We identified and cloned a novel 9,078-bp cDNA, designated TPRDI, from the Down syndrome-critical region by exon trapping. The cDNA encodes a putative protein (TPRDI) of 2,025 amino acid residues. Two isoforms, TPRDII (8,992 bp) and TPRDIII (7,416 bp), were also isolated. TPRDII, which is probably an alternative splicing product from the TPRD gene transcript, encodes two large open reading frames (ORFs) of 200 amino acid residues and 1,792 amino acid residues, respectively. TPRDIII, which is probably generated by transcription from an alternative start site of the TPRD gene, encodes a putative protein of 1,715 amino acid residues (TPRDIII). Northern blot analysis revealed that TPRDI and its isoforms are present in 7-17 day mouse embryo and in all the human adult and fetal tissues examined. TPRDI has three units of a 34-amino-acid repeat similar to the tetratricopeptide repeat (TPR) motif, which may mediate interaction with various proteins. A larger ORF encoded by TPRDII also has three units of TPR motif, but TPRDIII has only two-thirds of this motif unit. Thus, the TPRD gene may belong to the TPR gene family. Near-central and C terminal regions of TPRDs showed some homology to several matrix proteins such as trichohyalin and bullous pemphigoid antigen. It is possible that the TPRD gene is one of the genes whose overexpression causes several morphological anomalies observed in Down syndrome.