UASt regulatory sequences drive expression of the 'pexo-QC' reporter, which can be used to measure pexophagy (autophagy of peroxisomes). The reporter consists of the EGFP and mCherry coding sequences in tandem and fused to the Tag:PTS(SKL) peroxisome targeting signal. Under normal conditions, fluorescence from both EGFP and mCherry occurs. Upon pexophagy and fusion of the peroxisome and a lysosome, the low pH of the lysosome quenches the EGFP signal but not the mCherry signal.