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An allele (UK // or US //), or allel, is one of a number of alternative forms of the same gene or same genetic locus (generally a group of genes). It is the alternative form of a gene for a character producing different effects. Sometimes different alleles can result in different observable phenotypic traits, such as different pigmentation. However, many genetic variations result in little or no observable variation.
Most multicellular organisms have two sets of chromosomes, that is, they are diploid. These chromosomes are referred to as homologous chromosomes. Diploid organisms have one copy of each gene (and therefore one allele) on each chromosome. If both alleles are the same, they and the organism are homozygous, and the organisms are homozygotes. If the alleles are different, they and the organism are heterozygous and the organisms are heterozygotes.
A population or species 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.
For example, at the gene locus for the ABO blood type carbohydrate antigens in humans, classical genetics recognizes three alleles, IA, IB, and IO, that determine compatibility of blood transfusions. Any individual has one of six possible genotypes (AA, AO, BB, BO, AB, and OO) that produce one of four possible phenotypes: "A" (produced by AA homozygous and AO heterozygous genotypes), "B" (produced by BB homozygous and BO heterozygous genotypes), "AB" heterozygotes, and "OO" homozygotes. 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. An individual with "Type A" blood may be an AO heterozygote, an AA homozygote, or an AA heterozygote with two different "A" alleles.
The word "allele" is a short form of allelomorph ("other form"), which was used in the early days of genetics to describe variant forms of a gene detected as different phenotypes. It derives from the Greek prefix ἀλλήλ- ["allel-"], meaning "reciprocal" or "each other", which itself is related to the Greek adjective ἄλλος (allos; cognate with Latin "alius"), meaning "other".
In many cases, genotypic interactions between the two alleles at a locus can be described as dominant or recessive, according to which of the two homozygous genotypes the phenotype of the heterozygote most resembles. Where the heterozygote is indistinguishable from one of the homozygotes, the allele involved is said to be dominant to the other, which is said to be recessive to the former. The degree and pattern of dominance varies among loci. For a further discussion see Dominance (genetics). This type of interaction was first formally described by Gregor Mendel. However, many traits defy this simple categorization and the phenotypes are modeled by polygenic inheritance.
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 dominant, common, and normal, in contrast to "mutant" alleles regarded as recessive, rare, and frequently deleterious. It was commonly 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.
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:
where p is the frequency of one allele and q is the frequency of the alternative allele, which necessarily sum to unity. Then, p2 is the fraction of the population homozygous for the first allele, 2pq is the fraction of heterozygotes, and q2 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 p2 + 2pq, and the fraction with the recessive phenotype is q2.
With three alleles:
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:
A number of genetic disorders are caused when an individual inherits two recessive alleles for a single-gene trait. Recessive genetic disorders include Albinism, Cystic Fibrosis, Galactosemia, Phenylketonuria (PKU), and Tay-Sachs Disease. 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 disease, occur when an individual inherits only one dominant allele.