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Collagen, type IX, alpha 1

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(Redirected fromCOL9A1)

Protein found in humans

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)^[1]

Band	6q13	Start	70,216,040bp^[1]
Band	6q13	End	70,303,084bp^[1]

Gene location (Mouse)

Chr.	Chromosome 1 (mouse)^[2]

Band	1 A5\|1 9.95 cM	Start	24,216,691bp^[2]
Band	1 A5\|1 9.95 cM	End	24,291,765bp^[2]

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

^[3]

^[4]

Wikidata

View/Edit Human

View/Edit Mouse

Collagen alpha-1(IX) chain is aprotein that in humans is encoded by theCOL9A1gene.^[5]^[6]

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.^[6]

References

[edit]

^^a ^b ^cGRCh38: Ensembl release 89: ENSG00000112280 –Ensembl, May 2017
^^a ^b ^cGRCm38: Ensembl release 89: ENSMUSG00000026147 –Ensembl, May 2017
^"Human PubMed Reference:".National Center for Biotechnology Information, U.S. National Library of Medicine.
^"Mouse PubMed Reference:".National Center for Biotechnology Information, U.S. National Library of Medicine.
^Wu JJ, Woods PE, Eyre DR (Dec 1992)."Identification of cross-linking sites in bovine cartilage type IX collagen reveals an antiparallel type II-type IX molecular relationship and type IX to type IX bonding".J Biol Chem.267 (32):23007–14.doi:10.1016/S0021-9258(18)50048-X.PMID 1429648.
^^a ^b"Entrez Gene: COL9A1 collagen, type IX, alpha 1".

External links

[edit]

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.

v t e PDB gallery
2uur: N-TERMINAL NC4 DOMAIN OF COLLAGEN IX

Protein:scleroproteins

Extracellular
matrix

Collagen

Fibril forming	type I COL1A1 COL1A2 type II (COL2A1) type III type V COL5A1 COL5A2 COL5A3 COL24A1 COL26A1
Other	FACIT:type IX COL9A1 COL9A2 COL9A3 type XII (COL12A1) COL14A1 COL16A1 COL19A1 COL20A1 COL21A1 COL22A1 basement membrane:type IV COL4A1 COL4A2 COL4A3 COL4A4 COL4A5 COL4A6 multiplexin:COL15A1 type XVIII COL18A1 Endostatin transmembrane:COL13A1 COL17A1 COL23A1 COL25A1 other:type VI COL6A1 COL6A2 COL6A3 COL6A5 type VII (COL7A1) type VIII COL8A1 COL8A2 type X (COL10A1) type XI COL11A1 COL11A2 COL27A1 COL28A1
Enzymes	Prolyl hydroxylase/Lysyl hydroxylase Cartilage associated protein/Leprecan ADAMTS2 Procollagen peptidase Lysyl oxidase

Laminin

Other

See also: diseases

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