Gene Nomenclature

Lynn Miesel

Standard nomenclature

1. Mutational alleles

Enter allele followed by locus letter (if appropriate) followed by the allele number (e.g. hisD201). For alleles lacking a locus letter, insert a dash in place of the letter (e.g. his-203).

2. Insertions

a. mutational insertions:
If the insertion is located within a gene, enter the allele, the locus letter, then the allele number, followed by two colons and the insertion element (e.g. hisH9601::MudA).

b. z-- numbers

Many insertions have been isolated that are not known to be mutations of any particular gene. All such insertions are designated by a three-letter symbol starting with z; the second and third letters designated approximate map position in minutes. The second position designates 10-minutes map segments numbered clockwise from minute 0 (a=0-10; b=10-20; c=20-30, etc.); the third letter similarly designated minutes within any 10 minute segment. For example, an insertion located between minutes 2 and 3 would be designated by the symbol "zac".

Allele numbers are assigned serially to such insertions regardless of the letters appearing in positions 2 and 3. Thus, if more refined mapping data warrants a new three-letter symbol, the numerical identity of the insertion is not lost. As with other alleles, "z" numbers are assigned from the stock book.

For proper nomenclature, the three letter symbol is followed by a dash, the "z" allele number, a double colon, then the insertion element. For example, a Tn10 insertion located between minutes 2 and 3 would be designated zac-1::Tn10. Insertions on extra-chromosomal elements are designated with "zz" followed by letter denoting the element used. For example, zzf denotes insertions on a F'plasmid.

c. currently accepted designations for insertion elements.

Our lab's established designations for common insertion elements are listed below. Published designations may differ from one journal to another.

Tn10d-tet; Tn10d-can; Tn10d-kan
MudA; MudF; MudJ; MudP; MudQ

3. Rearrangements

Since chromosomal rearrangements involve more than one gene or gene cluster, they are distinguished from standard mutational alleles by a three capital letter symbol, CRR, in they are given a three letter symbol, CRR. A CRR symbol is assigned with an allele number regardless of the type of rearrangement. Upon characterization, it may be redesignated as a inversion (INV), a duplication (DUP), a deletion (DEL) or a transposition (TNP). It remains the same allele number to prevent confusion. The allele number is followed by a detailed description of the genotype in brackets.

Deletions are designated either by standard mutation nomenclature (above) or be rearrangement nomenclature according to the following rules. Standard mutation nomenclature may be used to describe deletions which remove one or more genes within an operon. Rearrangement nomenclature is appropriate when two or more unrelated genes are involved or for deletions generated by a transposable element and the gene.

The nomenclature for rearrangement formed from homologous recombination between Mud prophages for other transposons is illustrated by the following examples.

a. deletions

DEL443[(hisD9953)*Mud*(hisF9954)] is a deletion caused by recombination between the MudA insertions in hisD and hisF. This deletion would have its end points at the site of the original Mud insertions (hisD and hisF) and would have a MudA at the join point.

b. duplications

The same nomenclature is used for duplications. DUP442[(hisD9953)*MudA*(hisF9954) is a duplication of the material between the Mud insertions in hisD and hisF where a MudA exists at the join point.

4. Nomenclature references

Demerec M.; Adelber, E,; Clark, A.J.; Hartman, P.E. A proposal for a uniform nomenclature in bacterial genetics. Genetics 54:61-76, 1966.

Hughes, K.; Roth, J. Directed formation of deletions and duplications using Mud(Ap, lac). Genetics 109:263-282, 1985.

Schmidt, M. Bacterial rearrangement nomenclature. Thesis, Appendix II: 163-175.

Last Update: Friday February 22 2019
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