During cellularization, the zygotic transcription of RapGAP1 displays a complex pattern that consists of four distinct, spatially restricted expression domains, overlapping the presumptive region of the cephalic furrow, the ventral furrow, the posterior midgut, and the posterior dorsal fold, respectively. This last expression domain centers on the initiating cells of the posterior fold and encompasses both the anterior and posterior flanking regions. Thus, across the dorsal epithelium, the levels of RapGAP1 zygotic transcription are high in the region surrounding the posterior fold but low in the cells near the anterior fold.

RapGAP1 transcripts are first detected in the posterior pole of the embryo. They are observed in the pole cells as they form. They are detected in pole cells until they migrate through the midgut wall. During germ band extension, they are found in groups of cells in the neurectoderm. After germ band retraction, they are detected in cells of the PNS, in the garland cells and in the gut. In larvae, RapGAP1 transcripts are observed in imaginal discs. In the eye disc, they are observed in most cells of the morphogenetic furrow. Immediate y posterior to the furrow, expression is rapidly restricted to the developing ommatidial clusters.

Strong expression is observed in the larval central nervous system but not in motor neuron axons or body wall sensor neurons. Strong expression is also seen in the eye disc and optic lobes. Strong expression is also observed in the larval brain neuropil, both in the ventral nerve cord and in the mushroom body neuropil in the brain. Expression is additionally seen in the soma of dorsal medial motor neurons.

RapGAP1 protein is first detected in the posterior pole of the embryo in the pole cells as they form. It is detected in pole cells until they migrate through the midgut wall. During germ band extension, RapGAP1 protein is found in groups of cells in the neurectoderm. After germ band retraction, it is detected in cells of the PNS, in the garland cells and in the gut. In larvae, RapGAP1 protein is observed in imaginal discs. In the eye disc, it is observed in most cells of the morphogenetic furrow. Immediately posterior to the furrow expression is rapidly restricted to the developing ommatidial clusters. It is also detected in the axons of the optic nerve and in the optic lobe.