To elucidate regulatory mechanisms triggering early mammalian differentiation, 17 retinoic acid (RA)-inducible clones were isolated from 1.4 x 10(5) plaques of cDNA libraries prepared from mouse embryonal carcinoma F9 cells, using the differential plaque hybridization method. Partial nucleotide sequences of these clones demonstrated that ten clones correspond to known genes. Interestingly, only 2 of the 17 clones are among the previously documented up-regulated genes. Therefore, there are many more unidentified genes up-regulated in the course of RA-induced differentiation of F9 cells. As RNAs hybridizable with one of the seven unidentified clones were induced in F9 cells after 3 h of RA treatment, we chose this 'Rae-28' clone as being representative of developmentally up-regulated unidentified clones and its properties were characterized. We determined the Rae-28 cDNA sequence and deduced the RAE-28 protein structure. The deduced RAE-28 protein shared several motifs and highly homologous regions with a Drosophila polyhomeotic protein. As the Drosophila polyhomeotic gene is involved in regulating morphogenesis, the rae-28 gene may participate in regulating early mammalian development.