A gene locus is a particular position or region on a chromosome associated with a gene. Homologous chromosomes carry corresponding loci in the same general order.

Different DNA sequence versions found at the same locus are called alleles.

For a diploid organism, the two homologous chromosomes can therefore carry two allele copies at one locus. Genetic notation often uses letters such as $A$ and $a$ to distinguish alleles.

Genotype describes allele composition

The genotype at a locus is the allele combination an individual carries.

For a two-allele example, possible diploid genotypes include

$$AA,\qquad Aa,\qquad aa.$$

An individual with two copies of the same allele is homozygous at that locus:

$$AA\text{ or }aa.$$

An individual with two different alleles is heterozygous:

$$Aa.$$

The order $Aa$ versus $aA$ does not represent different genotypes unless additional parental-origin information is being tracked.

Phenotype describes an observable or measurable state

A phenotype is a measurable characteristic of an organism, cell or molecule. Examples include flower color, enzyme activity, blood-cell shape or expression level of a protein.

Genotype and phenotype are not synonyms. Genotype describes inherited sequence state; phenotype describes an outcome produced through molecular and developmental processes in an environment.

Two individuals can sometimes share a phenotype despite different genotypes, and the same genotype can sometimes produce different quantitative phenotypes under different environmental conditions.

Alleles are not whole genes that appear or disappear

If one allele is written $A$ and another $a$, both normally refer to versions of the same locus. The lowercase notation does not mean that the gene is absent, weaker or physically smaller.

This vocabulary separates four questions:

• locus: where in the genome is the gene?
• allele: which sequence version is present?
• genotype: which allele copies does the individual carry?
• phenotype: what measurable state results?

Keeping those levels distinct is the foundation for reasoning about inheritance.