Q14050 (CO9A3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Collagen alpha-3(IX) chain

Gene names

Name:

COL9A3

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	684 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Structural component of hyaline cartilage and vitreous of the eye.
Subunit structure	Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain.
Subcellular location	Secreted › extracellular space › extracellular matrix By similarity.
Post-translational modification	Covalently linked to the telopeptides of type II collagen by lysine-derived cross-links. Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
Involvement in disease	Multiple epiphyseal dysplasia 3 (EDM3) [MIM:600969]: A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal. Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.6 Intervertebral disc disease (IDD) [MIM:603932]: A common musculo-skeletal disorder caused by degeneration of intervertebral disks of the lumbar spine. It results in low-back pain and unilateral leg pain. Note: Disease susceptibility is associated with variations affecting the gene represented in this entry. Susceptibility to intervertebral disk disease is conferred by variant p.Arg103Trp (Ref.8). Ref.8
Sequence similarities	Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.

Ontologies

Keywords
Cellular component	Extracellular matrix Secreted
Coding sequence diversity	Polymorphism
Disease	Dwarfism
Domain	Collagen Repeat Signal
PTM	Glycoprotein Hydroxylation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	axon guidance Traceable author statement. Source: Reactome collagen catabolic process Traceable author statement. Source: Reactome extracellular matrix disassembly Traceable author statement. Source: Reactome female gonad development Inferred from electronic annotation. Source: Compara male gonad development Inferred from electronic annotation. Source: Compara
Cellular_component	collagen type IX Inferred from direct assay PubMed 8660302. Source: BHF-UCL endoplasmic reticulum lumen Traceable author statement. Source: Reactome
Molecular_function	extracellular matrix structural constituent conferring tensile strength Inferred by curator PubMed 8660302. Source: BHF-UCL
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 25	25	Potential
	Chain	26 – 684	659	Collagen alpha-3(IX) chain		PRO_0000005848
Regions
	Region	29 – 519	491	Triple-helical region 3 (COL3)
	Region	520 – 550	31	Nonhelical region 3 (NC3)
	Region	551 – 630	80	Triple-helical region 2 (COL2)
	Region	631 – 632	2	Nonhelical region 2 (NC2)
	Region	633 – 661	29	Triple-helical region 1 (COL1)
	Region	662 – 684	23	Nonhelical region 1 (NC1)
	Motif	423 – 425	3	Cell attachment site Potential
	Motif	601 – 603	3	Cell attachment site Potential
Amino acid modifications
	Glycosylation	483	1	N-linked (GlcNAc...) Potential
Natural variations
	Natural variant	94	1	P → S. Corresponds to variant rs35908728 [ dbSNP | Ensembl ].		VAR_048808
	Natural variant	103	1	R → Q. Ref.9		VAR_026467
	Natural variant	103	1	R → W Associated with an increased risk for intervertebral disk disease. Ref.9		VAR_026468
	Natural variant	296	1	P → L. Ref.9 Corresponds to variant rs45628843 [ dbSNP | Ensembl ].		VAR_026469
	Natural variant	402	1	R → Q. Ref.9		VAR_026470
	Natural variant	435	1	A → E. Ref.1 Ref.9 Corresponds to variant rs751557 [ dbSNP | Ensembl ].		VAR_026471
	Natural variant	563 – 565	3	Missing.		VAR_012660
	Natural variant	564 – 566	3	Missing.		VAR_012661
Experimental info
	Sequence conflict	18	1	E → Q in AAC41947. Ref.1
	Sequence conflict	18	1	E → Q in AAD47357. Ref.2
	Sequence conflict	39	1	P → R in AAC41947. Ref.1
	Sequence conflict	144	1	S → P in AAC41947. Ref.1
	Sequence conflict	524	1	R → H in CAA62495. Ref.5
	Sequence conflict	576	1	A → T in CAA62495. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Q14050 [UniParc]. Last modified January 23, 2002. Version 2. Checksum: 892F035CF6E06733	FASTA	684	63,616
	10 20 30 40 50 60 MAGPRACAPL LLLLLLGELL AAAGAQRVGL PGPPGPPGPP GKPGQDGIDG EAGPPGLPGP 70 80 90 100 110 120 PGPKGAPGKP GKPGEAGLPG LPGVDGLTGR DGPPGPKGAP GERGSLGPPG PPGLGGKGLP 130 140 150 160 170 180 GPPGEAGVSG PPGGIGLRGP PGPSGLPGLP GPPGPPGPPG HPGVLPEGAT DLQCPSICPP 190 200 210 220 230 240 GPPGPPGMPG FKGPTGYKGE QGEVGKDGEK GDPGPPGPAG LPGSVGLQGP RGLRGLPGPL 250 260 270 280 290 300 GPPGDRGPIG FRGPPGIPGA PGKAGDRGER GPEGFRGPKG DLGRPGPKGT PGVAGPSGEP 310 320 330 340 350 360 GMPGKDGQNG VPGLDGQKGE AGRNGAPGEK GPNGLPGLPG RAGSKGEKGE RGRAGELGEA 370 380 390 400 410 420 GPSGEPGVPG DAGMPGERGE AGHRGSAGAL GPQGPPGAPG VRGFQGQKGS MGDPGLPGPQ 430 440 450 460 470 480 GLRGDVGDRG PGGAAGPKGD QGIAGSDGLP GDKGELGPSG LVGPKGESGS RGELGPKGTQ 490 500 510 520 530 540 GPNGTSGVQG VPGPPGPLGL QGVPGVPGIT GKPGVPGKEA SEQRIRELCG GMISEQIAQL 550 560 570 580 590 600 AAHLRKPLAP GSIGRPGPAG PPGPPGPPGS IGHPGARGPP GYRGPTGELG DPGPRGNQGD 610 620 630 640 650 660 RGDKGAAGAG LDGPEGDQGP QGPQGVPGTS KDGQDGAPGE PGPPGDPGLP GAIGAQGTPG 670 680 ICDTSACQGA VLGGVGEKSG SRSS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning of the alpha 3 chain of human type IX collagen: linkage of the gene COL9A3 to chromosome 20q13.3." Brewton R.G., Wood B.M., Ren Z.-X., Gong Y., Tiller G.E., Warman M.L., Lee B., Horton W.A., Olsen B.R., Baker J.R., Mayne R. Genomics 30:329-336(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLU-435. Tissue: Cartilage.
[2]	"Complete sequence of the 23-kilobase human COL9A3 gene. Detection of Gly-X-Y triplet deletions that represent neutral variants." Paassilta P., Pihlajamaa T., Annunen S., Brewton R.G., Wood B.M., Johnson C.C., Liu J., Gong Y., Warman M.L., Prockop D.J., Mayne R., Ala-Kokko L. J. Biol. Chem. 274:22469-22475(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANTS 563-GLY--PRO-565 DEL AND 564-PRO--GLY-566 DEL.
[3]	"The DNA sequence and comparative analysis of human chromosome 20." Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E. , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J. Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Skin.
[5]	"Developmental regulation of mRNA species for types II, IX and XI collagens during mouse embryogenesis." Peraelae M., Savontaus M., Metsaeranta M., Vuorio E. Biochem. J. 324:209-216(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 522-667. Tissue: Cartilage.
[6]	"COL9A3: A third locus for multiple epiphyseal dysplasia." Paassilta P., Lohiniva J., Annunen S., Bonaventure J., Le Merrer M., Pai L., Ala-Kokko L. Am. J. Hum. Genet. 64:1036-1044(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INVOLVEMENT IN EDM3.
[7]	Erratum Paassilta P., Lohiniva J., Annunen S., Bonaventure J., Le Merrer M., Pai L., Ala-Kokko L. Am. J. Hum. Genet. 65:1214-1214(1999)
[8]	"Identification of a novel common genetic risk factor for lumbar disk disease." Paassilta P., Lohiniva J., Goring H.H., Perala M., Raina S.S., Karppinen J., Hakala M., Palm T., Kroger H., Kaitila I., Vanharanta H., Ott J., Ala-Kokko L. JAMA 285:1843-1849(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INVOLVEMENT IN SUSCEPTIBILITY TO IDD.
[9]	"A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity." Czarny-Ratajczak M., Lohiniva J., Rogala P., Kozlowski K., Peraelae M., Carter L., Spector T.D., Kolodziej L., Seppaenen U., Glazar R., Krolewski J., Latos-Bielenska A., Ala-Kokko L. Am. J. Hum. Genet. 69:969-980(2001) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS GLN-103; TRP-103; LEU-296; GLN-402 AND GLU-435.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases
EMBL GenBank DDBJ	L41162 mRNA. Translation: AAC41947.1. AF026802, AF026801 Genomic DNA. Translation: AAD47357.1. AL035669 Genomic DNA. Translation: CAC12750.1. BC011705 mRNA. Translation: AAH11705.1. X91013 mRNA. Translation: CAA62495.1.
IPI	IPI00289999.
RefSeq	NP_001844.3. NM_001853.3.
UniGene	Hs.716639.
3D structure databases
ProteinModelPortal	Q14050.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q14050. 1 interaction.
STRING	9606.ENSP00000341640.
PTM databases
PhosphoSite	Q14050.
Polymorphism databases
DMDM	20137327.
Proteomic databases
PaxDb	Q14050.
PRIDE	Q14050.
Protocols and materials databases
DNASU	1299.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000343916; ENSP00000341640; ENSG00000092758.
GeneID	1299.
KEGG	hsa:1299.
UCSC	uc002ydm.3. human.
Organism-specific databases
CTD	1299.
GeneCards	GC20P061447.
HGNC	HGNC:2219. COL9A3.
HPA	HPA040125.
MIM	120270. gene. 600969. phenotype. 603932. phenotype.
neXtProt	NX_Q14050.
Orphanet	166002. Multiple epiphyseal dysplasia due to collagen 9 anomaly.
PharmGKB	PA26735.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG297550.
HOGENOM	HOG000085653.
HOVERGEN	HBG004933.
InParanoid	Q14050.
KO	K08131.
OMA	PAGSIGH.
OrthoDB	EOG43N7D8.
PhylomeDB	Q14050.
Enzyme and pathway databases
Reactome	REACT_111045. Developmental Biology. REACT_111102. Signal Transduction. REACT_118779. Extracellular matrix organization.
Gene expression databases
ArrayExpress	Q14050.
Bgee	Q14050.
CleanEx	HS_COL9A3.
Genevestigator	Q14050.
GermOnline	ENSG00000092758. Homo sapiens.
Family and domain databases
InterPro	IPR008160. Collagen. [Graphical view]
Pfam	PF01391. Collagen. 9 hits. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	COL9A3. human.
GenomeRNAi	1299.
NextBio	5275.
SOURCE	Search...

Entry information

Entry name

CO9A3_HUMAN

Accession

Primary (citable) accession number: Q14050
Secondary accession number(s): Q13681, Q9H4G9, Q9UPE2

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 23, 2002
Last sequence update:	January 23, 2002
Last modified:	May 29, 2013
This is version 131 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.