Alternative splicing of mouse alpha1(XIII) collagen RNAs results in at least 17 different transcripts, predicting alpha1(XIII) collagen chains with length varying between 651 and 710 amino acid residues.

The alpha1(XIII) collagen chain has three collagenous domains (COL1-COL3) and four noncollagenous domains (NC1-NC4). A hydrophobic sequence in the extreme amino-terminal noncollagenous domain suggests that type XIII collagen is a transmembrane protein. The alpha1(XIII) collagen RNA is characterized by complex alternative splicing. In this study, expression of the alpha1(XIII) collagen chain was detected in 12 mouse tissues using reverse transcription (RT) and the polymerase chain reaction (PCR). Alternative splicings affecting the COL1, NC2, and COL3 domains were first evaluated separately. Subsequently, sequences spanning from the NC1 domain to the NC4 domain were studied for the first time to elucidate how the alternative splicing of type XIII collagen transcripts affects the structures of the entire mRNAs. A total of 10 alternatively spliced exons, which were freely combinatory, and 9 new exon combinations encoding parts of the COL1, NC2, and COL3 domains have been found. The sequences for the COL1 domain involved two common variants, one containing all the known COL1 exons and the other lacking exon 4B. Exons 12 and 13, encoding most of the NC2 domain, were subject to an alternative splicing that was found to display marked tissue-specific differences. The most common variant of the COL3 sequences lacked exons 28B and 33, or only the exon 33, which was found to be 100% identical to the corresponding human sequences. A total of 17 splice combinations of nine exons were characterized. The results suggest that the predicted length of the corresponding polypeptide varies between 710 and 651 residues.