Involved in the first step of peroxisomal beta-oxidation by catalyzing the desaturation of fatty acid-derived side chains of ascaroside pheromones, which regulates development and behavior (PubMed:20610393, PubMed:25775534, PubMed:29537254). Specifically, shortens ascarosides with a 7-carbon side chain (asc-C7) (PubMed:25775534, PubMed:29537254). Does not catalyze the desaturation of fatty acids or hydroxylated fatty acids (PubMed:25775534, PubMed:29537254). Involved in the biosynthesis of asc-C6-MK (daumone 2) and asc-delta-C9 (daumone 3) but not asc-C7 (daumone 1); daumones are pheromones produced during unfavourable growth conditions which promote entry into the dauer stage (PubMed:20610393). asc-C7-CoA + O2 = asc-DeltaC7-CoA + H2O2 Activated by ATP (By similarity). ATP binding leads to a conformational change that promotes FAD cofactor binding and enzyme activity (By similarity). ATP binding likely occurs during acox-1.3 folding and/or dimer formation (By similarity). kcat is 144 sec(-1) with asc-C7-CoA (at 30 degrees Celsius, pH 7.4 and in complex with acox-1.1). Lipid metabolism; peroxisomal fatty acid beta-oxidation. Forms a heterodimer with acox-1.1; the interaction may be important for the stability of acox-1.3. Induced by high temperatures (25 degrees Celsius) (PubMed:20610393). Induced by starvation (PubMed:25775534). RNAi-mediated knockdown abolishes production of dauer pheromone daumone 2, severely reduces production of daumone 3 and increases production of daumone 1. Belongs to the acyl-CoA oxidase family.