Genomic organisation, alternative splicing and primary structure of human matrilin-4

We have recently cloned a cDNA for mouse matrilin-4. By sequence comparison we identified the 12 kb long human matrilin-4 gene as a part of a high-throughput genomic sequence (HS453C12) in the databases. Additionally we found a human matrilin-4 expressed sequence tag (H54037) in the database that had been mapped to chromosome 20q13.1-2. The gene contains 10 exons and, like the matrilin-1 gene, the human matrilin-4 gene contains an AT-AC intron between the two exons encoding the coiled-coil domain. The cDNA sequence of human matrilin-4 was determined by sequencing of RT-PCR products obtained from mRNA of the human embryonic kidney cell line HEK 293. At the amino acid level it showed an overall sequence identity to the mature mouse matrilin-4 of 91% with a maximum of 97% in the second vWFA-like module. Alternative splicing leads to three different mRNAs. They all encode the putative signal peptide, the two vWFA-like domains and the potential coiled-coil alpha-helical oligomerisation domain but differ in that either one, two or three EGF-like domains are retained in the mature mRNA. Due to a G to A mutation at the splice donor site of intron C, the third exon encodes an untranslated pseudo-exon specifying the first EGF-like domain when compared to mouse matrilin-4.