An allele is one of two or more alternative versions of a DNA sequence at a particular location, or locus, in a genome. The term commonly describes a version of a gene, but it also applies to variants at noncoding sites and other defined DNA regions. Alleles may differ at a single base or across a longer sequence. In diploid organisms, an individual ordinarily carries two alleles at an autosomal locus, one inherited from each biological parent. (genome.gov)
Alleles, loci, and genotypes
A locus identifies a genomic position; an allele identifies the sequence present there. These concepts distinguish the location of genetic information from its alternative forms. Alleles occupy corresponding positions on paired chromosomes, rather than being separate genes at unrelated locations. An individual's allele combination at a locus constitutes its genotype. For a locus with alleles designated A and a, the possible diploid genotypes are AA, Aa, and aa. (genome.gov)
An individual with two matching alleles is homozygous at that locus; one with two different alleles is heterozygous. These descriptions are locus-specific: the same individual can be homozygous at some sites and heterozygous at others. Although a diploid individual ordinarily carries only two alleles at a particular autosomal locus, a population may contain many alternative alleles. Consequently, “two alleles per individual” does not mean “only two alleles per gene.” (genome.gov)
Molecular origins and effects
New alleles arise through mutation, meaning changes in DNA sequence. Mutations can result from errors during DNA replication or from other processes that alter DNA. In humans, germline mutations occurring in eggs or sperm can be transmitted to offspring, whereas mutations confined to somatic cells are not transmitted through ordinary reproduction. This distinction separates inherited allelic variation from variation acquired in particular body-cell lineages. (genome.gov)
At a single-base locus, alleles might be represented by nucleotide letters such as C and T. Such variation includes single-nucleotide polymorphisms, or SNPs. A gene-level allele, however, may contain several sequence differences rather than just one. For example, the major A and B forms of the ABO gene differ at multiple positions, producing enzymes with different substrate specificities. The scale at which an allele is defined therefore matters when comparing genetic results. (genome.gov)
Sequence differences do not necessarily produce observable differences. Some variants alter biological function, while others have no identified biological effect. Changes in protein-coding DNA can alter the amino acid sequence of a protein, but different DNA sequences can also encode the same amino acid. The phenotype—an organism's observable or measurable characteristics—reflects interactions between its genetic constitution and environment, not simply the name assigned to an allele. (genome.gov)
Inheritance and dominance
The segregation of alleles is central to the inheritance patterns investigated by Gregor Mendel. During meiosis, paired chromosomes separate so that a gamete normally receives one allele at each autosomal locus. Fertilization restores the paired condition. Under simple Mendelian segregation, a heterozygous Aa parent transmits either allele with a probability of one-half. Crossing two such parents gives expected offspring genotype proportions of one-quarter AA, one-half Aa, and one-quarter aa. These are probabilities, not guaranteed proportions in a small family. (openstax.org)
Dominance describes the relationship between alleles with respect to a specified phenotype. In complete dominance, the heterozygote resembles one homozygote for that trait; the other allele is described as recessive. Dominance does not mean that an allele is more common or more likely to enter a gamete. A dominant allele can be rare, and a recessive allele can be frequent: inheritance probabilities and population frequencies are distinct from phenotypic dominance. (genome.gov)
The ABO blood group system illustrates multiple alleles and codominance. Its major functional allele categories are conventionally written Iᴬ, Iᴮ, and i. A and B alleles produce different enzymes involved in forming cell-surface blood-group antigens. In the usual pattern, IᴬIᴮ individuals express both antigen types and have group AB, while Iᴬi and Iᴮi individuals have groups A and B, respectively. These categories simplify a locus containing additional molecular variation. (ncbi.nlm.nih.gov)
Alleles in populations
Population genetics examines allele distributions and their changes over generations. Allele frequency is the proportion of copies of a locus represented by a particular allele, rather than the proportion of individuals carrying it. For a diploid autosomal locus sampled in N individuals,
where and count the corresponding genotypes. Each homozygote contributes two copies of A, while each heterozygote contributes one. (openstax.org)
For two alleles with frequencies and , . Under Hardy–Weinberg equilibrium, expected genotype frequencies are , , and . This idealized model assumes random mating, no selection, mutation, or migration, and a population sufficiently large to neglect random sampling effects. Allele frequencies can change through natural selection, genetic drift, mutation, and gene flow. These processes connect allelic variation with evolution. (openstax.org)
Identification and linked variation
DNA sequencing and other genotyping methods identify alleles at specified genomic positions. Results may be expressed as symbolic genotypes or explicit nucleotide combinations. A haplotype is a grouping of variants on one chromosome that tends to be inherited together. Unlike a diploid genotype, which records the alleles present across chromosome copies, a haplotype describes their arrangement along a particular copy; it may encompass one gene or a larger region. (genome.gov)