Genes that have been designated the name "MUC" code for proteins comprising mucin domains. These proteins may be involved in barrier and protective functions. The first such gene to be characterized and sequenced is the MUC1 gene. Here we report a novel small protein derived from the MUC1 gene by alternative splicing that does not contain the hallmark of mucin proteins, the mucin domain. This protein termed MUC1/ZD retains the same N-terminal MUC1 sequences as all of the other known MUC1 protein isoforms. The common N-terminal sequences comprise the signal peptide and a subsequent stretch of 30 amino acids. In contrast, the MUC1/ZD C-terminal 43 amino acids are novel and result from a reading frameshift engendered by a splicing event that forms MUC1/ZD. The expression of MUC1/ZD at the protein level in human tissues is demonstrated by Western blotting, immunohistochemistry, immunoprecipitation, and an ELISA. Utilization was made of affinity-purified MUC1/ZD-specific polyclonal antibodies as well as two different monoclonal antibodies that are monospecific for the MUC1/ZD protein. The MUC1/ZD protein is expressed in tissues as an oligomeric complex composed of monomers linked by disulfide bonds contributed by MUC1/ZD cysteine residues. MUC1/ZD protein expression did not parallel that of the tandem-repeat array-containing MUC1 protein. Results presented here demonstrate for the first time the expression of a novel MUC1 protein isoform MUC1/ZD, which is generated by an alternative splicing event that both deletes the tandem-repeat array and leads to a C-terminal reading frameshift.Genes classified, for the most part, as MUC genes code for proteins that comprise mucin domains rich in proline, threonine, and serine residues (1). The heavily glycosylated mucin proteins derived from the MUC genes can be divided into those that are secreted from the cell (secreted mucins) and mucins that comprise a transmembrane domain that anchors them to the cell membrane (transmembrane mucins). The archetype membrane-tethered mucin, which was the one to be first characterized and sequenced, is derived from the MUC1 gene (2-5). It is a transmembrane protein that contains the serine-threonine-rich tandem-repeat region in its extracellular domain (Fig. 1A, MUC1/REP) and also comprises a 72 amino acid tail that can be tyrosine-phosphorylated (6, 7). The phosphorylated cytoplasmic domain subsequently interacts with second messenger proteins (6 -23), thereby relaying a signal to the nucleus that modifies gene expression.Challenging the classical definition of a mucin gene is the discovery of MUC1 mRNAs, which although transcribed from a mucin gene are devoid of a tandem-repeat array (24 -32). Alternative splicing generates these MUC1-derived mRNAs that no longer code for tandem-repeat array-containing mucin proteins. The prime example is the tandem-repeat array-deleted MUC1/Y isoform, which is expressed both as mRNA and protein (24 -26, 30, 31). The MUC1/Y protein is similar to MUC1/ REP in that it also contains the transmembrane and cytop...