Phenotypes are sometimes denoted by cognate symbols in roman type and by the superscripts + and -. For example, the independence and requirement for arginine can be denoted by Arg⁺ and Arg^-, respectively. Proteins encoded by ARG2, for example, can be denoted Arg2p, or simply Arg2 protein. However, gene symbols are generally used as adjectives for other nouns, for example, ARG2 mRNA, ARG2 strains, etc.

Although superscript letters should be avoided, it is sometimes expedient to distinguish genes conferring resistance and sensitivity by superscript R and S, respectively. For example, the genes controlling resistance to canavanine sulphate (can1) and copper sulphate (CUP1) and their sensitive alleles could be denoted, respectively, as can^R1, CUP^R1, CAN^S1, and cup^S1.

Dominant and recessive suppressors should be denoted, respectively, by three uppercase or three lowercase letters, followed by a locus designation, e.g., SUP4, SUF1, sup35, suf11, etc. In some instances UAA ochre suppressors and UAG amber suppressors are further designated, respectively, o and a following the locus. For example, SUP4-o refers to suppressors of the SUP4 locus that insert tyrosine residues at UAA sites; SUP4-a refers to suppressors of the same SUP4 locus that insert tyrosine residues at UAG sites. The corresponding wild-type locus that encodes the normal tyrosine tRNA and that lacks suppressor activity can be referred to as sup4⁺. Intragenic mutations that inactivate suppressors can denoted, for example, sup4^- or sup4-o-1. Frameshift suppressors are denoted as suf (or SUF), whereas metabolic suppressors are denoted with a variety of specialized symbols, such as ssn (suppressor of snf1), srn (suppressor of rna1-1), and suh (suppressor of his2-1)

Capital letters are also used to designate certain DNA segments whose locations have been determined by a combination of recombinant DNA techniques and classical mapping procedures, e.g., RDN1, the segment encoding ribosomal RNA.

The general form YCRXXw is now used to designate genes uncovered by systematically sequencing the yeast genome, where Y designates yeast; C (or A, B, etc.) designates the chromosome III (or I, II, etc.); R (or L) designates the right (or left) arm of the chromosome; XX designates the relative position of the start of the open-reading frame from the centromere; and w (or c) designates the Watson (or Crick) strand. For example, YCR5c denotes CIT2, a previously known but unmapped gene situated on the right arm of chromosome III, fifth open reading-frame from the centromere on the Crick strand.

E. coli genes inserted into yeast are usually denoted by the prokaryotic nomenclature, e. g., lacZ.

A list of gene symbols are tabulated in the book edited by Wheals et al. (1995), whereas a current list can be found in the Internet file
ftp://genome-ftp.stanford.edu/pub/yeast/gene_registry/registry.genenames.tab

Special consideration should be made of the nomenclature describing mutations of mitochondrial components and function that are determined by both nuclear and mitochondrial DNA genes. The growth on media containing nonfermentable substrates (Nfs) as the sole energy and carbon source (such as glycerol or ethanol) is the most convenient operational procedure for testing mitochondrial function. Lack of growth on nonfermentable media (Nfs^- mutants), as well as other mitochondrial alterations, can be due to either nuclear or mitochondrial mutations as outlined in Table 3. Nfs^- nuclear mutations are generally denote by the symbol pet; however, more specific designations have been used instead of pet when the gene products were known, such as cox4, hem1, etc.

The complexity of nomenclatures for mitochondrial DNA genes, outlined in Table 6.2, is due in part to complexity of the system, polymorphic differences of mitochondrial DNA, complementation between exon and intron mutations, the presence of intron-encoded maturases, diversed phenotypes of mutations within the same gene, and the lack of agreement between various workers. Unfortunately, the nomenclature for most mitochondrial mutations do not follow the rules outline for nuclear mutations. Furthermore, confusion can occur between phenotypic designations, mutant isolation number, allelic designations, loci, and cistrons (complementation groups).