Remembering that there is a specific order in which all colour genotypes are written [See the above linked page for more info on the genotype order]...
When the genetic shorthand for the Extension Gene and Agouti Gene is written, they are always written before the other genes in the genotype due to their being the initial phase in determing horse colour. Some prefer to write the Agouti Alleles prior to the Extension, and some prefer the Extension to be written first, however, they will/should be written at the beginning of the genotype as the interaction of the Extension and Agouti Genes is the most important process in the genotype. [I personally prefer to write the Extension first & Agouti second, and have done so throughout this site. This is simply a personal preference, each to their own.] The Extension and Agouti Genes determine the Base Colour and are the initial Building Blocks used to determine the end colour result [when the end colour is not one of the three Bases]. The Extension Locus/Gene, followed by the Agouti Locus/Gene, or vice versa, are always written at the beginning of the genotype, irrespective of whether there are additional genes modifying the end colour.
[The one exception to the Extension Gene and the Agouti Gene being the first & second rule is when the Grey Gene is accounted for in the written genotype. This is essentially due to the Grey Genes' dominance over all other genes. When the Grey Gene is accounted for [whether the horse is grey or not] it is written first, moving the Extension to second and the Agouti to third - More information on the Grey Gene can be found on the Grey Gene Page.]

A Chestnut horse's written genotype would therefore look like this: [EeEe, A-A-] with the hyphens representing the two Agouti Alleles that cannot be determined solely by phenotype of the horse due to the horse being chestnut [Agouti Gene instructions overridden due to no black pigment production].
A Bay horses' written genotype would look like: [EEE-, A-A-] with the hyphens again representing the unknown alleles not seen in the phenotype.
A Black horses' written genotype would look like: [EEE-, AaAa], with the underscore once again representing the unknown.
(Note that these examples are the simplest versions of written genotype. The above results can be determined purely by looking at a horses' phenotype alone. Further assessment of the individual, the sire and dam, siblings, progeny produced and extended family members provides the additional information required to fill in many, if not all, of the blanks. In doing so, it is quite possible to predict the colour outcomes of future breedings of that individual. Further information on how to determine the genotype of individuals as well as predicting progeny inheritance will be added to this site soon.)

Below is a list of the possible allelic combinations resultant of the interaction at the Extension Gene and Agouti Gene Loci. Every horses' genotype will begin with one of these following allele combinations - If the horse is not one of the three Base Colours, then the horse possesses alleles at consecutive gene loci that have modified that individuals' Base Colour to give the resultant outcome colour seen in the phenotype of the horse.

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The Base Colours

The Base Colours' Rules of Genetic Inheritance

Black Rules of Genetic Inheritance
* Heterozygous Extension Blacks can produce Chestnut, Bay and Black Based progeny
[EEEe, AaAa] x [E-Ee, A-A-] > [EeEe, A-A-] // [EEEe, AaAa] x [EEE-, AAA-] > [EEE-, AAAa] // [EEEe, AaAa] x [EEE-, AaAa] > [EEE-, AaAa]

* Black x Black does not necessarily produce Black progeny - To guarantee Black progeny when breeding Black x Black both parents must also be Homozygous Dominant Extension as well as Homozygous Recessive Agouti.
[EEEE, AaAa] x [EEEE, AaAa] = [EEEE, AaAa]

 

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The Extension Gene

All horses, no matter their final colour, are one of three Base Colours - Chestnut, Bay or Black. These three colours are the fundamental foundation of all horse colours. If the final colour of a horse is not visibly identifiable as Chestnut, Bay or Black, then the horse has what are termed "Modifying" gene/s which act, or 'build' upon the original Base Colour to achieve the final colour outcome we see in the phenotype of the horse.
The Genes that control the expression of the three bases are called the Extension Gene and the Agouti Gene. Understanding the interaction of these two genes is essential in order to understand how all other colours are achieved. They are the trickiest to master of all genes - But once the interactions of the Extension and Agouti Genes are grasped it becomes easier to understand how all horse colours are built upon from the three base colours.

The Extension Gene & The Agouti Gene

The Extension Gene appears at the Extension Locus. It controls the production of eumelanin, the black pigment of the hair shaft.
Ie - The Extension Gene controls whether or not the horse has black hair. The shorthand abbreviation for the Extension Locus is an uppercase 'E' - [E-].
The Dominant Extension Allele is represented by an uppercase letter 'E' - [EE]. The Dominant Extension Allele is the wild type allele occurring at the Extension Locus and so is sometimes respresented by a + symbol instead of an uppercase 'E'. [E+] is the wild type allele respresentation.
The Recessive Extension Allele is represented by a lower case letter [Ee]. There is a recently discovered third colour variation present at the Extension Locus, that has been named Dominant Black. The Dominant Black Extension Allele is respresented by an uppercase 'D' - [ED]

The Agouti Gene

The Agouti Gene appears at the Agouti Locus. It controls the distrubution of eumelanin, the black pigment coverage over the body, on those horses that are capable of producing eumelanin. Ie - The Agouti Gene controls where a horse with black hair has black hair.
The shorthand abbreviation for the Agouti Locus is an uppercase 'A' - [A-].
The Dominant Agouti Allele is represented by an upper case letter 'A' - [AA]. The Recessive Agouti Allele is represented by the lower case letter 'a' - [Aa].
The wild type allele occurring at the Agouti Locus is a third variant possible at this locus. The Wild Type Agouti Allele is represented by a + symbol - [A+]

The Extension & Agouti Loci Instructions

The process that determines a horses' colour is easiest to understand when viewed as a series of building blocks. Each gene locus is a single building block, with each gene representing a switch that enables or disables a specific instruction depending on whether the switch is on [enabled] or off [disabled]. In the 'off' position, the specified gene consists of two recessive alleles, and the purpose of the gene - The instruction contained within - Is effectively bypassed. In the 'on' position, the gene has at least one dominant allele and the specific instruction contained within that gene is enabled.

The third colour options, or variations, mentioned above - the Dominant Black Extension Allele and the Wild Type Agouti Allele are both relatively rare and have been proven to exist only in limited breeds. I have therefore excluded these two alleles from the basic Extension and Agouti Locus 'Building Blocks' and have discussed them in detail further down the page.

The Extension Gene Building Block

The process that occurs at the Extension Gene is the first building block for a horses' colour.
All of the Base Colours are made up of either pheomelanin [red pigmentation] and/or eumelanin [black pigmentation].
The process of determining a horses' colour begins with the Pheomelanin - Red Pigmentation
A horse with Pheomelanin only is the colour we know as Chestnut.
{See the sections under Pigment Production on the Introduction Page for more information on the above.}

The initial phase of the first Building Block for colour is the instruction contained at the Extension Locus. The Extension Locus instruction is "Produce Eumelanin" or "Produce Black Pigmentation" and this instruction is either on or off, depending on the alleles that form the gene.

When the Extension Gene "switch" is in the OFF position there are two recessive alleles located at the Extension Locus - [EeEe] - and the horse can produce only pheomelanin as the instruction of "Produce Black Pigmentation" located at the Extension Locus is bypassed.
The horse has two recessive extension alleles, therefore it is Homozygous Recessive Extension, and the Base Colour is Chestnut.

When the Extension Gene switch is in the ON position, the horse has at least one dominant allele at the Extension Locus - [EEEe] or [EEEE] and the instruction "Produce Eumelanin" is enabled - Resulting in a horse that IS NOT Chestnut as it will produce black pigmentation.
The horse has either A) One dominant extension allele, and therefore is Heterozygous Extension [EEEe], OR, B) Has two dominant extension alleles, and therefore is Homozygous Dominant Extension [EEEE] - In either case, the Base Colour is not Chestnut as it will have black pigmentation and therefore will be Bay or Black. Once the Extension Gene switch is on, and the horse is able to produce eumelanin, the instruction contained at the Agouti Locus is seen in the phenotype of the horse.

The Agouti Gene Building Block

The Agouti Gene can be viewed as the "switch" for the distribution of eumelanin. If the Extension Locus is "switched on", and the production of eumelanin [black pigment] instruction at the Extension Locus is enabled, the Agouti Locus instruction is then responsible for where black pigment can develop.
While all horses carry an Agouti genotype, it will only be expressed in the phenotype of the horse if the Extension Gene switch has been enabled.
The Agouti Gene cannot be visibly determined on a Chestnut based horse due to the instruction of the Agouti Locus pertaining only to eumelanin.

The second phase of the first Building Block for colour is the instruction contained at the Agouti Locus. If the Extension Locus instruction is ON then this second phase instruction will be visible in the horses' phenotype.
The Agouti Locus Instruction can be viewed as - "Restrict Eumelanin Production" OR "Restrict Black Pigment Production".

When the Agouti Locus switch is in the OFF position, there are two recessive alleles at the Agouti Locus - [AaAa] - and there is no restriction placed on the production of eumelanin, and so black pigmentation extends throughout all hair shafts, resulting in the Base Colour Black.

When the Agouti Locus switch is in the ON position, there is one [AAAa] or two [AAAA] dominant alleles and the instruction "Restrict Black Pigmentation Production" is enabled. The production of Black pigment is subsequently restricted to the points of the horse only, leaving the pheomelanin [red] pigmentation that we originally started with throughout the body area of the horse - Resulting in the Base Colour Bay.

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The Extension Gene & Agouti Gene Written Sequence & Abbreviations

See the Genetic Shorthand page for further information on the following section.

Which brings us to the genetic inheritance of the three Base Colours. Remembering that all gene pairs are inherited from the parents, one allele from each gene being inherited from each parent, you should immediately see, from the list above, that there are some 100% inheritance possibilities in regards to the Base Colours. There are rules that apply in circumstances where only the specific genotype of one parent is taken into account, and other circumstances where the genotype of both parents are taken into account.
It should be noted that these rules apply to all horses' because all colours are derived from the Base Colours - Even those carrying additional modifying genes have certain rules that apply to their Base Colours, and therefore rules that apply to their progenys' inheritance of such.

Chestnut Rules of Genetic Inheritance

* It is genetically impossible for Chestnut x Chestnut to produce anything other than Chestnut as there is no alternative but for the progeny to inherit two recessive alleles at the extension locus - Chestnut x Chestnut = Chestnut - [EeEe, A-A-] x [EeEe, A-A-] = [EeEe, A-A-]

* All Progeny of Chestnut is able to produce Chestnut - [EeEe, A-A- ] > [E-Ee, A-A-]

* All Chestnuts are capable of producing non Chestnut [Bay & possibly Black in some cases] progeny when bred to a NON Chestnut.
[EeEe, AAAa] x [EEEe, AAAa] > [EEEe, AAAa]

Bay Rules of Genetic Inheritance

*A Heterozygous Extension Bay [EEEe, AAA-] can produce Chestnut progeny.
[EEEe, AAAa] > [EeEe, AAA-] or [EeEe, A-Aa] // [EEEe, AAAA] > [EeEe, AAA-]

* Bay x Bay can produce Chestnut progeny.
[EEEe, AAAa] x [EEEe, AAAa] > [EeEe, AAAa]

* Homozygous Dominant Extension Bays [EEEE, AAAa] cannot produce Chestnut progeny - Regardless of the colour of the other parent.
[EEEE, AAAa] > [EEE-, AAA-] or [EEE-, A-Aa] // [EEEE, AAAA] > [EEE-, AAA-]

* Homozygous Dominant Agouti Bays cannot produce Black progeny - Regardless of the colour of other parent.
[EEEe, AAAA] > [E-E-, AAA-] // [EEEE, AAAA] > [EEE-, AAA-]

* A Bay Homozygous Dominant at both the Extension and Agouti loci [EEEE, AAAA] will always produce Bay progeny - Regardless of the colour of the other parent.
[EEEE, AAAA] > [EEE-, AAA-]

Black Rules of Genetic Inheritance

See the Genetic Shorthand page for further information on the following section.

So what comes next? At this stage you should be asking just how the infinite number of different shades, tones and highlights of the three basic Base Colours are achieved - How is Liver Chestnut genetically different to Flaxen Chestnut? What about the rare Wild Bay & the more common Bright Bay?
The answer to each of those questions is quite different, but similar in that they have similar genetic processes behind them.
The following two genetic groups are only mentioned briefly here as each are discussed in detail on their relevant pages within this site.

 

The different shades and tones of the Base Colours are the result of what are termed "Basic Modifying Genes". It is technically correct that all colours other than the three Bases are the result of additional genes [ie. Building Blocks"] whose instructions are essentially to modify, in some way and to a certain degree, the Base Colour of a horse. However, these genes modify the Base Colours to the extent that the end result is a completely different colour, with a more complicated genetic process, and susequently, a different name - Such as Base Colour Chestnut + Single Cream Dilution Gene = Palomino. Whereas the genes that are commonly known [and I refer to throughout this site] as the "Basic Modifying Genes" are those that alter the Base Colours to a limited, certain degree only, that result in a change of shade or a certain characteristic of a Base Colour, that will result in a more descriptive name but not a complete change in name - Such as Base Colour Chestnut + Flaxen Gene = Flaxen Chestnut. To assist with differentiating between the two, I refer to the latter group of 'Basic Modifying Genes' as the "Basic Modifying Factors" and reserve "Modifying Genes" for the former group.
There are a number of Basic Modifying Factors, and while the genetic processes behind all of them are not yet fully understood, I have set up a page to cover those we do know about HERE.

The Extension Locus controls the Production of Eumelanin - Whether the Hair Shaft has Black Pigmentation

The Agouti Locus controls the Distribution of Eumelanin - Where the Black Pigmented Hairs are able to develop

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All Colours are built upon from the first Building Block - Pheomelanin - Red Pigmentation - The Colour Chestnut

Other Base Colour Variants

Dominant Black Extension Allele

Basic Colours

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The Genetic Processes of the Extension & Agouti Loci

A rare allelic mutation only recently discovered is "Dominant Black" occurring at the Extension Locus.
Dominant Black Extension results in a completely Black, or almost Black [Ie. Brown], horse regardless of the Agouti genotype.
The Dominant Black Allele at the Extension Locus is represented by an uppercase 'D' - [ED]
While this allele has been proven to exist in the Arabian breed, it is said to be present though extremely rare in other breeds - But - As the Arabian breed has been used to improve other breeds for centuries, and there are several now recognized breeds derived from the Purebred Arabian, it only stands to reason that the Dominant Black genotype has been inherited by the breeds improved by, and derived from, the Purebred Arabian.

Once again, the easiest way to understand the genetic process of the Dominant Black Extension Allele is to view the Extension Gene as a "switch" that, when in the on position, enables the production of eumelanin, and disables the production of eumelanin in the off position.
With the Dominant Black Allele included along with the regular Dominant Extension Allele [eumelanin switch on] and Recessive Extension Allele [eumelanin switch off] discussed above, we then have a three-way switch, with the third option, the Dominant Black Allele, being the "locked on" switch.
The result is that the Extension Gene is geared for the production of eumelanin regardless of the Agouti genotype [See Genetic Processes section below].

The Dominant Black Allele is dominant over the Dominant Extension Allele, which in turn is dominant over the Recessive Extension Allele - Meaning that if a horse has a genotype with a Dominant Black Allele, then this is what will be expressed in the phenotype regardless of whether the counterpart allele is a Dominant Extension or a Recessive Extension. Dominant Black is also epistatic to Agouti, much the same as Recessive Extension is epistatic to Agouti - Meaning that a horse with the genotype for Dominant Black will not express their Agouti genotype in their phenotype, as is the case with Chestnut.

Wild Type Agouti Allele

As with the Extension Locus, there is also a third alternative allele at the Agouti Locus in some breeds of horse - the "Wild Type" Allele occurring at the Agouti Locus. Other names commonly used for this allele are "Wild Type Agouti" and/or "Wild Bay". It is respresented by a + symbol - [A+].
This third allele is also proven to exist in the Arabian breed, and is thought to be present in some other breeds, mainly those also with an Arabian heritage.
Wild Type Agouti is also considered to be rare in most of the breeds it exists in - Though it is not held to be as uncommon as the Dominant Black genotype.

The Wild Type Allele that occurs at the Agouti Locus is the primitive subtype of the colour we know as Bay. It is the original, primitive counterpart to the more common Bay colouring [though the evolution of true wild breeds saw most of them further modify their colour to their final, generally pale, colours].
Genetically, the Wild Type Agouti Allele operates in much the same way as the Dominant Agouti Allele, though to a more excessive degree. Where the Dominant Agouti Allele instruction is "Restrict Black Pigment", the Wild Type Agouti Alleles' instruction can be viewed as "Restrict Black Pigment further".
The Agouti Locus/Gene becomes a three-way switch with the instruction of "Restrict Black Pigment Production" now having the three options of "OFF" for the Recessive Agouti Allele, "ON COMMON" for the Dominant Agouti Allele, and "ON WILD" for the Wild Type Agouti Allele".
The result of the Wild Type Agouti instruction of

The Wild Type Agouti Allele is dominant to the Dominant Agouti Allele, which in turn is Dominant to the Recessive Agouti Allele - Meaning that an individual with a Wild Type Agouti Allele in thier genotype will express the Wild Bay colouring in their phenotype rather than/over the more common Bay colouring. An individual that displays the more common Bay colouring does not possess a Wild Type Agouti Allele or genotype. There is a distinct difference between the common Bay and Wild Bays, so much so that some countries, mostly those prolific with wild breeds, have separate names for the two colours.

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"Royal Court Satin"
Purebred Arabian Mare
Owned By Chetar Arabians.

Note the restricted black pigment on the lower legs, with interspersed black & red pigmented hairs, the lack of black pigment on the head & the reddish & 'not quite black' tinge to mane & tail

Photo: WILD BAY

Following on from the Pigment Production Section - Pigment Cell Function
Remembering that the surface receptor, and whether its' activated or not, determine whether melanocytes place pheomelanin or eumelanin in the cells, and that there are multiple ways in which the surface receptor and the melanocyte-stimulating hormone are manipulated by the genotype...

The Extension Locus is the first "switch" that manipulates the surface receptor. The Agouti Locus represents the second "switch" also able to manipulate the receptor. The Agouti Locus affect on the receptor, however, is external to the cell, whilst the Extension Locus is internal to the cell - The main result of this is that the Extension Locus affect is dominant to the Agouti Locus affect.

The Extension Gene in Homozygous Recessive Alleles [EeEe] results in a mutation of the receptor, leaving it completely inactive, and unable to respond to the presence of melanocyte-stimulating hormone, and thus causing the uninhibited production of pheomelanin, resulting in a Chestnut horse.
The Extension Gene in Heterozygous [EEEe] or Homozygous Dominant [EEEE] Allelic form causes a normal receptor able to react to the presence of the hormone, and thus able to produce eumelanin. The subsequent colour [Bay or Black as the melanocytes are able to produce eumelanin] is then determined at the Agouti Locus. The third option at the Extension Locus of Dominant Black [EDE-] causes the surface receptor to lock in the ON position, resulting in a completely eumelanic [black] phenotype. Because this locked on position is internal, the eumelanin production overrides the Agouti Locus.

The Agouti Locus works to block the surface receptor externally by producing a protein [agouti protein] that where/when present inhibits the receptors' activation even though there is melanocyte-stimulating hormone present. Where the Agouti protein is present, only pheomelanin is produced. Where the protein is absent the receptor is activated and eumelanin is produced. One Dominant Agouti Allele [AAAa] or [AAAA] results in the production of this inhibiting protein. Homozygous Recessive Alleles [AaAa] at the Agouti Locus leaves a normal receptor that's subsequently activated by the melanocyte-stimulating hormone and the production of eumelanin is unhibited across the body. The Wild Type Agouti Allele, the third option occurring at the Agouti Locus, while it has not yet been proven to act thus, is widely accepted to be dominant to the more regular Agouti, working in the same way as the counterpart Heterozygous/Homozygous Dominant allelic forms, producing the receptor inhibiting protein and thus restricting the production of eumelanin, though to a more excessive degree than its' counterpart. Which would [and does] result in a larger bodily areas with the protein and a more restricted area of eumelanin production.

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See the sections under Pigment Production on the Introduction Page for further information on the following.

The Colour "Dominant Black"

Please note that the existence of this allele has only recently been confirmed. It is evidenced as being present only in a few breeds & is rare in the breeds it does exist in. Arabians are one of those few breeds & the following information is taken from the researched facts of Arabians only.

While the colour "Dominant Black" is still considered somewhat rare, this seems to be only due to a lack of people actually realizing what they are looking at - Meaning that many Dominant Blacks are mistakenly identified as Recessive Blacks, most especially in the Purebred Arabian breed.
The colour Dominant Black had many Arabian enthusiasts confounded until this allele was recently confirmed to exit in the breed for two simple reasons.
Anyone familiar with the breeding and pedigrees of Arabians would likely know that there are Arabian families that are reknowned for producing Black on a relatively consistent basis. Families that appear to inherit the genotype for Black as a dominant trait, with many Black x non-Black and non-Black x non-Black matings producing Black offspring throughout the generations.This mode of inheritance is the opposite to the way in which Recessive Black operates. The other tell tale signature of Dominant Black is that many horses with this genotype are born a colour very similar - almost identical - to Bay. These horses may end up Black at the first shedding of the foal coat, but just as many will remain this 'almost Bay' colour until they're fully mature, until four or five, sometimes even six plus years old.

There are, in almost all cases, some subtle differences between the Black colours resulting from the two different Black genotypes.
Dominant Black is considered to be somewhat "weaker" than the Black resulting from the Recessive Agouti Locus genotype. Many of those with the Dominant Black genotype generally tend to be more of a Dark Brown in colour rather than true Black, often appearing as though the pigment in the hair shaft is not quite as strong in the former as compared to the latter. Dominant Black accounts for a large portion of "Brown" coloured horses with Arabian breeding. Whilst most Dominant Blacks do have the tendancy to be more brownish in colour, the expression can range from a very jet black right through to a lighter Brown Black colour, with this difference not seemingly attributed to the remainder of the genotype.
The main difference between horses with the different Black genotypes though, is that Dominant Blacks are almost always born a colour similar to Bay and then darken to Black at a later stage, whereas the Recessive Blacks are born a ash grey colour and turn Black when they shed their foal coats.

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Dominant Black at the Extension Locus

Wild Type Allele at the Agouti Locus

The Colour "Wild Bay"

The colour resulting from the Wild Type Agouti genotype is distinctly different from the more common Bay colouring resulting from the Dominant Agouti genotype. As mentioned above, the Wild Type Agouti results in a more excessive restriction of black pigmentation on the body.
The black pigment on the legs of common Bays extends from the coronet to the knee and is regularly seen as far up as the forearm and gaskin in some individuals. The black pigmentation on the legs of an individual with the Wild Type Agouti genotype is further restricted to the lower legs only. They may have as little as a few black hairs intermingled with the red body colour at the coronet to pastern area only, through to solid black from coronet to fetlock that appears to "fade" as it extends towards the cannon region. This "faded" appearance is caused by an interplay of red and black pigmentation and is a typical characteristic of Wild Bays. Common Bays usually have a more crisp, clean edge to their black leg markings where they meet their red body colour. Most Wild Bays have very little black on their legs, only to the fetlock with the interplay of red and black hairs extending partially onto the lower cannon region. The other tell tale sign of a Wild Bay is a mane and tail not completely solid in black pigmentation. Many Wild Bays will have a mane and/or tail that is more red than black, and usually always have a reddish tinge to the mane [most especially in direct sunlight] as aposed to the Black manes and tails of common Bays. This characteristic can also extend to the facial markings, with Wild Bays usually having little to no black pigmented hairs on the head.

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Please note that the existence of this allele has only recently been confirmed. It is evidenced as being present only in a few breeds & is rare in the breeds it does exist in. Arabians are one of those few breeds & the following information is taken from the researched facts of Arabians only.

Reading that may assist with Understanding the Information contained on this page:
~ Introduction to Genetics ~ Genetic Terminology ~ Genetic Shorthand ~

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Genotype: E+E-, A+A-

Possible Allelic Combinations at the Extension Locus & the Agouti Locus

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