An alternatively spliced variant of a testis-specific nuclear orphan receptor TR2-11 was identified and designated as TR2-11-t. As a result of retaining intron 5 of this gene, TR2-11-t mRNA encoded a truncated receptor with the complete ligand-binding domain deleted. Protein expression of both isoforms was confirmed using a prokaryotic expression system. In the mouse, the expression of the two TR2 isoforms was elevated in the testis with distinct profiles beginning at puberty. TR2-11 expression increased at postnatal day 18, peaked between day 20 and day 24 and remained at high levels throughout adulthood, whereas TR2-11-t expression was elevated transiently at postnatal day 24. Among separated primary germ cells and established testicular cell lines, TR2-11 was expressed highly in meiotic and postmeiotic germ cells and weakly in a Leydig cell line and a germ cell line, but not expressed in a Sertoli cell line. In contrast, TR2-11-t was expressed at a much lower level in all the testicular cell types examined. In adult testes blocked at germ cell development by vitamin A depletion or hypophysectomy, TR2-11 expression was dramatically reduced whereas TR2-11-t was highly elevated. Based upon the RNA expression patterns of these isoforms, it was suggested that TR2-11 was specific to meiotic and postmeiotic germ cells whereas TR2-11-t was enriched in early germ cell populations such as premeiotic cells. The biological activities of TR2-11 and TR2-11-t on a direct repeat 5-type retinoic acid (RA) response element (RARE)-containing reporter gene was examined in Cos cells. TR2-11 repressed RA induction of this reporter whereas TR2-11-t enhanced RA induction of the same reporter, and the opposite biological effects of these isoforms were dose-dependent. Gel-shift experiments provided evidence for a direct interaction of TR2-11, but not TR2-11-t, with DNA fragments containing this RARE. Opposite roles of TR2-11 and TR2-11-t on RA induction of promoters containing this particular RARE are suggested.