The bay gene is often marked as capital A (a for agouti) for the dominant bay allele and lower case a for the recessive non-bay allele. The bay gene modifies production of black pigment (eumelanin) restricting black in some areas causing the bay pattern. Only black pigment is modified leaving the red pigment pheomelanin to show through.
ASIPA the allele that causes bay and ASIPa the turned off version that causes a fully black horse are the only documented mutations of ASIP. However there is evidence to support that some bay horses may have slightly different alleles of the bay gene. Wild bay ASIP+ is proposed to be a very dominant and aggressive mutation of the ASIPA allele causing heavily reduced black points. Brown ASIPt is proposed to be a very recessive mutation of the ASIPA allele causing heavy black areas to remain on the body. This is supported by evidence from other species that have similar documented ASIP alleles.
Order of Dominance
Each ASIP allele removes a certain amount of black pigment. ASIP can only remove pigment not add it, so alleles that remove more pigment are more dominant then those that remove less. These more aggressive and dominate alleles mask less dominant ones.
ASIP+ (wild bay) always masks other versions of ASIP
ASIPA (classic bay) masks everything but ASIP+
ASIPt (brown) is masked by ASIPA and ASIP+
ASIPa (black) is masked by all other ASIP alleles.
Official abbreviated name is ASIP
Proper full name is agouti signaling protein
ASIPa (black) Identified by only black hairs over the whole body. No lighter hairs on the mane, flanks etc.
ASIPA (classic bay) Identified by a warm red tone over the whole body with clear black legs. Can have darker shading along the top line but not as clear as in ASIPt horses.
ASIPt (brown) Identified by darker then normal coloring, particularly along the neck, shoulders and haunches. Can range from rich bay to nearly black.
ASIP+ (wild bay). Identified by limited black on the legs and a more washed out over all body color.