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An allele is one of at least two alternative forms of a particular gene. Alleles provide the genetic instructions for organisms that, although similar in type, are visibly different (phenotypically different). The term allele is derived from the Greek term alleon, used to describe a difference in morphology or form. At the genetic level, alleles contain differing base sequences in their nucleic acid (e.g., DNA). As a form of a gene, an allele carries the instructions for a particular variation of the genes protein product. At its most basic molecular level, an allele is an ordered sequence of bases (part of nucleotides) that code for a specific genetic product (protein, enzyme, RNA molecule, etc.).

Although underlying genetic molecular complexities sometimes blur the differences in expression; nature provides simple examples of alleles. For example, a single gene may control the flower color of some plants. In such cases, one allele of the gene produces one color (e.g., red flowers) while another allele of flower color gene may produce another color (e.g., white flowers).

Alleles reside at corresponding locations on the chromosomes that constitute a chromosomal pair. Because alleles reside in specific regions of chromosomes, they can act as markers and are subject to the laws of inheritance resulting from the apportionment of homologous chromosomes (chromosomes that match in terms of size, shape, and gene content) during meiosis. The alternative alleles that comprise an organisms genome are inherited, one allele from each parent. The allele contained on the homologous chromosome derived from the mother is termed the maternal allele. The allele on the homologous chromosome derived from the father is termed the paternal allele.

All diploid organisms have two alleles at a given locus on a pair of homologous chromosomes. Because haploid cells (e.g., oocyte and spermatozoa in humans) contain half the chromosome compliment, such cells contain only one allele of each gene. When fertilization occurs, the pair of alleles can be described as homologous (alike) or heterologous (different). Accordingly, organisms that are homologous, with respect to the alleles for a particular gene, carry identical alleles for that gene. In contrast, organisms described as heterozygous for a particular gene carry alleles that differ. Alleles may also be dominant or recessive with respect to their interaction and expression.

A population with stable allele frequencies is in genetic equilibrium. Accordingly, changes in allele frequencies (the percentage of respective alleles in a population) are characteristic indicators of evolving populations. The Hardy-Weinberg theorem states that: in the absence of selection pressures, the types and frequencies of alleles in a population remain constant. The Hardy-Weinberg equation can be used to mathematically predict allele frequencies.

See also Adaptation; Chromosome mapping; Codons; Genetic engineering.