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. 1984 Aug 10;12(15):6117–6125. doi: 10.1093/nar/12.15.6117

Location of the 11 bp exon in the chicken pro alpha 2(I) collagen gene.

S Aho, V Tate, H Boedtker
PMCID: PMC320061  PMID: 6473103

Abstract

During the fine structural analysis of the 5' end of the 38 kb chicken pro alpha 2(I) collagen gene, we failed to locate an exon, only 11 bp in size, which had been predicted from the DNA sequence analysis of a cDNA clone complementary to the 5' end of the pro alpha 2(I) collagen mRNA (1). We know report the location of this 11 bp exon, exon 2, at the 5' end of a 180 bp Pst I fragment, 1900 bp 3' to exon 1 and 600 bp 5' to exon 3. Its sequence, ATGTGAGTGAG, is highly unusual in that it contains two overlapping consensus donor splice sequences. Moreover, it is flanked by two overlapping donor splice sequences but only one of the four splice sequences is actually spliced (1). The first half of intron 1 also has an unusual sequence: it is 68% GC, contains 88 CpG dinucleotides and 11 Hpa II sites. The second half is more like other intron sequences in the collagen gene with a GC content of 41%, 19 CpG, and no Hpa II sites. However it contains two sequences with 7 and 9 bp homology to the 14 bp SV40 enhancer core sequence. It is suggested that some part of intron 1 may be involved in regulation.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bentz H., Morris N. P., Murray L. W., Sakai L. Y., Hollister D. W., Burgeson R. E. Isolation and partial characterization of a new human collagen with an extended triple-helical structural domain. Proc Natl Acad Sci U S A. 1983 Jun;80(11):3168–3172. doi: 10.1073/pnas.80.11.3168. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boedtker H., Fuller F., Tate V. The structure of collagen genes. Int Rev Connect Tissue Res. 1983;10:1–63. doi: 10.1016/b978-0-12-363710-9.50007-1. [DOI] [PubMed] [Google Scholar]
  4. Catterall J. F., Stein J. P., Kristo P., Means A. R., O'Malley B. W. Primary sequence of ovomucoid messenger RNA as determined from cloned complementary DNA. J Cell Biol. 1980 Nov;87(2 Pt 1):480–487. doi: 10.1083/jcb.87.2.480. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Finer M. H., Fodor E. J., Boedtker H., Doty P. Endonuclease S1-sensitive site in chicken pro-alpha 2(I) collagen 5' flanking gene region. Proc Natl Acad Sci U S A. 1984 Mar;81(6):1659–1663. doi: 10.1073/pnas.81.6.1659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Frischauf A. M., Garoff H., Lehrach H. A subcloning strategy for DNA sequence analysis. Nucleic Acids Res. 1980 Dec 11;8(23):5541–5549. doi: 10.1093/nar/8.23.5541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fuller F., Boedtker H. Sequence determination and analysis of the 3' region of chicken pro-alpha 1(I) and pro-alpha 2(I) collagen messenger ribonucleic acids including the carboxy-terminal propeptide sequences. Biochemistry. 1981 Feb 17;20(4):996–1006. doi: 10.1021/bi00507a054. [DOI] [PubMed] [Google Scholar]
  8. Geiser M., Mattaj I. W., Wilks A. F., Seldran M., Jost J. P. Structure and sequence of the promoter area and of a 5' upstream demethylation site of the estrogen-regulated chicken vitellogenin ii gene. J Biol Chem. 1983 Jul 25;258(14):9024–9030. [PubMed] [Google Scholar]
  9. Gibson G. J., Kielty C. M., Garner C., Schor S. L., Grant M. E. Identification and partial characterization of three low-molecular-weight collagenous polypeptides synthesized by chondrocytes cultured within collagen gels in the absence and in the presence of fibronectin. Biochem J. 1983 May 1;211(2):417–426. doi: 10.1042/bj2110417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Harbers K., Kuehn M., Delius H., Jaenisch R. Insertion of retrovirus into the first intron of alpha 1(I) collagen gene to embryonic lethal mutation in mice. Proc Natl Acad Sci U S A. 1984 Mar;81(5):1504–1508. doi: 10.1073/pnas.81.5.1504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Jander R., Rauterberg J., Glanville R. W. Further characterization of the three polypeptide chains of bovine and human short-chain collagen (intima collagen). Eur J Biochem. 1983 Jun 1;133(1):39–46. doi: 10.1111/j.1432-1033.1983.tb07427.x. [DOI] [PubMed] [Google Scholar]
  12. Lehrach H., Frischauf A. M., Hanahan D., Wozney J., Fuller F., Crkvenjakov R., Boedtker H., Doty P. Construction and characterization of a 2.5-kilobase procollagen clone. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5417–5421. doi: 10.1073/pnas.75.11.5417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  14. McKeon C., Ohkubo H., Pastan I., de Crombrugghe B. Unusual methylation pattern of the alpha 2 (l) collagen gene. Cell. 1982 May;29(1):203–210. doi: 10.1016/0092-8674(82)90104-0. [DOI] [PubMed] [Google Scholar]
  15. Merlino G. T., McKeon C., de Crombrugghe B., Pastan I. Regulation of the expression of genes encoding types I, II, and III collagen during chick embryonic development. J Biol Chem. 1983 Aug 25;258(16):10041–10048. [PubMed] [Google Scholar]
  16. Miller E. J., Gay S. Collagen: an overview. Methods Enzymol. 1982;82(Pt A):3–32. doi: 10.1016/0076-6879(82)82058-2. [DOI] [PubMed] [Google Scholar]
  17. Sage H., Trüeb B., Bornstein P. Biosynthetic and structural properties of endothelial cell type VIII collagen. J Biol Chem. 1983 Nov 10;258(21):13391–13401. [PubMed] [Google Scholar]
  18. Sandell L. J., Yamada Y., Dorfman A., Upholt W. B. Identification of genomic DNA coding for chicken type II procollagen. J Biol Chem. 1983 Oct 10;258(19):11617–11621. [PubMed] [Google Scholar]
  19. Schmid T. M., Linsenmayer T. F. A short chain (pro)collagen from aged endochondral chondrocytes. Biochemical characterization. J Biol Chem. 1983 Aug 10;258(15):9504–9509. [PubMed] [Google Scholar]
  20. Showalter A. M., Pesciotta D. M., Eikenberry E. F., Yamamoto T., Pastan I., DeCrombrugghe B., Fietzek P. P., Olsen B. R. Nucleotide sequence of a collagen cDNA-fragment coding for the carboxyl end of pro alpha 1(I)-chains. FEBS Lett. 1980 Feb 25;111(1):61–65. doi: 10.1016/0014-5793(80)80761-7. [DOI] [PubMed] [Google Scholar]
  21. Stein J. P., Catterall J. F., Kristo P., Means A. R., O'Malley B. W. Ovomucoid intervening sequences specify functional domains and generate protein polymorphism. Cell. 1980 Oct;21(3):681–687. doi: 10.1016/0092-8674(80)90431-6. [DOI] [PubMed] [Google Scholar]
  22. Tate V. E., Finer M. H., Boedtker H., Doty P. Chick pro alpha 2 (I) collagen gene: exon location and coding potential for the prepropeptide. Nucleic Acids Res. 1983 Jan 11;11(1):91–104. doi: 10.1093/nar/11.1.91. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Tate V., Finer M., Boedtker H., Doty P. Procollagen genes: further sequence studies and interspecies comparisons. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1039–1049. doi: 10.1101/sqb.1983.047.01.117. [DOI] [PubMed] [Google Scholar]
  24. Yamada Y., Kühn K., de Crombrugghe B. A conserved nucleotide sequence, coding for a segment of the C-propeptide, is found at the same location in different collagen genes. Nucleic Acids Res. 1983 May 11;11(9):2733–2744. doi: 10.1093/nar/11.9.2733. [DOI] [PMC free article] [PubMed] [Google Scholar]

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