TheInfoList

An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is one of two, or more, forms of a given
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

variant. For example, the ABO blood grouping is controlled by the ABO gene, which has six common alleles. Nearly every living human's
phenotype In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular inter ...

for the ABO gene is some combination of just these six alleles. An allele is one of two, or more, versions of the same gene at the same place on a
chromosome A chromosome is a long DNA molecule with part or all of the genome, genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by Chaperone (protein), chaperone proteins, bind to and ...

. It can also refer to different sequence variations for several-hundred base-pair or more region of the genome that codes for a protein. Alleles can come in different extremes of size. At the lowest possible size an allele can be a
single nucleotide polymorphism In genetics, a single-nucleotide polymorphism (SNP ; plural ) is a substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of the population (e.g. 1% or more). For example, at a s ...
(SNP). At the higher end, it can be up to several thousand base-pairs long. Most alleles result in little or no observable change in the function of the protein the gene codes for. However, sometimes, different alleles can result in different observable
phenotypic trait A phenotypic trait, simply trait, or character state is a distinct variant of a phenotypic right , Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of petal color in pea plants. Th ...
s, such as different
pigmentation A pigment is a colored material that is completely or nearly insoluble in water. In contrast, dyes 300px, Yarn drying after being dyed in the early American tradition, at living_history_museum.html"_;"title="Conner_Prairie_living_history_muse ...
. A notable example of this is discovery that the white and purple flower colors in
pea The pea is most commonly the small spherical seed A seed is an embryonic plant enclosed in a protective outer covering. The formation of the seed is part of the process of reproduction Reproduction (or procreation or breeding) is ...

plants were the result of "pure line" traits, that is a single gene with two alleles. Nearly all
multicellular organism A multicellular organism is an organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biol ...
s have two sets of
chromosome A chromosome is a long DNA molecule with part or all of the genome, genetic material of an organism. Most eukaryotic chromosomes include packaging proteins called histones which, aided by Chaperone (protein), chaperone proteins, bind to and ...

s at some point in their
life cycle Life cycle, life-cycle, or lifecycle may refer to: Science and academia *Biological life cycle, the sequence of life stages that an organism undergoes from birth to reproduction ending with the production of the offspring *Life-cycle hypothesis, ...
; that is, they are
diploid Ploidy () is the number of complete sets of chromosomes in a cell (biology), cell, and hence the number of possible alleles for Autosome, autosomal and Pseudoautosomal region, pseudoautosomal genes. Sets of chromosomes refer to the number of mate ...
. 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 Zygosity (the noun, zygote A zygote (from Greek ζυγωτός ''zygōtos'' "joined" or "yoked", from ζυγοῦν ''zygoun'' "to join" or "to yoke") is a eukaryotic cell formed by a fertilization event between two gamete A gamete ( /ˈ ...
with respect to that gene. If the alleles are different, they, and the organism, are
heterozygous Zygosity (the noun, zygote, is from the Greek zygotos "yoked," from zygon "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 or ...

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 William Bateson (8 August 1861 – 8 February 1926) was an English biology, biologist who was the first person to use the term genetics to describe the study of heredity, and the chief populariser of the ideas of Gregor Mendel following their red ...

and
Edith Rebecca Saunders Edith Rebecca Saunders (14 October 1865 – 6 June 1945) was a British geneticist A geneticist is a biologist who studies genetics, the science of genes, heredity, and variation of organism In biology, an organism (from Ancient Greek ...
), which was used in the early days of
genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, ...

to describe variant forms of a
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

detected as different
phenotypes right , Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of petal color in pea plants. The letters B and b represent genes for color, and the pictures show the resultant phenotypes. Ill ...
. It derives from the
Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is approximately 10.7 million as of ...
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 spoken in the area around Rome, known as Latium. Through the power of the Roman Republic, it became ...

''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 Domination or dominant may refer to: Society * World domination, which is mainly a conspiracy theory * Colonialism in which one group (usually a nation) invades another region for material gain or to eliminate competition * Chauvinism in which a p ...
or
recessive In genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Mendel, Moravia, Moravian scientist ...
, according to which of the two homozygous phenotypes the
heterozygote Zygosity (the noun, zygote A zygote (from Greek ζυγωτός ''zygōtos'' "joined" or "yoked", from ζυγοῦν ''zygoun'' "to join" or "to yoke") is a eukaryotic cell formed by a fertilization event between two gamete A gamete ( /ˈ ...
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 Gregor Johann Mendel (; cs, Řehoř Jan Mendel; 20 July 1822 – 6 January 1884) was a meteorologist, mathematician, biologist, AugustinianAugustinian may refer to: *Augustinians Augustinians are members of Christian religious orders th ...

. However, many traits defy this simple categorization and the phenotypes are modeled by
co-dominance In genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) Though heredity had been observed for millennia, Gregor Mendel, Moravia, Moravian scientis ...
and
polygenic inheritance A quantitative trait locus (QTL) is a locus Locus (plural loci) is Latin for "place". It may refer to: Entertainment * Locus (comics), a Marvel Comics mutant villainess, a member of the Mutant Liberation Front * Locus (magazine), ''Locus'' (ma ...
. The term "
wild type Unlike culinary bananas, wild-type bananas have numerous large, hard seeds. The wild type (WT) is the phenotype right , Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of petal col ...
" 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 (''''). Such a "wild type" allele was historically regarded as leading to a dominant (overpowering - always expressed), common, and normal phenotype, in contrast to "
mutant In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechan ...

" 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 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 In biology, a gene (from ''genos'' "...Wilhelm Johannsen coined the word gene to describe the Men ...
, 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 biological classification, 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 individu ...

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 The ABO blood group system is used to denote the presence of one, both, or neither of the A and B antigen In immunology Immunology is a branch of biology that covers the study of immune systems in all organisms. Immunology charts, meas ...

blood type A blood type (also known as a blood group) is a classification of blood Blood is a body fluid Body fluids, bodily fluids, or biofluids are liquid A liquid is a nearly incompressible In fluid mechanics or more generally continuum ...
carbohydrate A carbohydrate () is a biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a ...
antigen In immunology Immunology is a branch of biology that covers the study of immune systems in all organisms. Immunology charts, measures, and contextualizes the Physiology, physiological functioning of the immune system in states of both health ...
s 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 product A blood product is any therapeutic substance prepared from human blood. This includes whole blood; blood components; and plasma derivatives. Whole blood is not commonly used in t ...

s. Any individual has one of six possible
genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a specific ...
s (IAIA, IAi, IBIB, IBi, IAIB, and ii) which produce one of four possible
phenotype In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular inter ...

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 In population genetics, the Hardy–Weinberg principle, also known as the Hardy–Weinberg equilibrium, model, theorem, or law, states that allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is one of two, o ...
). 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 In the fields of molecular biology Molecular biology is the branch of biology that seeks to understand the molecule, molecular basis of biologi ...
are caused when an individual inherits two recessive alleles for a single-gene trait. Recessive genetic disorders include
albinism Albinism is the congenital absence of any pigmentation or colouration in a person, animal or plant, resulting in white hair, feathers, scales and skin and pink eyes in mammals, birds, reptiles, amphibians and fish and invertebrates as well. V ...
,
cystic fibrosis Cystic fibrosis (CF) is a genetic disorder 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 In biology, a gene (from ''genos'' "...Wilhelm Johan ...
,
galactosemia Galactosemia (British galactosaemia, from Greek γαλακτόζη + αίμα, meaning galactose + blood, accumulation of galactose in blood) is a rare genetic metabolic disorder that affects an individual's ability to metabolize the sugar galact ...

,
phenylketonuria Phenylketonuria (PKU) is an that results in decreased of the . Untreated, PKU can lead to , s, behavioral problems, and s. It may also result in a musty smell and lighter skin. A baby born to a mother who has poorly treated PKU may have hear ...
(PKU), and
Tay–Sachs disease Tay–Sachs disease is a genetic disorder 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 In biology, a gene (from ''genos'' "...Wilhelm Johannse ...
. 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 Zygosity (the noun, zygote, is from the Greek zygotos "yoked," from zygon "yoke") () is the degree to which both copies of a chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. Most euk ...
), they are more frequent in males than in females. Examples include red-green
color blindness Color blindness (color vision deficiency) is the decreased ability to see color or differences in color Color (American English American English (AmE, AE, AmEng, USEng, en-US), sometimes called United States English or U.S. Eng ...

and
fragile X syndrome Fragile X syndrome (FXS) is a genetic disorder A genetic disorder is a health problem caused by one or more abnormalities in the genome In the fields of molecular biology and genetics Genetics is a branch of biology concerned ...
. Other disorders, such as
Huntington's disease Huntington's disease (HD), also known as Huntington's chorea, is a neurodegenerative disease that is mostly Genetic disorder#Autosomal dominant, inherited. The earliest symptoms are often subtle problems with mood or mental abilities. A gener ...
, occur when an individual inherits only one dominant allele.

# Epialleles

While are typically studied in terms of genetic alleles,
epigenetic In biology, epigenetics is the study of heritability, heritable phenotype changes that do not involve alterations in the DNA sequence. The Ancient Greek, Greek prefix ''wikt:epi-, epi-'' ( "over, outside of, around") in ''epigenetics'' implies f ...
marks such as
DNA methylation DNA methylation is a biological process by which methyl group A methyl group is an alkyl derived from methane, containing one carbon atom chemical bond, bonded to three hydrogen atoms — CH3. In chemical formula, formulas, the ...

can be inherited at specific genomic regions in certain species, a process termed transgenerational epigenetic inheritance. The term ''epiallele'' is used to distinguish these heritable marks from traditional alleles, which are defined by
nucleotide sequence A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monom ...

. 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.