Each gene has both a unique name and a unique gene symbol that is usually shorter than the name and contains no spaces, allowing genotypes to be described in an unambiguous and manageable way. Both are italicized in print. In general, genes are named in one of three ways:

Genes may be named according to a mutant phenotype of the gene (generally the phenotype of the first mutant allele identified), e.g., white (w), Shaker (Sh), cubitus interruptus (ci). The name and symbol are capitalized if the phenotype of the mutant allele for which the gene was named is dominant to a wild-type allele. Be aware, however, that many nominally 'dominant genes' have recessive alleles and many 'recessive genes' have dominant alleles.

Genes may be named according to a category of phenotypic effect, such as suppressor, enhancer, lethal, sterile, along with identifying information relevant to the class (the name of the gene that is suppressed or enhanced, or the chromosomal location of lethals and steriles). For example: suppressor of forked (su(f)), Enhancer of Star (E(S)), lethal (3) 85Eb (l(3)85Eb), male sterile (2)LY1 (ms(2)LY1).

When the product of a gene is known, the gene is typically named according to the product encoded, with a chromosomal location or series number if part of a multigene family. For example: α-Tubulin at 67C (αTub67C), Superoxide dismutase 1 (Sod1), transfer RNA:Arginine-ACG 1-1 (tRNA:Arg-ACG-1-1). Superscripts identify individual mutant alleles of a gene: wa, l(2)40Fg1, AntpLC. On the BDSC website, superscripts are placed within square brackets [ ]. A "+" superscript indicates a wild-type allele of the gene. A "+" in place of a gene symbol indicates that the chromosome or the complete genotype, depending on the context, is wild type.

Chromosome aberrations are named according to the type of rearrangement, the chromosome or chromosomes involved, and an identifying symbol. The basic types of aberrations and their abbreviations are: deficiency (Df), duplication (Dp), inversion (In), transposition (Tp), translocation (T), compound (C), ring (R), levosynaptic element (LS) and dextrosynaptic element (DS). These are written as: Type(Chromosome)Identifier. The identifier may or may not convey information about the rearrangement. For example, Df(3R)by10 is the name of a deficiency in the right arm of the third chromosome; in this case the identifier reflects the inclusion of the blistery (by) gene within the deficiency and the 10 distinguishes it from others in a series. Superscripts, which define unique alleles, are not used with symbols of genes deleted by deficiencies (they are used only when the gene is interrupted, rather than removed, by the aberration). Df(3R)by10, Df(3R)by62, and Df(3R)by77 represent three unique deficiencies, but not unique alleles of by - the gene is equally absent in all three aberrations. T(2;3)apXa refers to a translocation between chromosomes 2 and 3; here the translocation is named for the mutant allele of the apterous gene that results from one of the translocation breakpoints. Tp(1;3)O4 names a three-break event that resulted in the insertion of a piece of chromosome 1 into chromosome 3. In this case the identifier, O4, is arbitrary, formed from the name of the person who recovered the aberration and a series number.

Balancers are an important class of aberration and one for which shorthand is commonly used. Lindsley and Zimm define a set of core balancer symbols that are commonly used to represent a particular set of aberrations and markers. The most popular balancers exist in a variety of marker combinations, all with at least one dominant visible marker. There are three different standard ways of representing balancer chromosomes:

Balancer symbol - A single symbol represents a unique set of aberrations and markers, e.g., TM3-Sb.

Balancer short genotype - A core balancer symbol is combined with aberration, transposon and allele symbols to describe a unique balancer variant,e.g., TM3, Sb1. This is the type of symbol used in BDSC genotypes.

Balancer full genotype - All aberration, transposon and allele symbols that comprise the unique balancer variant are explicitly stated, e.g., In(3LR)TM3, kniri-1 pp vvlsep l(3)89Aa1Sb1 Ubxbx-34ee1.

Transposon nomenclature has four basic parts: source of transposon ends, included genes, construct symbol, and insertion identifier. A transposon symbol is composed of ends{symbol}. A full transposon genotype adds the geneallele symbols of all visible marker genes, with the form ends{genes=symbol}. The symbol for a specific insertion of a given transposon has the form ends{symbol}identifier.

A properly assembled genotype represents all mutant components of the stock in the order 1;Y;2;3;4. Within a chromosome, aberrations precede gene symbols. A comma and space separate aberrations from gene symbols and genes are listed in the left-right order of the unrearranged chromosome. Gene symbols are separated by a space. Homologues are separated by a solidus (/) and heterologous chromosomes are separated by a semicolon. Homozygous chromosomes are defined only once: cn bw implies cn bw/cn bw, and + implies +/+. For example:

cv1; sp1; Diap1 - The stock is homozygous for three recessive mutations, crossveinless 1 on chromosome 1, speck 1 on 2, and Death-associated inhibitor of apoptosis 1 on 3.

In(1)dl-49+BM1, sc1vOf - This stock is homozygous for two inversions on the X, delta-49 and Bar of Muller, and two recessive mutations, scute 1 and vermillion Of.

Df(3L)Ar14-8, red1/TM2, emc2ppUbx1es - The stock is heterozygous for a deficiency on the left arm of chromosome 3. The deficiency chromosome also carries a mutation in the red gene. Adults will express the recessive emc phenotype as well as the dominant Ubx phenotype because emc is deleted in Df(3L)Ar14-8 and the balancer carries a mutant allele of emc in addition to the standard TM2 markers pink peach, Ultrabithorax 1, and ebony sooty.

T(2;3)CyO-TM6, CyO: TM6/pr1cn1AdhUF; mwh1ry506e1 - A translocation is superimposed on two balancer chromosomes, CyO and TM6. The normal sequence homologues carry mutations in the 2nd chromosome genes purple, cinnabar and Alcohol dehydrogenase and the 3rd chromosome genes multiple wing hair, rosy and ebony.

y1w1118 P{ry+t7.2=hsFLP}1; TM3ryRKSb1Ser1/TM6BryCBTb1ca1 - This stock carries mutant alleles of yellow and white on the X as well as a P element transposon that is marked with a functionally wild-type allele of the rosy gene. The transposon also carries an allele that expresses the yeast FLP gene, but in most cases only visible markers are shown in transposon genotypes. You will need to look up the transposon in FlyBase to find the complete genotype of the construct. The symbol for this specific construct is P{hsFLP}, and the identifier for this particular insertion of the P{hsFLP} construct is 1. Both balancers carry loss-of-function rosy mutations in addition to other markers.

The rules for designating autosomal homologues can't be strictly applied to sex chromosomes. Sometimes the genotypes of both sexes are explicitly defined, using the form X/X x X/Y or X/X & X/Y. More often a condensed notation is used and it is left to the user to apply the rules of segregation and sex determination to identify the genotype of each sex. For example, compound 1st, or attached-X, chromosomes are commonly used to create balanced stocks of X-linked female sterile mutations. In a stock of the female sterile mutation Mycdiminutive 1, the genotypes of males and females are Mycdm-1/Y and C(1)DX/Y, respectively, but the stock genotype is usually written as Mycdm-1/C(1)DX. The latter seems to imply a stock of triplo-X flies, but triplo-X metafemales have extremely low viability and survivors are sterile. The only interpretation consistent with the biology is that females carry a maternally inherited compound X, males carry a paternally inherited Mycdm-1 X, and both sexes carry a wild-type Y chromosome inherited from the opposite sex.