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- eumelanin - the browning gene B/b/bl codes for TYRP1 (Q4VNX8), an enzyme involved in the metabolic pathway for eumelanin pigment production. Its dominant form, B, will produce black eumelanin. It has two recessive variants, b (chocolate) and bl (cinnamon), with bl being recessive to both B and b.
- phaeomelanin - the sex-linked red "Orange" locus, O/o; it determines whether a cat will produce eumelanin. In cats with orange fur, phaeomelanin (red pigment) completely replaces eumelanin (black or brown pigment). This gene is located on the X chromosome. The orange allele is O, and is codominant with non-orange, o. Males can typically only be orange or non-orange due to only having one X chromosome. Since females have two X chromosomes, they have two alleles of this gene. OO results in orange fur, oo results in fur without any orange (black, brown, etc.), and Oo results in a tortoiseshell cat, in which some parts of the fur are orange and others areas non-orange.
- dilution - the Dense pigment gene, D/d, codes for melanophilin (MLPH; A0SJ36), a protein involved in the transportation and deposition of pigment into a growing hair. When a cat has two of the recessive d alleles (Maltese dilution), black fur becomes "blue" (appearing grey), chocolate fur becomes "lilac" (appearing light, almost greyish brown-lavender), cinnamon fur becomes "fawn", and red fur becomes "cream".Similar to red cats, all cream cats are tabbies. The d allele is a single-base deletion that truncates the protein. If the cat has d/d genes, the coat is diluted. If the genes are D/D or D/d, the coat will be unaffected.
- Barrington Brown - it's a recessive browning gene that dilutes black to mahogany, brown to light brown and chocolate to pale coffee. It is different from the browning gene and has only been observed in laboratory cats.
- the Dilution modifier gene - Dm, "caramelizes" the dilute colours as a dominant trait. The existence of this phenomenon as a discrete gene is a controversial subject among feline enthusiasts.
- amber - a mutation at the extension locus E/e (the melanocortin 1 receptor, MC1R) changes black pigment to amber or light amber, similar in appearance to red and cream. Kittens are born dark but lighten up as they age. The paws and nose still exhibit the original undiluted colour, in contrast to other diluted colours, where the paws and nose have the diluted colour. This phenomenon was first identified in Norwegian Forest cats.
- Another recessive mutation at extension was discovered which causes the russet colour in Burmese cats. It is symbolized as er. Like amber cats, russet cats lighten as they age.
- agouti gene - determines if the cat is a tabby or not. The agouti gene, with its dominant A allele and recessive a allele, controls the coding for agouti signalling protein (ASIP; Q865F0). The wild-type A produces the agouti shift phenomenon, which causes hairs to be banded with black and an orangish/reddish brown, revealing the underlying tabby pattern (which is determined by the T alleles at the separate tabby gene). The non-agouti or "hyper melanistic" allele, a, does not initiate this shift in the pigmentation pathway and so homozygotes aa have pigment production throughout the entire growth cycle of the hair—along its full length. As a result, the non-agouti genotype (aa) is solid and has no obvious tabby pattern (sometimes a suggestion of the underlying pattern, called "ghost striping", can be seen, especially in bright slanted light on kittens and on the legs, tail and sometimes elsewhere on adults). Agouti is found on chromosome A3.
- tortoiseshells - they have patches of orange fur (pheomelanin-based) and black or brown (eumelanin-based) fur, caused by X-inactivation. Because this requires two X chromosomes, the vast majority of tortoiseshells are female, with approximately 1 in 3,000 being male. Tortoiseshells with a relatively small amount of white spotting are known as "tortoiseshell and white", while those with a larger amount are known in the United States as calicos. The basic tortoiseshell pattern has several different colours depending on the colour of the eumelanin (the B locus), and dilution (the D locus).
- tortoiseshell tabbies, also known as torbies, display tabby patterning on both red- and black-based colours. Calico tabbies are also called calibys or tabicos.
- the KIT gene - determines whether or not there will be any white in the coat, except when a solid white coat is caused by albinism.
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