A novel gene, ELKS, whose 5' portion was fused to the RET gene, was found in a papillary thyroid carcinoma. A cDNA of this gene obtained from a human-brain cDNA library revealed that it encoded a peptide of 948 amino acids, termed ELKSalpha. We identified four other isoforms, which encoded ELKSbeta, ELKSgamma, ELKSdelta, and ELKSepsilon proteins consisting, respectively, of 992, 720, 1088, and 1116 amino acid residues. Analysis of the gene structure revealed that the isoforms were generated by alternative splicing. Isoforms beta, gamma, delta, and epsilon all contain an optional exon (exon14a), but ELKSgamma, -delta, and -epsilon lack exon 1b. ELKSgamma lacks exons 3 to 6. ELKSdelta and -epsilon lack exons 12 and 17; ELKSepsilon contains an optional exon (exon 6a). Analysis by RT-PCR suggested that ELKSalpha and ELKSbeta mRNAs are abundant in the brain, ELKSdelta and ELKSepsilon mRNAs predominate in testis and thyroid, and ELKSepsilon mRNA predominates in other tissues. To prove whether the fusion of different ELKS isoforms to RET (between ELKS coiled-coil domains and the RET kinase domain) could produce chimeric proteins that could be autophosphorylated, we synthesized ELKSgamma-RET, ELKSdelta-RET, and ELKSepsilon-RET fusion proteins in vitro. Immunoblotting with anti-ELKS, anti-RET, and anti-phosphotyrosine antibodies demonstrated that the chimeric proteins were constitutively phosphorylated at tyrosine residues, whereas native RET protein was not. These results indicate that the ELKS gene is alternatively spliced, and that every type of ELKS-RET chimeric protein having oligomerization domains can activate RET's cytoplasmic tyrosine kinase.