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Lesson 4 - Advanced Nomenclature

In "Basic Naming", you learned that it's important to have a consistent method of creating gene names and using it to identify alleles. The best symbols communicate information to the reader. Single-letter codes can work, but what if you have several different traits that start with the same letter? And is there a way to let the symbol tell you if the mutant allele is dominant or not? The Basic scheme outlined tells if the allele is dominant, but you might not know, without extra context, whether the mutation is dominant or not.

Enter "Advanced Nomenclature". At first this will take some practice, but most students get the hang of it and find it useful when dealing with multiple traits.

The Ground Rules

This list will get you started. Some of them come from the "Basic Nomenclature" section.

The "normal" phenotype is described as "wildtype"; this is the default phenotype of the reference organism.
Any change from the wildtype phenotype is a mutation and must be named. The name must provide a clear description of the mutant trait. One or two words is best.
The gene symbol must be 3 letters derived from the trait name. Consider using the first three letters of the name you chose or use the first couple letters and last letter if it makes a word that reminds you of the mutant trait. If you use two words, you could replace the last letter of your symbol with the first letter of the second word.
Dominant mutant trait symbols must have the first letter capitalized. Recessive mutant traits must be all lower case.
The allele that is not mutant uses the exact same letters as the mutant: only a superscript ‘+” is added to the symbol.

Here is a printable four-page summary of how to use Advanced Nomenclature.

Exercise: Create a three-letter gene name

Proper format for writing genes and alleles

Always underline your gene names when writing them out. If you're typing them, you can underline or italicise them.

In science, it's conventional to set your text apart stylistically so you know when you're dealing with Latin or Greek words, or a special symbol - such as a gene name!

e.g. You should use Alb for a dominant mutant allele, and Alb⁺ for its wild-type counterpart.

Also note that the second and third letters are always lower case.

What makes a good gene name?

Now that we have the freedom to use three letters, let's make the best use of them. Before, if you had a bald mouse with big eyes and broken ear margins, you'd have to get really creative with the single letters you used. You might have to range far for descriptive terms that aren't intuitive, and it makes your analysis harder: you'll have to put everything you come up with through a filter.

Now, however, you can define the gene names as bld for "bald", bey for "big eyes", and bre for "broken ear". Note that each of these symbols indicates the mutant allele of this gene is recessive to wild-type. The wild-type alleles, of course, will have superscript "+" at the end: bld⁺, bey⁺, and bre⁺.

Note also that you have more control of the gene names than this example... perhaps you prefer bal for "bald"?

Finally, note that the gene name is essentially the long form of the mutant gene symbol. Thus, bld and bld⁺ both refer to the bald gene.

Don't forget these "basic" rules! (see earlier sections if you DID forget)

Homologous chromosome pairs are indicated with a ‘/’ (slash) symbol.
Genes on nonhomologous chromosomes are separated by a ‘;’ (semicolon) symbol.
Linked loci (loci that are on the same chromosome) are listed together on the same side of the slash.

If you forgot the rules, check out "linked genes".