Allele
An allele is one of the alternative versions of a gene; an organism inherits one allele for each gene from each parent.
Definition
An allele is one version of a gene, the specific answer to the question a gene asks, such as "what color are the seeds," and an organism inherits one allele for each gene from each parent, arriving at genotypes that are homozygous (two matching alleles) or heterozygous (two different ones). A dominant allele, written with a capital letter, masks a recessive allele, written in lowercase, when the two are paired in a heterozygote; at the molecular level, alleles are sequence variants at a locus that can differ by a single nucleotide, an insertion or deletion, or a larger structural change, with effects ranging from silent to a complete loss or gain of function. Dominance is a property of the phenotype being measured rather than of the allele itself, so incomplete dominance, codominance, and multiple-allele systems are common, and across a population allele frequencies are described by the Hardy-Weinberg principle ($p^2 + 2pq + q^2 = 1$) and shift under selection, drift, mutation, and migration.
Example
In pea plants, $YY$ and $Yy$ genotypes give yellow seeds and $yy$ gives green, so crossing two $Yy$ plants yields offspring in a $3:1$ yellow-to-green ratio. The human ABO blood group locus has three alleles, with $I^A$ and $I^B$ codominant and $i$ recessive to both, producing four phenotypes from six genotypes, while the sickle-cell allele of the beta-globin gene differs from the normal allele by a single base change that swaps glutamate for valine at position $6$.
Key Insight
A recessive allele is not weaker or rarer, just unexpressed when paired with a dominant one, and the same allele can even help in one context while harming in another: sickle-cell heterozygotes gain partial protection against malaria, a textbook case of balancing selection keeping an otherwise damaging allele common where malaria is widespread.