The Hox proteins play a role in development and cellular differentiation by regulating downstream target genes. Specifically, the Hox proteins direct DNA-protein and protein-protein interactions that assist in determining the morphologic features associated with the anterior-posterior body axis. The mammalian HOX gene complex consists of 39 genes that are located on four linkage groups, which are dispersed over four chromosomes. HOX genes that occupy the same relative position along the 5’ to 3’ coordinate (trans-paralogous genes) are more similar in sequence and expression pattern than adjacent HOX genes on the same chromosome. HoxA3, in conjunction with Pax1, mediates the development of the thymus, parathyroid gland, and carotid body. Its expression in the third pharyngeal arch and pouch is required for development of the third arch artery, and homozygous null HoxA3 mutants lack the carotid body. HoxA3 also regulates hindbrain development by controlling the axon projection pattern of motor neurons and sensory neurons of the proximal and distal ganglia.