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Genetic Alleles
Some basic vocabulary:
allele-a variety of a gene, either dominant or recessive in its simplest expression. Usually, dominant genes are indicated by a capital letter; recessive genes are indicated by a lower case letter, unless the abbreviation for the gene is more complex or would be duplicated by more than one gene.
homozygous-every horse has two copies of each gene. Homozygous means both are identical, AA for example.
heterozygous-This means having two different alleles of the gene, aA for example.

Here is a sample gene test from one of my horses, http://www.huntandjump.com/horse.php?horseid=2106164.
EE AA CC dd gg Ff SstySsty pP zz chch SaSa | KitKit SpSp PAX3+PAX3+ VVrn LL rbrb OO IiIi WF: Light PATN: Light

EE--his base gene coat color is black. ee would give a red coat color. E is dominant and any horse with at least one E will be referred to as black-based and be black, depending on other modifying genes. Horses with at least one dominant E and one dominant A (see next gene) are called bay-based.

AA--this is the agouti gene that makes bay horses by pushing the black pigment into the main, tail, and lower legs. So the horse with this test result is bay. Even with the dominant A gene present, a horse without the black E gene will not be bay because there is no black pigment in its coat.
There are now four alleles of agouti in the game.
A+ is Wild Bay, the most dominant allele. It pushes the black points lower down the legs and lightens coat and mane, like this horse: http://www.huntandjump.com/horse.php?horseid=2850414
A is normal bay. Any horse with at least one E and one A will be a normal bay, unless it has an A+.
At makes brown horses when is is homozygous or combined with recessive a. Heterozygous brown horses (Ata) are a darker brown than homozygous brown horses (AtAt). A horse that tests AtA will be a bay because the brown allele At is recessive to normal bay and wild bay.
a is the recessive form of agouti. A horse that tests aa will always be black if it has dominant E or chestnut if it does not, depending on what dilution genes it carries.

CC--this is the inactive Cream gene. It also has several varieties. Active Cream acts on red pigment to lighten the coat, mane and tail. It does not affect black pigment unless it is homozygous. Since the model horse is homozygous for inactive cream, he is bay, not buckskin.
Ccr stands for the active cream allele. It creates palomino horses out of chestnut ones, when heterozygous, buckskin horses out of bays, and smokey black horses out of blacks (there is no visible effect on the coat color in this case).
CcrCcr is homozygous cream. It lightens red-based coats even further and gives blue eyes. This produces cremello horses from chestnuts, perlino horse from bays, and smokey creams from blacks.
Cprl is the pearl variant of this gene. It also lightens coats in a slightly different way. This is the most recessive allele of the cream gene. It will be seen when it is homozygous, hidden when it is not.

dd--this is the dun gene. The dominant form D lightens the coat except for the points. It causes a dark dorsal stripe and zebra stripes on the legs. It produces red duns on chestnut, bay duns on bay, and grullos on black. The sample horse is recessive and therefor not dun.

gg--this is the gray gene. The dominant form G causes an increasing amount of white hairs to mix with base coat as the horse ages, until it all or nearly all the hair is white. Gray overrides any other color so the color name of a horse with G is always simply "gray" regardless of what its base color is otherwise. The sample horse is gg so not gray.

Ff--this is the flaxen gene. It only shows on red based horses. The recessive ff causes manes and tails to be flaxen, that is cream colored. Red based horses with dominant F will have manes and tails about the same color as their bodies. The sample horse is not ee, so this gene has no effect.

SstySsty--This is the sooty gene; Its dominant form affects all colors whether it is homozygous or heterozygous. It causes darkening of the coat from top to bottom. The sample horse is homozygous for sooty. The recessive allele is indicated by S, so a heterozygous sooty horse would be SstyS.
In the game we have an additional sooty allele, S+, or sooty plus. It causes additional dappled dark markings on all colors, although it is less noticeable on blacks. This horse is palomino sooty+. http://www.huntandjump.com/horse.php?horseid=1916650

pP--This is the pangare gene. When at least one dominant allele is present, it lightens the coat around the eyes, behind the legs, and gives a mealy muzzle on red and bay based horses.

zz--This is the silver gene. When at least one copy of the dominant allele is present, it lightens black pigment in both the coat and the mane and tail. Thus it creates black, bay, and buckskin horses with silvery manes and tails. Chestnut horses can carry and pass down dominant silver, even though it will not show up on them.

chch--This is the champagne gene. The sample horse does not carry champagne. With at least one copy of the dominant allele (Ch), it lightens the coat, gives a spotted muzzle and amber eyes to all base coat colors. Chestnuts carrying champagne are called gold champagnes, bays are amber champagnes, blacks are classic champagnes, browns are sable champagnes.

SaSa--This is the satin gene. Like flaxen, it only expresses when it is homozygous recessive (sasa). It is a game gene created to represent the metallic shimmer seen in Akhal Teke horses or their descendents. It is extremely rare. http://www.huntandjump.com/horse.php?horseid=2282147

Ok! Thank you so much for your help!