title: Characterization of the spectrum of alternative splicing of alpha 1 (XIII) collagen transcripts in HT-1080 cells and calvarial tissue resulted in identification of two previously unidentified alternatively spliced sequences, one previously unidentified exon, and nine new mRNA variants.
abstract: Amplification of a COL1-encoding region of alpha 1 (XIII) collagen transcripts of HT-1080 cell RNA suggested that exon 3 of the alpha 1 (XIII) collagen gene, which was previously deduced to be of 35 base pairs (bp) may consist of a constitutive 8-bp exon and an alternatively spliced 27-bp exon, termed here exons 3A and 3B, respectively. Furthermore, a previously unidentified alternatively spliced Gly-Xaa-Yaa-encoding exon designated as 4B was found between the sequences encoded by exons 4, redesignated here as 4A and 5. Six of the 16 potential combinations of the four consecutive alternatively spliced exons 3B, 4A, 4B, and 5 were found to exist in mRNAs, and as a result, the length of the COL1 domain may vary between 57 and 104 amino acid residues. Most of the NC2 domain is encoded by the alternatively spliced exons 12 and 13. Where previous analysis of cDNAs indicated that mRNA variants exist that contain either exon 12 or 13 sequences, amplification studies indicated here that there are also variants that lack both exons 12 and 13 but none that contain both exons simultaneously. Thus, the predicted length of this domain is either 12, 31, or 34 residues. Analyses covering both the COL1 and NC2 domains demonstrate that at least 12 mRNA species exist through the alternations of exons 3B-5, 12, and 13.
authors.affiliation: Collagen Research Unit, University of Oulu, Finland.
authors.forename: M
authors.initials: M
authors.lastname: Juvonen
authors.forename: T
authors.initials: T
authors.lastname: Pihlajaniemi
mesh_terms: D000022:Abortion, Spontaneous; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D001483:Base Sequence; D001842:Bone and Bones / Q000502:physiology*; D003094:Collagen / Q000235:genetics*; D005091:Exons; D005260:Female; D005333:Fetus; D005354:Fibrosarcoma; D014644:Genetic Variation; D006801:Humans; D007438:Introns; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides; D016133:Polymerase Chain Reaction; D011247:Pregnancy; D021382:Protein Sorting Signals / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D014158:Transcription, Genetic; D014407:Tumor Cells, Cultured
chemical_list: D009838:Oligodeoxyribonucleotides; D021382:Protein Sorting Signals; D012333:RNA, Messenger; D003094:Collagen