Identification of the promoter and first exon of the mouse alpha 1 (III) collagen gene

We have identified the promoter-proximal exon of the mouse alpha 1 (III) collagen gene using a synthetic oligonucleotide as a hybridization probe and have determined the DNA sequence of this exon and 380 base pairs 5' to it. The exact start site of transcription was localized with a primer extension experiment. The region upstream of the start of transcription shows only scattered homologies with the analogous sequences in the alpha 1(I) and alpha 2(I) mouse collagen genes although these genes are often co-expressed and co-regulated. The most striking homology with the type I gene is seen around the start of translation. This region contains an inverted repeat which could form a stem-loop structure with a calculated delta G of -30 kcal in the type III collagen mRNA. When compared to the alpha 1(I) and alpha 2(I) signal peptides, the signal peptide of mouse alpha 1(III) collagen presents less homology than when these segments are compared to each other.