The two splice variants of collagen XII share a common 5' end.

The short splice variant of collagen XII is composed of 1960 amino acid residues. This polypeptide contains the same signal peptide and the same carboxy-terminus as the long splice variant, but lacks an internal fragment of 1164 amino acid residues. Thus, the two variants of collagen XII are not created by the use of two different transcription initiation sites as generally assumed, but result from the inclusion or skipping of several exons located within the collagen XII gene.