Alleles are variant forms of the same gene: that is, they are different DNA sequences. Frequently, different alleles vary by just one or a few nucleotides but much more significant sequence differences have been observed. Of course, we could use the DNA sequence itself to represent an allele but that would be cumbersome even if we knew the DNA sequence. Therefore, we use a simple symbol to represent an allele. You may encounter some complex looking symbols or terms to represent an allele but there are some general conventions which are commonly followed, particularly in Introductory Genetics. These conventions are covered here for those cases when there are just 2 alleles for a gene (multiple alleles are covered elsewhere).

Italics: Gene names and alleles are generally given in italics. This distinguishes them from gene products which are not italicized. The most important convention is that the use of the same letter, or name, indicates alleles of the same gene. Therefore, different letters or names refer to different genes not different alleles.

Common allele designation systems

A, a	An upper case and lower case letter are used when we know that one allele is dominant (and, by definition, the other is recessive). The upper case letter designates the dominant allele. Any letter can be used.
B₁, B₂ or B¹, B²	Subscripts or superscripts of the same letter indicate different alleles of the same gene. (A₁ and B₂ would indicate different genes) No information about dominance is conveyed by these symbols. As you might guess, this usage is easier to extend to cases when there are more than two alleles.
d⁺, d	The + is used to designate the wild type allele. Sometimes, just the + is used when the letter is obvious. The use of lower case indicates that the d allele is recessive to d⁺.
E⁺, E	This is similar to the a⁺, a case but the use of an upper case E indicates that E is dominant to the wild type E⁺.
fun¹, fun²	We can also use words, rather than just letters, to designate a gene. The same applications of superscripts and subscripts apply to the words. And, if we use fun and Fun then the second is the dominant allele (Upper case!).

Intro to Mendel

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