vector also includes a gene for the lac repressor (lacI) and a gene conferring resistance to the antibiotic kanamycin (KanR), as well as various promoters for driving the expression of these genes.
expressivity
For a given genotype associated with a variable non-binary phenotype, the proportion of individuals with that genotype who show or express the phenotype to a specified extent, usually given as a percentage. Because of the many complex interactions that govern gene expression, the same allele may produce a wide variety of possible phenotypes of differing qualities or degrees in different individuals; in such cases, both the phenotype and genotype may be said to show variable expressivity. Expressivity attempts to quantify the range of possible levels of phenotypic variation in a population of individuals expressing the phenotype of interest. Compare penetrance.
extein
Any part of an amino acid sequence which is retained within a precursor polypeptide, i.e. not excised by post-translational protein splicing, and is therefore present in the mature protein, analogous to the exons of RNA transcripts. Contrast intein.
extrachromosomal DNA

Also extranuclear DNA and cytoplasmic DNA.

Any DNA that is not found in chromosomes or in the nucleus of a cell and hence is not genomic DNA. This may include the DNA contained in plasmids or organelles such as mitochondria or chloroplasts, or, in the broadest sense, DNA introduced by viral infection. Extrachromosomal DNA usually shows significant structural differences from nuclear DNA in the same organism.


F

facultative expression
The transcription of a gene only as needed, as opposed to constitutive expression, in which a gene is transcribed continuously. A gene that is transcribed as needed is called a facultative gene.
fluorescence in situ hybridization (FISH)
five-prime cap
See 5' cap.
five-prime end
See 5'-end.
five-prime untranslated region
See 5' untranslated region.
fixation
The process by which a single allele for a particular gene with multiple different alleles increases in frequency in a given population such that it becomes permanently established at 100% frequency – that is, the only allele at that locus within the population's gene pool. In the absence of mutation and heterozygote advantage, any given allele is eventually destined to become either permanently fixed over all other variants or completely lost from the population, though how long this takes depends on selection pressures and chance fluctuations in allele frequencies.
forward genetics
forward mutation
frameshift mutation
A type of mutation in a nucleic acid sequence caused by the insertion or deletion of a number of nucleotides that is not divisible by three. Because of the triplet nature by which nucleotides code for amino acids, a mutation of this sort causes a shift in the reading frame of the nucleotide sequence, resulting in the sequence of codons downstream of the mutation site being completely different from the original.
Functional Genomics Data (FGED) Society

Formerly known by the abbreviation MGED.

An organization that works with others "to develop standards for biological research data quality, annotation and exchange" as well as software tools that facilitate their use. [10]


G

G banding

Also Giemsa banding or G-banding.

A technique used in cytogenetics to produce a visible karyotype by staining the condensed chromosomes with Giemsa stain. The staining produces consistent and identifiable patterns of dark and light "bands" in regions of chromatin, which allows specific chromosomes to be easily distinguished.
gamete
A haploid cell that is the meiotic product of a progenitor germ cell and the final product of the germ line in sexually reproducing multicellular organisms. Gametes are the means by which an organism passes its genetic information to its offspring; during fertilization, two gametes (one from each parent) are fused into a single diploid zygote.
gDNA
See genomic DNA.
gene
Any segment or set of segments of a nucleic acid molecule that contains the information necessary to produce a functional RNA transcript in a controlled manner. In living organisms, genes are often considered the fundamental units of heredity and are typically encoded in DNA. A particular gene can have multiple different versions, or alleles, and a single gene can result in a gene product that influences many different phenotypes.
gene dosage
The number of copies of a particular gene present in a genome. Gene dosage directly influences the amount of gene product a cell is able to express, though a variety of controls have evolved which tightly regulate gene expression. Changes in gene dosage caused by mutations include copy-number variations.
gene drive
gene duplication

Also gene amplification.

A type of mutation defined as any duplication of a region of DNA that contains a gene. Compare chromosomal duplication.
gene expression
The set of processes by which the information encoded in a gene is used in the synthesis of a gene product, such as a protein or non-coding RNA, or otherwise made available to influence one or more phenotypes. Canonically, the first step is transcription, which produces a messenger RNA molecule complementary to the DNA molecule in which the gene is encoded; for protein-coding genes, the second step is translation, in which the messenger RNA is read by the ribosome to produce a protein. The information contained within a DNA sequence need not necessarily be transcribed and translated to exert an influence on molecular events, however; broader definitions encompass a huge variety of other ways in which genetic information can be expressed.
Gene Expression Omnibus (GEO)
A database of high-throughput functional genomics and gene expression data derived from experimental chips and next-generation sequencing and managed by the National Center for Biotechnology Information. [11] [12]
gene fusion
The union, either by natural mutation or by recombinant laboratory techniques, of two or more previously independent genes that code for different gene products such that they become subject to control by the same regulatory systems. The resulting hybrid sequence is known as a fusion gene. [5]
gene mapping
Any of a variety of methods used to precisely identify the location of a particular gene within a DNA molecule (such as a chromosome) and/or the physical or linkage distances between it and other genes.
gene of interest (GOI)
A gene being studied in a scientific experiment, especially one that is the focus of a genetic engineering technique such as cloning.
gene pool
The sum of all of the various alleles shared by the members of a single population.
gene product
Any of the biochemical material resulting from the expression of a gene, most commonly interpreted as the functional mRNA transcript produced by transcription of the gene or the fully constructed protein produced by translation of the transcript, though non-coding RNA molecules such as transfer RNAs may also be considered gene products. A measurement of the quantity of a given gene product that is detectable in a cell or tissue is sometimes used to infer how active the corresponding gene is.
gene regulation
The broad range of mechanisms used by cells to control the activity of their genes, especially to allow, prohibit, increase, or decrease the production or expression of specific gene products, such as RNA or proteins. Gene regulation increases an organism's versatility and adaptability by allowing its cells to express different gene products when required by changes in its environment. In multicellular organisms, the regulation of gene expression also drives cellular differentiation and morphogenesis in the embryo, enabling the creation of a diverse array of cell types from the same genome.
gene silencing
Any mechanism of gene regulation which drastically reduces or completely prevents the expression of a particular gene. Gene silencing may occur naturally during either transcription or translation. Laboratory techniques often exploit natural silencing mechanisms to achieve gene knockdown.
gene therapy
The insertion of a functional or wild-type gene or part of a gene into an organism (especially a patient) with the intention of correcting a genetic defect, either by direct substitution of the defective gene or by supplementation with a second, functional version. [8]
gene trapping
A high-throughput technology used to simultaneously inactivate, identify, and report the expression of a target gene in a mammalian genome by introducing an insertional mutation consisting of a promoterless reporter gene and/or a selectable genetic marker flanked by an upstream splice site and a downstream polyadenylated termination sequence.
generation
1.  In any given organism, a single reproductive cycle, or the phase between two consecutive reproductive events, i.e. between an individual organism's reproduction and that of the progeny of that reproduction; or the actual or average length of time required to complete a single reproductive cycle, either for a particular lineage or for a population or species as a whole.
2.  In a given population, those individuals (often but not necessarily living contemporaneously) who are equally removed from a given common ancestor by virtue of the same number of reproductive events having occurred between them and the ancestor. [8]
genetic association
The co-occurrence within a population of one or more alleles or genotypes with a particular phenotypic trait more often than might be expected by chance alone; such statistical correlation may be used to infer that the alleles or genotypes are responsible for producing the given phenotype.
genetic background
genetic code
A set of rules by which information encoded within nucleic acids is translated into proteins by living cells. These rules define how sequences of nucleotide triplets called codons specify which amino acid will be added next during protein synthesis. The vast majority of living organisms use the same genetic code (sometimes referred to as the "standard" genetic code) but variant codes do exist.
genetic counseling
The process of advising individuals or families who are affected by or at risk of developing genetic disorders in order to help them understand and adapt to the physiological, psychological, and familial implications of genetic contributions to disease. Genetic counseling integrates genetic testing, genetic genealogy, and genetic epidemiology. [13]
genetic disorder
genetic distance
A measure of the genetic divergence between species, populations within a species, or individuals, used especially in phylogenetics to express either the time elapsed since the existence of a common ancestor or the degree of differentiation in the DNA sequences comprising the genomes of each population or individual.
genetic diversity

Sometimes used interchangeably with genetic variation.

The total number of genetic traits or characteristics in the genetic make-up of a population, species, or other group of organisms. It is often used as a measure of the adaptability of a group to changing environments. Genetic diversity is similar to, though distinct from, genetic variability.
genetic drift

Also allelic drift or the Sewall Wright effect.

A change in the frequency with which an existing allele occurs in a population due to random variation in the distribution of alleles from one generation to the next. Genetic drift is often interpreted as the role that random chance plays in determining whether a given allele becomes more or less common with each generation, regardless of the influence of natural selection. Such randomness may cause certain alleles, even otherwise advantageous ones, to disappear completely from the gene pool, thereby reducing genetic variation, or it may cause initially rare alleles, even neutral or deleterious ones, to become much more frequent or even fixed.
genetic engineering

Also genetic modification or genetic manipulation.

The direct, deliberate manipulation of an organism's genetic material using any of a variety of biotechnology methods, including the insertion or removal of genes, the transfer of genes within and between species, the mutation of existing sequences, and the construction of novel sequences using artificial gene synthesis. Genetic engineering encompasses a broad set of technologies by which the genetic composition of individual cells, tissues, or entire organisms may be altered for various purposes, commonly in order to study the functions and expression of individual genes, to produce hormones, vaccines, and other drugs, and to create genetically modified organisms for use in research and agriculture.
genetic epidemiology
The study of the role played by genetic factors in determining health and disease, in particular through the interaction of genetic factors with environmental factors, and typically as observed in genetically related individuals, often families or lineages but also populations and subpopulations.
genetic genealogy
The use of genealogical DNA testing in combination with traditional genealogical methods to infer the level and type of genetic relationships between individuals, to find ancestors, and to construct family trees, genograms, or other genealogical charts.
genetic hitchhiking

Also genetic draft or the hitchhiking effect.

A type of linked selection by which the positive selection of an allele undergoing a selective sweep causes alleles for different genes at nearby loci to change frequency as well, allowing them to "hitchhike" to fixation along with the positively selected allele. If selection at the first locus is strong enough, neutral or even slightly deleterious alleles within the same linkage group may undergo the same positive selection because the physical distance between the nearby loci is small enough that a recombination event is unlikely to occur between them. Genetic hitchhiking is often considered the opposite of background selection.
genetic marker
A specific, easily identifiable, and usually highly polymorphic gene or other DNA sequence with a known location on a chromosome that can be used to identify the individual or species possessing it.
genetic recombination
Any reassortment or exchange of genetic material within an individual organism or between individuals of the same or different species, especially that which creates genetic variation. In the broadest sense, the term encompasses a diverse class of naturally occurring mechanisms by which nucleic acid sequences are copied or physically transferred into different genetic environments, including homologous recombination during meiosis or mitosis or as a normal part of DNA repair; horizontal gene transfer events such as bacterial conjugation, viral transduction, or transformation; or errors in DNA replication or cell division. Artificial recombination is central to many genetic engineering techniques which produce recombinant DNA.
genetic redundancy
The redundant encoding of two or more distinct gene products that ultimately perform the same biochemical function. Mutations in one of these genes may have a smaller effect on fitness than might be expected, since the redundant genes often compensate for any loss of function and obviate any gain of function.
genetic regulatory network (GRN)
A graph that represents the regulatory complexity of gene expression. The vertices (nodes) are represented by various regulatory elements and gene products while the edges (links) are represented by their interactions. These network structures also represent functional relationships by approximating the rate at which genes are transcribed.
genetic testing

Also DNA testing or genetic screening.

A broad class of various procedures used to identify features of an individual's particular chromosomes, genes, or proteins in order to determine parentage or ancestry, diagnose vulnerabilities to heritable diseases, or detect mutant alleles associated with increased risks of developing genetic disorders. Genetic testing is widely used in human medicine, agriculture, and biological research.
genetic variability

Sometimes used interchangeably with genetic variation.

The formation or the presence of individuals differing in genotype within a population or other group of organisms, as opposed to individuals with environmentally induced differences, which cause only temporary, non-heritable changes in phenotype. Barring other limitations, a population with high genetic variability has a greater potential for successful adaptation to changing environmental conditions than a population with low genetic variability. Genetic variability is similar to, though distinct from, genetic diversity.
genetic variation

Sometimes used interchangeably with genetic diversity and genetic variability.

The genetic differences both within and between populations, species, or other groups of organisms. It is often visualized as the variety of different alleles in the gene pools of different populations.
genetically modified organism (GMO)
Any organism whose genetic material has been altered using genetic engineering techniques, particularly in a way that does not occur naturally by mating or by natural genetic recombination.
genetics
The field of biology that studies genes, genetic variation, and heredity in living organisms.
genic balance
A mechanism of sex determination that depends upon the ratio of the number of X chromosomes (X) to the number of sets of autosomes (A). Males develop when the X/A ratio is 0.5 or less, females when it is 1.0 or more, and an intersex develops when it is between 0.5 and 1.0. [5]
genome
The entire complement of genetic material contained within the chromosomes of an organism, organelle, or virus. The term is also used to refer to the collective set of genetic loci shared by every member of a population or species, regardless of the different alleles that may be present at these loci in different individuals.
genome size
The total amount of DNA contained within one copy of a genome, typically measured by mass (in picograms or daltons) or by the total number of base pairs (in kilobases or megabases). For diploid organisms, genome size is often used interchangeably with C-value.
genomic DNA (gDNA)

Also chromosomal DNA.

The DNA contained in chromosomes, as opposed to the extrachromosomal DNA contained in separate structures such as plasmids or organelles such as mitochondria or chloroplasts.
genomic imprinting
An epigenetic phenomenon that causes genes to be expressed in a manner dependent upon the particular parent from which the gene was inherited. It occurs when epigenetic marks such as DNA or histone methylation are established or "imprinted" in the germ cells of a parent organism and subsequently maintained through cell divisions in the somatic cells of the organism's progeny; as a result, a gene in the progeny that was inherited from the father may be expressed differently than another copy of the same gene that was inherited from the mother.
genomics
An interdisciplinary field that studies the structure, function, evolution, mapping, and editing of entire genomes, as opposed to individual genes.
genotoxicity
The ability of certain chemical agents to cause damage to genetic material within a living cell (e.g. through single- or double-stranded breaks, crosslinking, or point mutations), which may or may not result in a permanent mutation. Though all mutagens are genotoxic, not all genotoxic compounds are mutagenic.
genotype
The entire complement of alleles present in a particular individual's genome, which gives rise to the individual's phenotype.
genotype frequency
genotyping
The process of determining differences in the genotype of an individual by examining the DNA sequences in the individual's genome using bioassays and comparing them to another individual's sequences or a reference sequence.
germ cell
Any cell that gives rise to the gametes of an organism that reproduces sexually. Germ cells are the vessels for the genetic material which will ultimately be passed on to the organism's descendants and are usually distinguished from somatic cells, which are entirely separate from the germ line.
germ line
1.  In multicellular organisms, the population of cells which are capable of passing on their genetic material to the organism's progeny and are therefore (at least theoretically) distinct from somatic cells, which cannot pass on their genetic material except to their own immediate mitotic daughter cells. Cells of the germ line are called germ cells.
2.  The lineage of germ cells, spanning many generations, that contains the genetic material which has been passed on to an individual from its ancestors.
Goldberg-Hogness box
See TATA box.
gRNA
See guide RNA.
guanine (G)
A purine nucleobase used as one of the four standard nucleobases in both DNA and RNA molecules. Guanine forms a base pair with cytosine.
guanine-cytosine content

Also abbreviated GC-content.

The proportion of nitrogenous bases in a nucleic acid that are either guanine (G) or cytosine (C), typically expressed as a percentage. DNA and RNA molecules with higher GC-content are generally more thermostable than those with lower GC-content due to molecular interactions that occur during base stacking. [14]
guanosine (G, Guo)
One of the four standard nucleosides used in RNA molecules, consisting of a guanine base with its N9 nitrogen bonded to the C1 carbon of a ribose sugar. Guanine bonded to deoxyribose is known as deoxyguanosine, which is the version used in DNA.
guide RNA (gRNA)


H

hairpin
See stem-loop.
haplodiploidy
A sex-determination system in which the sex of an individual organism is determined by the number of sets of chromosomes it possesses: offspring which develop from fertilized eggs are diploid and female, while offspring which develop from unfertilized eggs are haploid and male, with half as many chromosomes as the females. Haplodiploidy is common to all members of the insect order Hymenoptera and several other insect taxa.
haplogroup
haploid

Denoted in shorthand with the somatic number n.

(of a cell or organism) Having one copy of each chromosome, with each copy not being part of a pair. Contrast diploid and polyploid.
haploinsufficiency
haplotype
A set of alleles in an individual organism that were inherited together from a single parent.
helicase
Any of a class of ATP-dependent motor proteins that move directionally along the DNA backbone and catalyze the separation of the two complementary strands of double-stranded molecules, permitting a wide variety of vital processes to take place, e.g. transcription, replication, and repair. [8]
hemizygous
In a diploid organism, having just one allele at a given genetic locus (where there would ordinarily be two). Hemizygosity may be observed when only one copy of a chromosome is present in a normally diploid cell or organism, or when a segment of a chromosome containing one copy of an allele is deleted, or when a gene is located on a sex chromosome in the heterogametic sex (in which the sex chromosomes do not exist in matching pairs); for example, in human males with normal chromosomes, almost all X-linked genes are said to be hemizygous because there is only one X chromosome and few of the same genes exist on the Y chromosome.
heredity

Also inheritance.

The storage, transfer, and expression of molecular information in biological organisms, [8] as manifested by the passing on of phenotypic traits from parents to their offspring, either through sexual or asexual reproduction. Offspring cells or organisms are said to inherit the genetic information of their parents.
heritability
1.  The ability to be inherited.
2.  A statistic used in quantitative genetics that estimates the proportion of variation within a given phenotypic trait that is due to genetic variation between individuals in a particular population. Heritability is estimated by comparing the individual phenotypes of closely related individuals in the population.
heterochromatin
heterochromosome
See allosome.
heterogeneous nuclear RNA (hnRNA)
heterologous expression
The expression of a foreign gene or any other foreign DNA sequence within a host organism which does not naturally contain the same gene. Insertion of foreign transgenes into heterologous hosts using recombinant vectors is a common biotechnology method for studying gene structure and function.
heterosis

Also hybrid vigor and outbreeding enhancement.

The improved or increased function or quality of any biological trait in a hybrid offspring, with respect to the same trait in its genetically distinct parents. If any one or more of the parents' traits are noticeably enhanced in the offspring as a result of the mixing of the parents' genetic contributions, the offspring is said to be heterotic.
heterozygous
In a diploid organism, having two different alleles at a given genetic locus. In genetics shorthand, heterozygous genotypes are represented by a pair of non-matching letters or symbols, often an uppercase letter (indicating a dominant allele) and a lowercase letter (indicating a recessive allele), such as "Aa" or "Bb". Contrast homozygous.
high-throughput
histone
Any of a class of highly alkaline proteins responsible for packaging nuclear DNA into structural units called nucleosomes in eukaryotic cells. Histones are the chief protein components of chromatin, where they associate into complexes which act as "spools" around which the linear DNA molecule winds. They play a major role in gene regulation and expression.
hnRNA
See heterogeneous nuclear RNA.
holocentric
(of a linear chromosome or chromosome fragment) Having no single centromere but rather multiple kinetochore assembly sites dispersed along the entire length of the chromosome. During cell division, the chromatids of holocentric chromosomes move apart in parallel and do not form the classical V-shaped structures typical of monocentric chromosomes.
homeobox
homologous chromosomes

Also homologs.

A set of two matching chromosomes, one maternal and one paternal, which pair up with each other inside the nucleus during meiosis. They have the same genes at the same loci, but may have different alleles.
homologous recombination
A type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical ("homologous") molecules of DNA, especially that which occurs between homologous chromosomes. The term may refer to the recombination that occurs as a part of any of a number of distinct cellular processes, most commonly DNA repair or chromosomal crossover during meiosis in eukaryotes and horizontal gene transfer in prokaryotes. Contrast nonhomologous recombination.
homozygous
In a diploid organism, having two identical alleles at a given genetic locus. In genetics shorthand, homozygous genotypes are represented by a pair of matching letters or symbols, such as "AA" or "aa". Contrast heterozygous.
horizontal gene transfer (HGT)

Also lateral gene transfer (LGT).

Any process by which genetic material is transferred between unicellular and/or multicellular organisms other than by vertical transmission from parent to offspring, e.g. bacterial conjugation.
housekeeping gene
Any constitutive gene that is transcribed at a relatively constant level across many or all known conditions and cell types. The products of housekeeping genes typically play critical roles in the maintenance of cellular integrity and basic metabolic function. It is generally assumed that their expression is unaffected by experimental or pathological conditions.
Hox genes
A subset of highly conserved homeobox-containing genes which are essential for the proper organization of the body plan in developing animal embryos, ensuring that the correct structures are formed in the correct places. Hox genes are usually arranged on a chromosome in tandem arrays and are expressed sequentially during development, with the sequence of gene activation corresponding to the physical layout of the tissues in which they are expressed along the organism's anterior–posterior axis. [5]
Human Genome Project (HGP)
A collaborative international scientific research project with the goal of sequencing all of the chromosomal DNA and identifying and mapping all of the genes within human cells, and ultimately of assembling a complete reference genome for the human species. The project was launched in 1990 by a consortium of federal agencies, universities, and research institutions and was declared complete in 2003. Because each individual human being has a unique genome, the finished reference genome is a mosaic of sequences obtained by sampling DNA from thousands of individuals across the world and does not represent any one individual.
hybrid
The offspring that results from combining the qualities of two organisms of different genera, species, breeds, or varieties through sexual reproduction. Hybrids may occur naturally or artificially, as during selective breeding of domesticated animals and plants. Reproductive barriers typically prevent hybridization between distantly related organisms, or at least ensure that hybrid offspring are sterile, but fertile hybrids may result in speciation.
hybridization
1.  The process by which a hybrid organism is produced from two organisms of different genera, species, breeds, or varieties.
2.  The process by which two or more single-stranded nucleic acid molecules with complementary nucleotide sequences pair with each other in solution, creating double-stranded or triple-stranded molecules via the formation of hydrogen bonds between the complementary nucleobases of each strand. In certain laboratory contexts, especially ones in which long strands hybridize with short oligonucleotide primers, hybridization is often referred to as annealing.
3.  A step in some experimental assays in which a single-stranded DNA or RNA preparation is added to an array surface and anneals to a complementary probe.
hybridization probe
hypoxanthine (I)
A naturally occurring non-canonical purine nucleobase that is used in some RNA molecules and pairs with standard nucleobases in a phenomenon known as wobble base pairing. Its nucleoside form is known as inosine, which is the reason it is commonly abbreviated with the letter I in sequence reads.


I

idiochromosome
See allosome.
idiomere
See chromomere.
in silico
(of a scientific experiment or research) Conducted, produced, or analyzed by means of computer modeling or simulation, as opposed to a real-world trial.
in situ
(of a scientific experiment or biological process) Occurring or made to occur in a natural, uncontrolled setting, or in the natural or original position or place, as opposed to in a foreign cell or tissue type or in an artificial environment.
in situ hybridization
in vitro
(of a scientific experiment or biological process) Occurring or made to occur in a laboratory vessel or other controlled artificial environment, e.g. in a test tube or a petri dish, as opposed to inside a living organism or in a natural setting.
in vivo
(of a scientific experiment or biological process) Occurring or made to occur inside the cells or tissues of a living organism; or, in the broadest sense, in any natural, unmanipulated setting. Contrast ex vivo and in vitro.
inbred line
Any lineage of a particular species in which individuals are nearly or completely genetically identical to each other due to a long history of repeated inbreeding, either by natural or artificial means. Lineages are typically considered inbred after at least 20 generations of inbreeding (e.g. by self-fertilization or sib mating), at which point nearly all loci across the genome are homozygous and all individuals can therefore effectively be treated as clones (despite the fact that individuals are still produced by sexual reproduction).
inbreeding

Also incrossing.

Sexual reproduction between breeds or individuals that are closely related genetically. Inbreeding results in homozygosity, which can increase both the probability of offspring being affected by deleterious recessive traits and the probability of fixing beneficial traits within the breeding population. The reproductive event and the resulting progeny may both be referred to as an incross, and the progeny is said to be inbred. Contrast outbreeding.
incidence
The frequency of new occurrence of a genetic disorder (or more broadly any genetic condition or trait, deleterious or otherwise) among the members of a particular population and within a particular period of time. [8]
incomplete dominance
indel
A term referring to either an insertion or a deletion of one or more bases in a nucleic acid sequence.
inducer
A protein that binds to a repressor (to disable it) or to an activator (to enable it).
inducible gene
A gene whose expression is either responsive to environmental change or dependent on its host cell's position within the cell cycle.
inheritance
See heredity.
initiation codon
See start codon.
inosine
insertion
A type of mutation in which one or more bases are added to a nucleic acid sequence. Contrast deletion.
insertion sequence (IS)

Also insertion element or simply insert.

Any nucleotide sequence that is inserted naturally or artificially into another sequence. The term is used in particular to refer to the part of a transposable element that codes for those proteins directly involved in the transposition process, e.g. the transposase enzyme. The coding region in a transposable insertion sequence is usually flanked by short inverted repeats, and the structure of larger transposable elements may include a pair of flanking insertion sequences which are themselves inverted.
insertional mutagenesis
The alteration of a DNA sequence by the insertion of one or more nucleotides into the sequence, either naturally or artificially. Depending on the precise location of the insertion within the target sequence, insertions may partially or totally inactivate or even upregulate a gene product or biochemical pathway, or they may be neutral, leading to no substantive changes at all. Many genetic engineering techniques rely on the insertion of exogenous genetic material into host cells in order to study gene function and expression. [5]
insulator
A specific DNA sequence that prevents a gene from being influenced by the activation or repression of nearby genes.
integron
A mobile genetic element consisting of a gene cassette containing the gene for a site-specific recombinase, integrase-specific recognition sites, and a promoter that governs the expression of one or more genes conferring adaptive traits on the host cell. Integrons usually exist in the form of circular episomal DNA fragments, through which they facilitate the rapid adaptation of bacteria by enabling horizontal gene transfer of antibiotic resistance genes between different bacterial species. [5]
intein
Any sequence of one or more amino acids within a precursor polypeptide that is excised by protein splicing during post-translational modification and is therefore absent from the mature protein, analogous to the introns spliced out of RNA transcripts. [5] Contrast extein.
intercalating agent
Any chemical compound (e.g. acridine dyes) that disrupts the alignment and pairing of bases in the complementary strands of a DNA molecule by inserting itself between the bases. [3]
intercalation
The insertion, naturally or artificially, of chemical compounds between the planar bases of a DNA molecule, which generally disrupts the hydrogen bonding necessary for base pairing.
intercistronic region
Any DNA sequence that is located between the stop codon of one gene and the start codon of the following gene in a polycistronic transcription unit. [5] See also intergenic region.
intercross
A cross in which both the male and female parents are heterozygous at a particular locus. [5]
intergenic region (IGR)
Any sequence of non-coding DNA that is located between functional genes.
intergenic spacer (IGS)
See spacer.
interkinesis

Also interphase II.

The abbreviated pause in activities related to cell division that occurs during meiosis in some species, between the first and second meiotic divisions (i.e. meiosis I and meiosis II). No DNA replication occurs during interkinesis, unlike during the normal interphase that precedes meiosis I and mitosis. [5]
interphase
All stages of the cell cycle excluding cell division. A typical cell spends most of its life in interphase, during which it conducts everyday metabolic activities as well as the complete replication of its genome in preparation for mitosis or meiosis.
intragenic region
See intron.
intragenic suppression
intragenomic conflict
introgression

Also introgressive hybridization.

The movement of a gene from the gene pool of one population or species into that of another population by the repeated backcrossing of hybrids of the two populations with one of the parent populations. Introgression is a ubiquitous and important source of genetic variation in natural populations, but may also be practiced intentionally in the cultivation of domesticated plants and animals.
intron

Also intragenic region.

Any nucleotide sequence within a functional gene that is removed by RNA splicing during post-transcriptional modification of the mRNA primary transcript and is therefore absent from the final mature mRNA. The term refers to both the sequence as it exists within a DNA molecule and to the corresponding sequence in RNA transcripts. Contrast exon.
intron intrusion
intron-mediated recombination
See exon shuffling.
inverted repeat
A nucleotide sequence followed downstream on the same strand by its own reverse complement. The initial sequence and the reverse complement may be separated by any number of nucleotides, or may be immediately adjacent to each other; in the latter case, the composite sequence is also called a palindromic sequence. Inverted repeats are self-complementary by definition, a property which involves them in many biological functions and dysfunctions. Contrast direct repeat.
in-frame
1.  (of a gene or sequence) Read or transcribed in the same reading frame as another gene or sequence; not requiring a shift in reading frame to be intelligible or to result in a functional peptide.
2.  (of a mutation) Not causing a frameshift. [5]
isochore
A large region of genomic DNA with a relatively homogeneous composition of base pairs, distinguished from other regions by the proportion of pairs that are G- C or A- T. The genomes of most plants and vertebrates are composed of different classes of GC-rich and AT-rich isochores. [5]
isochromosome
A type of abnormal chromosome in which the arms of the chromosome are mirror images of each other. Isochromosome formation is equivalent to simultaneous duplication and deletion events such that two copies of either the long arm or the short arm comprise the resulting chromosome.
isomeric genes
Two or more genes that are equivalent and redundant in the sense that, despite coding for distinct gene products, they each result in the same phenotype when set within the same genetic background. If several isomeric genes are present in a single genotype they may be either cumulative or non-cumulative in their contributions to the phenotype. [8]


J

jumping gene
See transposable element.
junctional diversity
junk DNA
Any DNA sequence that appears to have no known biological function, or which serves a purpose that has no positive or a net negative effect on the fitness of the genome in which it is located. The term was once more broadly used to refer to all non-coding DNA, much of which was later discovered to have a function; in modern usage it typically refers to broken or vestigial sequences and selfish genetic elements, including introns, pseudogenes, intergenic DNA, and fragments of transposons and retroviruses, which together constitute a large proportion of the genomes of most eukaryotes. Despite not contributing productively to the host organism, these sequences are able to persist indefinitely inside genomes because the disadvantages of continuing to copy them are too small to be acted upon by natural selection.
junk RNA
Any RNA-encoded sequence, especially a transcript, that appears to have no known biological function, or whose function has no positive or a net negative effect on the fitness of the genome from which it is transcribed. Despite remaining untranslated, many non-coding RNAs still serve important functions, whereas junk RNAs are truly useless: often they are the product of accidental transcription of a junk DNA sequence, or they may result from post-transcriptional processing of primary transcripts, as with spliced-out introns. Junk RNA is usually quickly degraded by ribonucleases and other cytoplasmic enzymes.


K

Ka/Ks ratio
karyotype
The number and appearance of chromosomes within the nucleus of a eukaryotic cell, especially as depicted in an organized photomicrograph known as a karyogram or idiogram (in pairs and ordered by size and by position of the centromere). The term is also used to refer to the complete set of chromosomes in a species or individual organism or to any test that detects this complement or measures the chromosome number.
The karyotype of a typical human male, as visualized in a karyogram using Giemsa staining
kilobase (kb)
A unit of nucleic acid length equal to 1,000 base pairs in duplex molecules such as double-stranded DNA or 1,000 bases in single-stranded molecules.
kinetochore
A disc-shaped protein complex which assembles around the centromere of a chromosome during prometaphase of mitosis and meiosis, where it functions as the attachment point for microtubules of the spindle apparatus.
knob
In cytogenetics, an enlarged, heavily staining chromomere that can be used as a visual marker, allowing specific chromosomes to be easily identified in the nucleus. [5]
knockdown
A genetic engineering technique by which the normal rate of expression of one or more of an organism's genes is reduced, either through direct modification of a DNA sequence or through treatment with a reagent such as a short DNA or RNA oligonucleotide with a sequence complementary to either an mRNA transcript or a gene.
knockin
knockout
A genetic engineering technique in which an organism is modified to carry genes that have been made inoperative ("knocked out"), such that their expression is disrupted at some point in the pathway that produces their gene products and the organism is deprived of their normal effects. Contrast knockin.


L

labelling

Also tagging.

A laboratory technique involving the chemical attachment of a highly selective substance, known as a label, tag, or probe, to a particular cell, protein, amino acid, or other biomolecule of interest, either in vivo or in vitro. The label is typically a reactive derivative of a naturally fluorescent compound (e.g. green fluorescent protein) or any other substance that makes its target distinguishable in some way; other commonly used labels include dyes, enzymes, antibodies, and radioactive molecules. The labelled targets are thereby rendered distinct from their surroundings, allowing them to be easily detected, identified, quantified, or isolated for further study.
lagging strand
In DNA replication, the nascent strand for which DNA polymerase's direction of synthesis is away from the replication fork, which necessitates a complex and discontinuous process, in contrast to the streamlined, continuous synthesis of the other nascent strand that occurs simultaneously. Because DNA polymerase works only in the 5' to 3' direction, but the overall direction of chain elongation must ultimately be the opposite (i.e. 3' to 5', toward the replication fork), the elongation must occur by an indirect mechanism in which a primase synthesizes short RNA primers complementary to the template DNA, and DNA polymerase then extends the primed segments into short chains of nucleotides known as Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the Okazaki fragments are joined by DNA ligase.
lampbrush chromosome
lateral gene transfer (LGT)
See horizontal gene transfer.
Law of Dominance and Uniformity
One of three fundamental principles of Mendelian inheritance, which states that different alleles of the same gene may be dominant or recessive relative to others, and that an organism with at least one dominant allele will uniformly display the phenotype associated with the dominant allele.
Law of Independent Assortment
One of three fundamental principles of Mendelian inheritance, which states that genes responsible for different phenotypic traits are segregated independently during meiosis. Linked genes are a notable exception to this rule.
Law of Segregation
One of three fundamental principles of Mendelian inheritance, which states that during meiosis, the alleles of each gene segregate from each other such that each resulting gamete carries only one allele of each gene.
leader sequence
See 5' untranslated region.
leading strand
In DNA replication, the nascent strand for which both DNA polymerase's direction of synthesis and that of the overall chain elongation are toward the replication fork, i.e. both occur in the 5' to 3' direction, resulting in a single, continuous elongation process with few or no interruptions. By contrast, the other nascent strand, known as the lagging strand, is assembled in a discontinuous process involving the ligation of short DNA fragments which are synthesized in the opposite direction, away from the replication fork. [5]
left splicing junction

Also donor splicing junction or donor splicing site.

The boundary between the left end (by convention, the 5' end) of an intron and the right ( 3') end of an adjacent exon in a pre-mRNA transcript.
leptonema

Also leptotene stage.

In meiosis, the first of five substages of prophase I, following interphase and preceding zygonema. During leptonema, the replicated chromosomes condense from diffuse chromatin into long, thin strands that are much more visible within the nucleus.
lethal equivalent value
The average number of recessive deleterious genes existing in the heterozygous condition that is carried by a member of a population of diploid organisms, multiplied by the average probability that each such gene will cause premature lethality when homozygous. For example, an organism carrying eight recessive semilethal alleles, each of which produces only a 50% probability of premature death when homozygous, is said to carry a genetic burden of four "lethal equivalents". [5]
lethal mutation
Any mutation that results in the premature death of the organism carrying it. Recessive lethal mutations are fatal only to homozygotes, whereas dominant lethals are fatal even in heterozygotes. [5]
leucine zipper
ligase
A class of enzymes which catalyze the joining of large molecules such as nucleic acids by forming one or more chemical bonds between them, typically C–C, C–O, C–S, or C–N bonds via condensation reactions. An example is DNA ligase, which catalyzes the formation of phosphodiester bonds between adjacent nucleotides on one or both strands of a DNA molecule, a reaction known as ligation.
ligation
lineage

Also pedigree.

A linear evolutionary sequence connecting an ancestral cell, organism, or species to a particular descendant cell, organism, or species, including all intermediate organisms and spanning any number of generations; the direct progression of reproductive events (i.e. the line of descent) between two individuals, including vertically related individuals, e.g. parent(s) and offspring, but usually excluding horizontally related individuals who did not themselves directly contribute genetic material to any of the included individuals, e.g. siblings.
linkage
The tendency of DNA sequences which are physically near to each other on the same chromosome to be inherited together during meiosis. Because the physical distance between them is relatively small, the chance that any two nearby parts of a DNA sequence (often loci or genetic markers) will be separated on to different chromatids during chromosomal crossover is statistically very low; such loci are then said to be more linked than loci that are farther apart. Loci that exist on entirely different chromosomes are said to be perfectly unlinked. The standard unit for measuring genetic linkage is the centimorgan (cM).
linkage disequilibrium
linker DNA
1.  A short, synthetic DNA duplex containing the recognition sequence for a particular restriction enzyme. [5] In molecular cloning, linkers are often deliberately included in recombinant molecules in order to make them easily modifiable by permitting cleavage and insertion of foreign sequences at precise locations. A segment of an engineered plasmid containing many such restriction sites is sometimes called a polylinker.
2.  A section of chromosomal DNA connecting adjacent nucleosomes by binding to histone H1. [5]
linking number
The number of times that the two strands of a circular double-helical DNA molecule cross each other, equivalent to the twisting number (which measures the torsion of the double helix) plus the writhing number (which measures the degree of supercoiling). The linking number of a closed molecule cannot be changed without breaking and rejoining the strands. DNA molecules which are identical except for their linking numbers are known as topological isomers. [5]
lncRNA
See long non-coding RNA.
locus

Plural loci.

A specific, fixed position on a chromosome where a particular gene or genetic marker resides.
LOD score
long arm

Denoted in shorthand with the symbol q.

In condensed chromosomes where the positioning of the centromere creates two segments or "arms" of unequal length, the longer of the two arms of a chromatid. Contrast short arm.
long interspersed nuclear element (LINE)
Any of a large family of non- LTR retrotransposons which together comprises one of the most widespread mobile genetic elements in eukaryotic genomes. Each LINE insertion is on average about 7,000 base pairs in length.
long non-coding RNA (lncRNA)
A class of non-coding RNA consisting of all transcripts of more than 200 nucleotides in length that are not translated. This limit distinguishes lncRNA from the numerous smaller non-coding RNAs such as microRNA. See also long intervening non-coding RNA.
lyonization
See X-inactivation.


See also

References

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  4. ^ "NCI Dictionary of Genetics Terms". National Cancer Institute. PDQ® Cancer Genetics Editorial Board.
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  10. ^ "Functional Genomics Data Society – FGED Society".
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Further reading

External links