The use of rapid amplification of 5'-cDNA ends-PCR yielded two novel sequences for the rat orphan receptor, TR4, representing heterogeneity on the 5'-untranslated region. Genomic structure analysis revealed that the 5'-untranslated region of the longer messenger RNA fragment, rTR4-1, contained three exons, alpha, beta, and gamma. The skipping of exon gamma gave rise to rTR4-2, indicating that rTR4-1 and rTR4-2 are products of alternative splicing. We isolated another novel rat TR4 splice variant, rTR4-NS, which was found to diverge from rTR4-2 at codon 504. rTR4-NS contained an unspliced intronic sequence with in-frame codons for eight amino acids followed by a termination codon. The three TR4 messenger RNA variants were differentially expressed. rTR4-NS appeared to be a rare transcript found in limited areas of the brain. In situ hybridization detect prominent TR4 signals in brain areas known to be involved in stress response. In cerebellar granule cells, the rise in TR4 expression correlated with the progression of neuronal maturation. N-Methyl-D-aspartate treatment triggered a marked increase in TR4 expression. These results suggest a possible role for TR4 in neuronal differentiation.