Topographically graded molecules representing position-specific differences among otherwise similar cells are thought to play a role in the patterning of the developing nervous system. In the embryonic chick visual system, a 40 kDa protein, TOPAP, is expressed in a posterior > anterior gradient in the retina and in an inverted anterior > posterior gradient in the optic tectum, the major retinal projection area. Here we report the isolation and nucleotide sequencing of a complementary DNA clone encoding the chick TOPAP protein and demonstrate that the mRNA encoding this coiled-coil integral membrane protein is topographically graded within the retina and is present in a variety of chick tissues.