Genes
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, Minute, 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 Minutes, lethals and steriles). For example: suppressor of forked (su(f)), Enhancer of Star (E(S)), Minute (1)15D (M(1)15D), lethal (3)85Ea (l(3)85Ea), male sterile (2)1 (ms(2)1).

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: -Tubulin (3)67C (Tub67C), Superoxide dismutase (Sod), transfer RNA arginine (tRNA-Arg1). Superscripts identify individual mutant alleles of a gene: w^a, l(2)40Fg¹, Antp^LC. 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.

Aberrations
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)ap^Xa 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, Sb[1]

Balancer full genotype

All aberration, transposon and allele symbols that comprise the unique balancer variant are explicitly stated

e.g., In(3LR)TM3, kni^ri-1 p^p sep¹ l(3)89Aa¹ Sb¹ Ubx^bx-34e e¹

Transposon insertions
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 gene^allele symbols of all included genes, with the form ends{genes=symbol}. The symbol for a specific insertion of a given transposon has the form ends{symbol}identifier.

Genotypes
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 heterologues are separated by a semicolon. Homozygous chromosomes are defined only once: cn bw implies cn bw/cn bw, and + implies +/+.

For example:

cv¹; sp¹; th¹

The stock is homozygous for three recessive mutations, crossveinless 1 on chromosome 1, speck 1 on 2, and thread 1 on 3.

In(1)dl-49+B^M1, sc¹ v^Of

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)emc5, red¹ /TM2, emc² p^p Ubx¹ e^s

The stock is heterozygous for a deficiency on the left arm of chromosome 3 that includes the extra macrochaetae gene. 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 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)CyOTM6, CyO: TM6/pr¹ cn¹ Adh^ufs; mwh¹ ry⁵⁰⁶ e¹

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.

y¹ w¹¹¹⁸ P{ry^+t7.2=hsFLP}1; TM3, ry^RK Sb¹ Ser¹/TM6B, ry^CB Tb¹ ca¹

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 athe 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 hsFLP, and the identifier for this particular insertion of the 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 diminutive 1, the genotypes of males and females are dm¹/Y and C(1)DX/Y, respectively, but the stock genotype is usually written as dm¹/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 dm¹ X, and both sexes carry a wild-type Y chromosome inherited from the opposite sex.