What is an allele, and how can alleles of one gene differ?

An allele is one version of a gene. Think of “gene” as the name for the gene being discussed and “allele” as the particular version of it. OpenStax describes alleles as gene variants found at corresponding positions on homologous chromosomes. [S1]

For example, we could invent a gene called Gene X and label two imaginary versions A and a. In this teaching model, A and a are two allele labels for the same gene. The letters are just a convenient way to distinguish the versions; they do not tell us what the gene does or what trait it might be associated with.

For the simple model here, assume the organism is diploid. A diploid organism may have two copies of a gene, and those copies can encode the same version or different versions. [S1]

Using our fictional labels, the two copies could be written as A/A if both carry the version labeled A, or A/a if they carry different versions. Those slash-separated pairs are a notation for the example, not extra biological claims about what either version does. The useful distinction is that A and a are alleles; A/A and A/a describe pairs of alleles in this model.

Not by itself. A and a show a difference between two versions of one gene in the example. They do not describe every feature of an organism, and the letters alone do not establish whether any visible or other trait differs. Keep “allele variation” (different versions of a gene) separate from “organism variation” (differences between whole organisms).

Also, A and a are not a claim that only two versions can exist. OpenStax notes that more than two allele forms can occur in a population. [S1] Our model simply chooses two labels to make the idea easy to see; it leaves out any other possible versions.

Glossary entry: An allele is one version of a gene. Different alleles are different versions of the same gene, rather than names for different whole organisms. For the fictional example below, assume Gene X has two versions in the model, labeled A and a, and assume the organism being represented is diploid. The labels do not describe a real trait.

Worked example:

1. Name the gene in the model: Gene X.
2. Name the modeled versions: allele A and allele a.
3. Represent the two copies as A/A or A/a.
4. Read A/A as two copies with the same modeled version; read A/a as two copies with different modeled versions.
5. Stop there unless you have additional information: these labels alone do not say what a trait looks like or how it is inherited.

That last limit matters. The source supports the definition, the two-copy description for a diploid organism, and the possibility of more than two allele forms in a population. [S1] It does not establish what a particular allele does, what an organism would look like, or which allele pair a real organism has.