A segmentation gene whose expression subdivides the embryo into a series of stripes, and sets the boundaries of the parasegments. It also regulates the subsequent expression of segment polarity genes.
These genes are sequentially expressed next to the gap genes and before the segment polarity genes. In fact, the gene products of gap genes, together with those of maternal genes, activate pair-rule genes.
Examples of pair-rule genes are: even-skipped, hairy, runt, fushi-tarazu, odd-skipped, paired, odd-paired, sloppy-paired, and Tenascin major. Defect in any of these genes results in missing pattern elements in alternate segments. For instance, defective even-skipped gene results in even-numbered parasegments missing in the body pattern of the Drosophila larva.