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<h3> <br><b>Gene Symbols</b></h3>
<h4>by Paul Hollander<br>
Copyright 2001, 2004. Freely Distributable.<br> </h4></div>
Sometimes terms take up a lot of space. If they must be written over and over, it makes sense to shorten them in some way. For example, "United States of America" is often abbreviated to "USA".
Gregor Mendel, the father of genetics, used letter symbols for several reasons. He lacked words because "heterozygous" and other genetics terms had not been invented. And symbols were simple, clear, and easy to understand. While present day geneticists have words that Mendel lacked, they continue to use symbols because they are short and easy to understand.
Various groups of geneticists have agreed on rules for genetic symbols. These rules allow a few alphanumeric characters to indicate whether the gene is normal or mutant, dominant or recessive, allelic or independent, etc. That is quite a load of information to carry, but it can be done.
So far, there is no single set of rules for gene symbols for all species. The rules for the mouse are not exactly the same as the rules for the house cat. And the rules for the fruit fly are not exactly the same as for maize, though there is considerable agreement. As uniformity is desirable, these rules follow the <a href="http://www.informatics.jax.org/mgihome/nomen/gene.shtml">gene nomenclature for the mouse and rat</a>.
<ol>
<li>Give the mutant a unique name that is reasonably descriptive of the phenotype.<br><br>
Examples: amelanistic, axanthic, flame, piebald, striped.<br>
<li>Derive the unique one to four letter symbol from the unique mutant name, and italicize the symbol if possible.<br><br>Alphabet books for young children often start with "a is for apple". In the same way, <i>a</i> is for amelanistic. Because <i>a</i> is already used, <i>ax</i> is for axanthic.<br>
<li>Use lower case letters for all letters symbolizing a recessive mutant.<br><br>Again, <i>a</i> is for amelanistic, a recessive mutant gene in the corn snake. The symbol <i>a</i> can also stand for albino, the name given to the analogous recessive mutant gene in many snake species.<br>
<li>Use lower case letters for all letters except the first letter in the symbol for a dominant or codominant mutant. The first letter is an upper case letter.<br><br>The symbol <i>Sa</i> is for salmon, a dominant mutant in the boa constrictor.<br>
<li>The locus symbol is the same as the symbol given to the first mutant discovered at that locus.<br><br>The corn snake's <i>a</i> locus has the <i>a</i> (amelanistic) mutant gene and all of its alleles. And the boa constrictor's <i>Sa</i> locus has the <i>Sa</i> (salmon) mutant gene and all of its alleles.<br>
<li>The wild type allele is symbolized either by the + character alone or by + added to the locus symbol as a superscript.<br><br>The wild type allele at the <i>a</i> locus can be either +, if the useage is obvious, or <i>a<sup>+</sup></i>, to make useage absolutely clear.<br>
<li>Three or more alleles may occur at any locus. Symbolizing the first mutant allele and the wild type allele have been covered. All alleles share the same base letter(s), though the initial letter's case may be changed, depending on whether the mutant is recessive, dominant, or codominant to the wild type or normal allele. In addition, the second and later mutant alleles get a unique superscript made up of one or two lower case letters. The superscript should somehow be derived from the mutant's name.<br><br>
The <i>a</i> for agouti locus in the mouse has over a dozen alleles. (Note: The locus name and symbol predate the guidelines and were retained for stability.) Here are a few to show how symbols are assigned to multiple alleles:<br><ul>
<li><i>A<sup>vy</sup>.</i> Viable yellow. Dominant to the normal allele. Homozygotes and heterozygotes are variable in color, ranging from clear yellow through yellow spotted to agouti.<br>
<li><i>A<sup>y</sup>.</i> Dominant yellow. Codominant to the normal allele. Homozygotes die at birth. Heterozygotes are yellow.<br>
<li><i>a<sup>+</sup>.</i> Wild type. The normal allele. The normal or agouti color.<br>
<li><i>a.</i> Nonagouti. Recessive to the normal allele. Homozygotes are black with a little yellow around the nipples and anus.<br>
<li><i>a<sup>e</sup>.</i> Extreme nonagouti. Recessive to the normal allele. Homozygotes are black, including around the nipples and anus.<br> </ul>
<li>If possible, use the same symbols for similar mutants in closely related species.<br><br>
As <i>a</i> stands for amelanistic in the corn snake, it should be reserved for amelanistic or albino in all North American rat snakes and possibly in all snakes.
</ol>
<h3> <br><b>Gene Symbols</b></h3>
<h4>by Paul Hollander<br>
Copyright 2001, 2004. Freely Distributable.<br> </h4></div>
Sometimes terms take up a lot of space. If they must be written over and over, it makes sense to shorten them in some way. For example, "United States of America" is often abbreviated to "USA".
Gregor Mendel, the father of genetics, used letter symbols for several reasons. He lacked words because "heterozygous" and other genetics terms had not been invented. And symbols were simple, clear, and easy to understand. While present day geneticists have words that Mendel lacked, they continue to use symbols because they are short and easy to understand.
Various groups of geneticists have agreed on rules for genetic symbols. These rules allow a few alphanumeric characters to indicate whether the gene is normal or mutant, dominant or recessive, allelic or independent, etc. That is quite a load of information to carry, but it can be done.
So far, there is no single set of rules for gene symbols for all species. The rules for the mouse are not exactly the same as the rules for the house cat. And the rules for the fruit fly are not exactly the same as for maize, though there is considerable agreement. As uniformity is desirable, these rules follow the <a href="http://www.informatics.jax.org/mgihome/nomen/gene.shtml">gene nomenclature for the mouse and rat</a>.
<ol>
<li>Give the mutant a unique name that is reasonably descriptive of the phenotype.<br><br>
Examples: amelanistic, axanthic, flame, piebald, striped.<br>
<li>Derive the unique one to four letter symbol from the unique mutant name, and italicize the symbol if possible.<br><br>Alphabet books for young children often start with "a is for apple". In the same way, <i>a</i> is for amelanistic. Because <i>a</i> is already used, <i>ax</i> is for axanthic.<br>
<li>Use lower case letters for all letters symbolizing a recessive mutant.<br><br>Again, <i>a</i> is for amelanistic, a recessive mutant gene in the corn snake. The symbol <i>a</i> can also stand for albino, the name given to the analogous recessive mutant gene in many snake species.<br>
<li>Use lower case letters for all letters except the first letter in the symbol for a dominant or codominant mutant. The first letter is an upper case letter.<br><br>The symbol <i>Sa</i> is for salmon, a dominant mutant in the boa constrictor.<br>
<li>The locus symbol is the same as the symbol given to the first mutant discovered at that locus.<br><br>The corn snake's <i>a</i> locus has the <i>a</i> (amelanistic) mutant gene and all of its alleles. And the boa constrictor's <i>Sa</i> locus has the <i>Sa</i> (salmon) mutant gene and all of its alleles.<br>
<li>The wild type allele is symbolized either by the + character alone or by + added to the locus symbol as a superscript.<br><br>The wild type allele at the <i>a</i> locus can be either +, if the useage is obvious, or <i>a<sup>+</sup></i>, to make useage absolutely clear.<br>
<li>Three or more alleles may occur at any locus. Symbolizing the first mutant allele and the wild type allele have been covered. All alleles share the same base letter(s), though the initial letter's case may be changed, depending on whether the mutant is recessive, dominant, or codominant to the wild type or normal allele. In addition, the second and later mutant alleles get a unique superscript made up of one or two lower case letters. The superscript should somehow be derived from the mutant's name.<br><br>
The <i>a</i> for agouti locus in the mouse has over a dozen alleles. (Note: The locus name and symbol predate the guidelines and were retained for stability.) Here are a few to show how symbols are assigned to multiple alleles:<br><ul>
<li><i>A<sup>vy</sup>.</i> Viable yellow. Dominant to the normal allele. Homozygotes and heterozygotes are variable in color, ranging from clear yellow through yellow spotted to agouti.<br>
<li><i>A<sup>y</sup>.</i> Dominant yellow. Codominant to the normal allele. Homozygotes die at birth. Heterozygotes are yellow.<br>
<li><i>a<sup>+</sup>.</i> Wild type. The normal allele. The normal or agouti color.<br>
<li><i>a.</i> Nonagouti. Recessive to the normal allele. Homozygotes are black with a little yellow around the nipples and anus.<br>
<li><i>a<sup>e</sup>.</i> Extreme nonagouti. Recessive to the normal allele. Homozygotes are black, including around the nipples and anus.<br> </ul>
<li>If possible, use the same symbols for similar mutants in closely related species.<br><br>
As <i>a</i> stands for amelanistic in the corn snake, it should be reserved for amelanistic or albino in all North American rat snakes and possibly in all snakes.
</ol>