The invention provides isolated nucleic acids molecules that encode novel ubiquitin protease polypeptides. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing the ubiquitin protease nucleic acid molecules of the invention, host cells into which the expression vectors have been introduced, and nonhuman transgenic animals in which a ubiquitin protease sequence of the invention has been introduced or disrupted. The invention still further provides isolated ubiquitin protease proteins, fusion proteins, antigenic peptides and antibodies. Diagnostic methods utilizing compositions of the invention are also provided.