FlyBase:Nontraditional alleles

G.1. Nontraditional alleles

In addition to 'alleles' in the traditional sense, FlyBase now names and curates further classes of allele so that phenotypic or expression pattern data can be captured for in vitro construct alleles and alleles of reporter (e.g., Ecol\lacZ), effector (e.g., Scer\FLP) or toxin (e.g., Rcom\DT-A) genes. Since these alleles have not historically been named by researchers, and have been named by FlyBase, their presentation in FlyBase requires some explanation:

G.1.1. Alleles of reporter genes

Alleles of reporter genes currently fall into two main classes, those resulting from enhancer trap experiments, and those resulting from promoter (or other regulatory region) analysis, where a fragment is used to drive the expression of a reporter gene. Ecol\lacZ will be used for illustration.

Enhancer trap results:

The enhancer trap construct causes an allele of a gene and is expressed in a pattern consistent with insertion in that gene. The resulting insertion will be described with the format P{A92}hL43a, and the Ecol\lacZ allele symbol is of the format Ecol\lacZh-L43a.

The reporter gene reflects the expression of a gene without causing a mutant allele of that gene. The resulting insertion will be described with the format P{PZ}P2023-44, where P2023-44 reflects the insertion identifier, and the Ecol\lacZ allele symbol is of the format Ecol\lacZhh-P2023-44.

The reporter gene reflects the expression of an undescribed gene/enhancer. The resulting insertion will be described with the format P{lacW}1.28, and the Ecol\lacZ allele symbol is of the format Ecol\lacZ1.28.

Promoter analysis results:

Generally some fragment of a gene promoter/intron/3'-region is fused to the reporter gene. In this case the allele symbol is of the form 'gene symbol.fragment descriptor' e.g., Ecol\lacZeve.prox54. The fragment descriptor reflects that used in the publication, even though this may be long and cumbersome (this may not be strictly true for such alleles curated early in the FlyBase project).

Where a reporter gene is simply described in a publication as being driven by, e.g., an arm promoter, the symbol of the Ecol\lacZ allele is 'arm.PI', where I is the first letter of the surname of the first author of the paper, e.g., Ecol\lacZarm.PV for 'Ecol\lacZ arm promoter construct of Vincent'.

For logistical reasons some promoter fusions involving reporter genes such as Ecol\lacZ, though technically protein fusions, are simply treated as alleles of the reporter gene. The symbol for the additional gene(s) contributing to the fusion is indicated as part of a superscript, e.g., Ecol\lacZP\T.A92. In these special cases there is no distinction made between promoter fusions and protein fusions in the gene name.