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An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of
nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecu ...
s at the
same place ''Same Place'' is the debut mini-album from Australian-American hip hop artist, Bukkcity. Originally meant for released in October 2008, due to several delays it wasn't released until January 2009, through Australian hip hop label, Unda K9 and M ...
on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chromosomal or genomic location of a gene or any other genetic element is called a locus (plural: loci) and alternative DNA sequences at a locus are called alleles." The simplest alleles are single nucleotide polymorphisms (SNP). but they can also be insertions and deletions of up to several thousand base pairs. Popular definitions of 'allele' typically refer only to different alleles within genes. For example, the ABO blood grouping is controlled by the
ABO gene Histo-blood group ABO system transferase is an enzyme with glycosyltransferase activity, which is encoded by the ''ABO'' gene in humans. It is ubiquitously expressed in many tissues and cell types. ABO determines the ABO blood group of an individ ...
, which has six common alleles (variants). In population genetics, nearly every living human's
phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (biology), morphology or physical form and structure, its Developmental biology, developmental proc ...
for the ABO gene is some combination of just these six alleles. Most alleles observed result in little or no change in the function of the gene product it codes for. However, sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation. A notable example of this is Gregor Mendel's discovery that the white and purple flower colors in pea plants were the result of a single gene with two alleles. Nearly all multicellular organisms have two sets of
chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins ar ...
s at some point in their biological life cycle; that is, they are diploid. In this case, the chromosomes can be paired. Each chromosome in the pair contains the same genes in the same order, and place, along the length of the chromosome. For a given gene, if the two chromosomes contain the same allele, they, and the organism, are homozygous with respect to that gene. If the alleles are different, they, and the organism, are
heterozygous Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. ...
with respect to that gene.


Etymology

The word "allele" is a short form of allelomorph ("other form", a word coined by British geneticists William Bateson and
Edith Rebecca Saunders Edith Rebecca Saunders FLS (14 October 1865 – 6 June 1945) was a British geneticist and plant anatomist. Described by J. B. S. Haldane as the "Mother of British Plant Genetics", she played an active role in the re-discovery of Mendel's laws ...
), which was used in the early days of genetics to describe variant forms of a
gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
detected as different phenotypes. It derives from the Greek prefix ἀλληλο-, ''allelo-'', meaning "mutual", "reciprocal", or "each other", which itself is related to the Greek adjective ἄλλος, ''allos'' (cognate with
Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally a dialect spoken in the lower Tiber area (then known as Latium) around present-day Rome, but through ...
''alius''), meaning "other".


Alleles that lead to dominant or recessive phenotypes

In many cases, genotypic interactions between the two alleles at a locus can be described as dominant or
recessive In genetics, dominance is the phenomenon of one variant ( allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant an ...
, according to which of the two homozygous phenotypes the
heterozygote Zygosity (the noun, zygote, is from the Greek "yoked," from "yoke") () is the degree to which both copies of a chromosome or gene have the same genetic sequence. In other words, it is the degree of similarity of the alleles in an organism. M ...
most resembles. Where the heterozygote is indistinguishable from one of the homozygotes, the allele expressed is the one that leads to the "dominant" phenotype, and the other allele is said to be "recessive". The degree and pattern of dominance varies among loci. This type of interaction was first formally-described by Gregor Mendel. However, many traits defy this simple categorization and the phenotypes are modeled by co-dominance and
polygenic inheritance A quantitative trait locus (QTL) is a locus (section of DNA) that correlates with variation of a quantitative trait in the phenotype of a population of organisms. QTLs are mapped by identifying which molecular markers (such as SNPs or AFLPs ...
The term " wild type" allele is sometimes used to describe an allele that is thought to contribute to the typical phenotypic character as seen in "wild" populations of organisms, such as fruit flies ('' Drosophila melanogaster''). Such a "wild type" allele was historically regarded as leading to a dominant (overpowering – always expressed), common, and normal phenotype, in contrast to " mutant" alleles that lead to recessive, rare, and frequently deleterious phenotypes. It was formerly thought that most individuals were homozygous for the "wild type" allele at most gene loci, and that any alternative "mutant" allele was found in homozygous form in a small minority of "affected" individuals, often as genetic diseases, and more frequently in heterozygous form in " carriers" for the mutant allele. It is now appreciated that most or all gene loci are highly polymorphic, with multiple alleles, whose frequencies vary from population to population, and that a great deal of genetic variation is hidden in the form of alleles that do not produce obvious phenotypic differences.


Multiple alleles

A population or
species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriat ...
of organisms typically includes multiple alleles at each locus among various individuals. Allelic variation at a locus is measurable as the number of alleles ( polymorphism) present, or the proportion of heterozygotes in the population. A null allele is a gene variant that lacks the gene's normal function because it either is not expressed, or the expressed protein is inactive. For example, at the gene locus for the ABO blood type
carbohydrate In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may o ...
antigens in humans, classical genetics recognizes three alleles, IA, IB, and i, which determine compatibility of
blood transfusion Blood transfusion is the process of transferring blood products into a person's circulation intravenously. Transfusions are used for various medical conditions to replace lost components of the blood. Early transfusions used whole blood, but mo ...
s. Any individual has one of six possible genotypes (IAIA, IAi, IBIB, IBi, IAIB, and ii) which produce one of four possible
phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (biology), morphology or physical form and structure, its Developmental biology, developmental proc ...
s: "Type A" (produced by IAIA homozygous and IAi heterozygous genotypes), "Type B" (produced by IBIB homozygous and IBi heterozygous genotypes), "Type AB" produced by IAIB heterozygous genotype, and "Type O" produced by ii homozygous genotype. (It is now known that each of the A, B, and O alleles is actually a class of multiple alleles with different DNA sequences that produce proteins with identical properties: more than 70 alleles are known at the ABO locus. Hence an individual with "Type A" blood may be an AO heterozygote, an AA homozygote, or an AA heterozygote with two different "A" alleles.)


Genotype frequencies

The frequency of alleles in a diploid population can be used to predict the frequencies of the corresponding genotypes (see Hardy–Weinberg principle). For a simple model, with two alleles; : p + q=1 \, : p^2 + 2pq + q^2=1 \, where ''p'' is the frequency of one allele and ''q'' is the frequency of the alternative allele, which necessarily sum to unity. Then, ''p''2 is the fraction of the population homozygous for the first allele, 2''pq'' is the fraction of heterozygotes, and ''q''2 is the fraction homozygous for the alternative allele. If the first allele is dominant to the second then the fraction of the population that will show the dominant phenotype is ''p''2 + 2''pq'', and the fraction with the recessive phenotype is ''q''2. With three alleles: : p + q + r = 1 \, and : p^2 + q^2 + r^2 + 2pq + 2pr + 2qr = 1. \, In the case of multiple alleles at a diploid locus, the number of possible genotypes (G) with a number of alleles (a) is given by the expression: : G= \frac.


Allelic dominance in genetic disorders

A number of
genetic disorders A genetic disorder is a health problem caused by one or more abnormalities in the genome. It can be caused by a mutation in a single gene (monogenic) or multiple genes (polygenic) or by a chromosomal abnormality. Although polygenic disorde ...
are caused when an individual inherits two recessive alleles for a single-gene trait. Recessive genetic disorders include albinism, cystic fibrosis, galactosemia,
phenylketonuria Phenylketonuria (PKU) is an inborn error of metabolism that results in decreased metabolism of the amino acid phenylalanine. Untreated PKU can lead to intellectual disability, seizures, behavioral problems, and mental disorders. It may als ...
(PKU), and
Tay–Sachs disease Tay–Sachs disease is a genetic disorder that results in the destruction of nerve cells in the brain and spinal cord. The most common form is infantile Tay–Sachs disease, which becomes apparent around three to six months of age, with the baby ...
. Other disorders are also due to recessive alleles, but because the gene locus is located on the X chromosome, so that males have only one copy (that is, they are hemizygous), they are more frequent in males than in females. Examples include red-green color blindness and fragile X syndrome. Other disorders, such as
Huntington's disease Huntington's disease (HD), also known as Huntington's chorea, is a neurodegenerative disease that is mostly inherited. The earliest symptoms are often subtle problems with mood or mental abilities. A general lack of coordination and an uns ...
, occur when an individual inherits only one dominant allele.


Epialleles

While heritable traits are typically studied in terms of genetic alleles, epigenetic marks such as DNA methylation can be inherited at specific genomic regions in certain species, a process termed
transgenerational epigenetic inheritance Transgenerational epigenetic inheritance is the transmission of epigenetic markers from one organism to the next (i.e., from parent to child) that affects the traits of offspring without altering the primary structure of DNA (i.e. the sequence of ...
. The term ''epiallele'' is used to distinguish these heritable marks from traditional alleles, which are defined by nucleotide sequence. A specific class of epiallele, the metastable epialleles, has been discovered in mice and in humans which is characterized by stochastic (probabilistic) establishment of epigenetic state that can be mitotically inherited.


Idiomorph

The term “idiomorph”, from Greek ‘morphos’ (form) and ‘idio’ (singular, unique), was introduced in 1990 in place of “allele” to denote sequences at the same locus in different strains that have no sequence similarity and probably do not share a common phylogenetic relationship. It is used mainly in the genetic research of mycology.


See also


References and notes


External links


ALFRED: The ALlele FREquency Database
{{Genetics Classical genetics Genetic genealogy