Structure and mapping of the mouse matrilin-3 gene (Matn3), a member of a gene family containing a U12-type AT-AC intron

The gene for murine matrilin-3, an extracellular matrix protein present in cartilage, was isolated and further characterized. The gene spans 23.4 kb a nd comprises 8 exons; with one exception, this reflects the modular structu re of the protein. The major and a minor transcription start site were dete rmined by RNase protection assays to positions approximately 72 nt and 87 n t up stream of the ATG codon, respectively. The promoter contains a TATA-li ke box 32 bp upstream of the main transcription start ar; well as several p otential binding sites for eukaryotic transcription factors. As in all know n matrilin genes, the last intron, separating the exons coding for the coil ed-coil domain, does not follow the GT-AG rule and belongs to the subgroup of introns having AT-AC at the ends that are spliced by the U12-type splice osome. The mouse matrilin-3 gene does not contain hidden exon sequences cod ing for the second vWFA-like domain present in all other matrilins. The int ron that could possibly contain such sequences in stead shows 75% repetitiv e sequences, indicating an evolutionary process that has led to the loss of sequences coding for vWFA2. Single-strand conformation polymorphism analys is was used to map the Matn3 gene to the proximal end of Chr 12, linked to the genes Synd1, Apob, Dntb, and Kif3c.