Collagen, type IX, alpha 1

Collagen alpha-1(IX) chain is a protein that in humans is encoded by the COL9A1 gene.

COL9A1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2UUR
Identifiers
Aliases	COL9A1, DJ149L1.1.2, EDM6, MED, STL4, collagen type IX alpha 1, collagen type IX alpha 1 chain
External IDs	OMIM: 120210; MGI: 88465; HomoloGene: 1393; GeneCards: COL9A1; OMA:COL9A1 - orthologs
Gene location (Human) Chr. Chromosome 6 (human) Band 6q13 Start 70,216,040 bp End 70,303,084 bp
Gene location (Mouse) Chr. Chromosome 1 (mouse) Band 1 A5|1 9.95 cM Start 24,216,691 bp End 24,291,765 bp
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in tibia cartilage tissue ventricular zone sperm ganglionic eminence Epithelium of choroid plexus Amygdala gonad caudate nucleus cingulate gyrus Top expressed in vestibular sensory epithelium human fetus condyle fossa saccule calvaria mandibular prominence phalanx of finger lesser wing of sphenoid bone utricle More reference expression data BioGPS More reference expression data
Gene ontology Molecular function extracellular matrix structural constituent conferring tensile strength metal ion binding extracellular matrix structural constituent Cellular component collagen type IX trimer extracellular region collagen endoplasmic reticulum lumen extracellular space extracellular matrix collagen-containing extracellular matrix Biological process animal organ morphogenesis extracellular matrix organization Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 1297 12839 Ensembl ENSG00000112280 ENSMUSG00000026147 UniProt P20849 Q05722 RefSeq (mRNA) NM_001851 NM_078485 NM_001377289 NM_001377290 NM_001377291 NM_001290691 NM_007740 RefSeq (protein) NP_001842 NP_511040 NP_001364218 NP_001364219 NP_001364220 NP_001277620 NP_031766 Location (UCSC) Chr 6: 70.22 – 70.3 Mb Chr 1: 24.22 – 24.29 Mb PubMed search
Wikidata
View/Edit Human View/Edit Mouse

This gene encodes one of the three alpha chains of type IX collagen, a collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene may be associated with multiple epiphyseal dysplasia. Two transcript variants have been identified for this gene.

External links

• GeneReviews/NCBI/NIH/UW entry on Multiple Epiphyseal Dysplasia, Dominant
• GeneReviews/NCBI/NIH/UW entry on Stickler Syndrome

Further reading

• Muragaki Y, Nishimura I, Henney A, et al. (1990). "The alpha 1 (IX) collagen gene gives rise to two different transcripts in both mouse embryonic and human fetal RNA". Proc. Natl. Acad. Sci. U.S.A. 87 (7): 2400–4. Bibcode:1990PNAS...87.2400M. doi:10.1073/pnas.87.7.2400. PMC 53696. PMID 1690886.
• Muragaki Y, Kimura T, Ninomiya Y, Olsen BR (1990). "The complete primary structure of two distinct forms of human alpha 1 (IX) collagen chains". Eur. J. Biochem. 192 (3): 703–8. doi:10.1111/j.1432-1033.1990.tb19279.x. PMID 2209617.
• Fahrig T, Landa C, Pesheva P, et al. (1988). "Characterization of binding properties of the myelin-associated glycoprotein to extracellular matrix constituents". EMBO J. 6 (10): 2875–83. doi:10.1002/j.1460-2075.1987.tb02590.x. PMC 553721. PMID 2446864.
• Kimura T, Mattei MG, Stevens JW, et al. (1989). "Molecular cloning of rat and human type IX collagen cDNA and localization of the alpha 1(IX) gene on the human chromosome 6". Eur. J. Biochem. 179 (1): 71–8. doi:10.1111/j.1432-1033.1989.tb14522.x. PMID 2465149.
• Fitch JM, Mentzer A, Mayne R, Linsenmayer TF (1988). "Acquisition of type IX collagen by the developing avian primary corneal stroma and vitreous". Dev. Biol. 128 (2): 396–405. doi:10.1016/0012-1606(88)90301-6. PMID 3294062.
• McCormick D, van der Rest M, Goodship J, et al. (1987). "Structure of the glycosaminoglycan domain in the type IX collagen-proteoglycan". Proc. Natl. Acad. Sci. U.S.A. 84 (12): 4044–8. Bibcode:1987PNAS...84.4044M. doi:10.1073/pnas.84.12.4044. PMC 305018. PMID 3473493.
• Richardson GP, Russell IJ, Duance VC, Bailey AJ (1987). "Polypeptide composition of the mammalian tectorial membrane". Hear. Res. 25 (1): 45–60. doi:10.1016/0378-5955(87)90078-5. PMID 3542919. S2CID 42559806.
• Robertson NG, Khetarpal U, Gutiérrez-Espeleta GA, et al. (1995). "Isolation of novel and known genes from a human fetal cochlear cDNA library using subtractive hybridization and differential screening". Genomics. 23 (1): 42–50. doi:10.1006/geno.1994.1457. PMID 7829101.
• Warman ML, Tiller GE, Polumbo PA, et al. (1993). "Physical and linkage mapping of the human and murine genes for the alpha 1 chain of type IX collagen (COL9A1)". Genomics. 17 (3): 694–8. doi:10.1006/geno.1993.1391. PMID 8244386.
• Diab M, Wu JJ, Eyre DR (1996). "Collagen type IX from human cartilage: a structural profile of intermolecular cross-linking sites". Biochem. J. 314 (1): 327–32. doi:10.1042/bj3140327. PMC 1217044. PMID 8660302.
• Pihlajamaa T, Vuoristo MM, Annunen S, et al. (1998). "Human COL9A1 and COL9A2 genes. Two genes of 90 and 15 kb code for similar polypeptides of the same collagen molecule". Matrix Biol. 17 (3): 237–41. doi:10.1016/S0945-053X(98)90063-4. PMID 9707347.
• Paassilta P, Lohiniva J, Göring HH, et al. (2001). "Identification of a novel common genetic risk factor for lumbar disk disease". JAMA. 285 (14): 1843–9. doi:10.1001/jama.285.14.1843. PMID 11308397.
• Czarny-Ratajczak M, Lohiniva J, Rogala P, et al. (2001). "A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity". Am. J. Hum. Genet. 69 (5): 969–80. doi:10.1086/324023. PMC 1274373. PMID 11565064.
• Wistow G, Bernstein SL, Wyatt MK, et al. (2002). "Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants". Mol. Vis. 8: 205–20. PMID 12107410.
• Zhang P, Jimenez SA, Stokes DG (2003). "Regulation of human COL9A1 gene expression. Activation of the proximal promoter region by SOX9". J. Biol. Chem. 278 (1): 117–23. doi:10.1074/jbc.M208049200. PMID 12399468.
• Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. Bibcode:2002PNAS...9916899M. doi:10.1073/pnas.242603899. PMC 139241. PMID 12477932.
• Mungall AJ, Palmer SA, Sims SK, et al. (2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805–11. doi:10.1038/nature02055. PMID 14574404.
• Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40–5. doi:10.1038/ng1285. PMID 14702039.
• Pihlajamaa T, Lankinen H, Ylöstalo J, et al. (2004). "Characterization of recombinant amino-terminal NC4 domain of human collagen IX: interaction with glycosaminoglycans and cartilage oligomeric matrix protein". J. Biol. Chem. 279 (23): 24265–73. doi:10.1074/jbc.M402865200. PMID 15047691.
• Gerhard DS, Wagner L, Feingold EA, et al. (2004). "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)". Genome Res. 14 (10B): 2121–7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.