The discovery of the pair rule genes was rather unexpected. In mutants of the pair rule genes, every other segment is lost, indicating that the process of segmentation proceeds through an intermediate phase in which segments are organized in a double periodicity. Accordingly, pair rule genes are expressed in a pattern of 7 stripes, half of the number of segments in a wild-type larva.

Two different classes of pair rule genes are distinguished. The primary pair rule genes translate spatial information provided by the maternal and gap genes into a striped pattern. Stripes are regulated independently by a characteristic combination of gap genes. Secondary pair rule genes, like fushi tarazu, are regulated by the primary pair rule genes, with each stripe executing the same response. The expression of pair rule genes is very dynamic; expression patterns can change considerably over time. These changes are driven by interactions between all, primary and secondary pair rule genes.

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Pair rule genes

Gene	Type - Domains	Function	Links
even-skipped (eve)	transcription factor - homeodomain	pair rule gene establishing epidermal cell fate	Interactive Fly
fushi tarazu (ftz)	transcription factor - homeodomain - Antp class	pair rule gene	Interactive Fly
hairy (h)	transcription factor - bHLH - Hairy/E(spl) class	pair-rule gene, later it antagonizes sensory bristle formation	Interactive Fly
odd paired (opa)	transcription factor - zinc finger	pair rule gene activates engrailed and wingless during segmentation	Interactive Fly
odd skipped (odd)	transcription factor - zinc finger	pair rule gene - mutants associated with cuticle defects that are limited to alternate--odd-numbered--segments	Interactive Fly
paired (prd)	transcription factor - homeodomain, paired domain	pair rule gene, required for the progression from pair-rule directed segmentation to specifying positional information within segments (segment polarity genes)	Interactive Fly
runt (run)	transcription factor - novel	pair rule gene, also contributes to neuroblast cell identity	Interactive Fly
sloppy-paired (slp)	transcription factor - forkhead domain	has combined characteristics of a gap, pair rule and segment polarity gene	Interactive Fly
Tenascin major (Ten-m)	transmembrane - tenasin homolog - EGF and Fibronectin repeats	pair-rule gene product	Interactive Fly