EC cells are characterized by their potent capacity to differentiate into several cell types, such as mesoderm-like cells, endoderm-like cells, or ectoderm-like cells. By subtracting the mRNAs expressed by one EC cell clone, F9 cells, with the mRNAs expressed by another EC cell clone, P19 cells, we identified six novel genes that are expressed selectively by F9 cells. One of these genes (Nucling) encodes a polypeptide of 1411 amino acids containing an ankyrin repeat, aspartyl protease motif, a leucine zipper motif, and two t-SNARE coiled-coil domains. Northern blot analyses revealed the Nucling mRNA to be detected predominantly in heart, liver, kidney and testis, but not in brain or spleen. Immunostaining analyses revealed a unique feature of Nucling that the transiently expressed protein forms aggregates exclusively around nuclear membranes. Moreover, the expression level of the Nucling gene transcript increases progressively during the early developmental stages in mice, and specifically at cardiomuscular differentiation in vitro and in vivo. These results suggest that Nucling may play some role in the gene regulation of cell differentiation during embryonal development.