A 62-kDa (p62) mitotic apparatus-associated protein is important for the proper progression of mitosis in sea urchin embryos (Dinsmore, J. H., and Sloboda, R. D. (1989) Cell 53, 769-780). We have isolated and characterized a full-length p62 cDNA of 3374 base pairs which encodes an extremely acidic polypeptide of 411 amino acids having a calculated Mr of 46,388 and a pI of 4.01; p62 is a unique protein with no significant identity to any known proteins. Southern and Northern blot analyses demonstrate that the gene for p62 is present once in the sea urchin genome and the corresponding mRNA is present in unfertilized eggs and in early embryos through and up to the gastrula stage. Sequence analysis suggests certain regions may participate in chromatin association and microtubule binding, an observation that is consistent with previous immunological data (Ye, X., and Sloboda, R. D. (1995) Cell Motil. Cytoskeleton 30, 310-323) as well as data reported herein. Confocal microscopy reveals that during interphase the protein binds to chromatin in the nuclei of sea urchin eggs. In the germinal vesicles of clam oocytes at prophase of meiosis I, p62 binds to the condensed chromosomes. Currently, truncated clones of p62 are being used to identify the tubulin and chromatin binding domains.