Alx3 belongs to the large class of genes that encode a prd/Q50 homeodomain, denoting moderate similarity to the prd homeodomain but the presence of a glutamine at position 50. The authors found that Alx3 was expressed in mouse embryos from 8 days of gestation onward in a characteristic pattern, predominantly in neural crest-derived mesenchyme and in lateral plate mesoderm.

Prominent expression was seen in the frontonasal head mesenchyme and in the first and second pharyngeal arches and some of their derivatives. High expression was also seen in the tail and in many derivatives of the lateral plate mesoderm including the limbs, the body wall, and the genital tubercle.