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Protein

Collagen alpha-3(IX) chain

Gene

COL9A3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Structural component of hyaline cartilage and vitreous of the eye.

GO - Molecular functioni

  1. extracellular matrix structural constituent conferring tensile strength Source: BHF-UCL

GO - Biological processi

  1. axon guidance Source: Reactome
  2. collagen catabolic process Source: Reactome
  3. extracellular matrix disassembly Source: Reactome
  4. extracellular matrix organization Source: Reactome
  5. female gonad development Source: Ensembl
  6. male gonad development Source: Ensembl
Complete GO annotation...

Enzyme and pathway databases

ReactomeiREACT_121139. Collagen biosynthesis and modifying enzymes.
REACT_13552. Integrin cell surface interactions.
REACT_150401. Collagen degradation.
REACT_163906. ECM proteoglycans.
REACT_16888. Signaling by PDGF.
REACT_18312. NCAM1 interactions.

Names & Taxonomyi

Protein namesi
Recommended name:
Collagen alpha-3(IX) chain
Gene namesi
Name:COL9A3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 20

Organism-specific databases

HGNCiHGNC:2219. COL9A3.

Subcellular locationi

GO - Cellular componenti

  1. collagen type IX trimer Source: BHF-UCL
  2. endoplasmic reticulum lumen Source: Reactome
  3. extracellular region Source: Reactome
  4. proteinaceous extracellular matrix Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Extracellular matrix, Secreted

Pathology & Biotechi

Involvement in diseasei

Multiple epiphyseal dysplasia 31 Publication

The disease is caused by mutations affecting the gene represented in this entry.

Disease descriptionA 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.

See also OMIM:600969
Intervertebral disc disease1 Publication

Disease susceptibility is associated with variations affecting the gene represented in this entry. Susceptibility to intervertebral disk disease is conferred by variant p.Arg103Trp (PubMed:11308397).

Disease descriptionA common musculo-skeletal disorder caused by degeneration of intervertebral disks of the lumbar spine. It results in low-back pain and unilateral leg pain.

See also OMIM:603932

Keywords - Diseasei

Dwarfism

Organism-specific databases

MIMi600969. phenotype.
603932. phenotype.
Orphaneti250984. Autosomal recessive Stickler syndrome.
166002. Multiple epiphyseal dysplasia due to collagen 9 anomaly.
PharmGKBiPA26735.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2525Sequence AnalysisAdd
BLAST
Chaini26 – 684659Collagen alpha-3(IX) chainPRO_0000005848Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi483 – 4831N-linked (GlcNAc...)Sequence Analysis

Post-translational modificationi

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.

Keywords - PTMi

Glycoprotein, Hydroxylation

Proteomic databases

MaxQBiQ14050.
PaxDbiQ14050.
PRIDEiQ14050.

PTM databases

PhosphoSiteiQ14050.

Expressioni

Gene expression databases

BgeeiQ14050.
CleanExiHS_COL9A3.
ExpressionAtlasiQ14050. baseline and differential.
GenevestigatoriQ14050.

Organism-specific databases

HPAiHPA040125.
HPA058323.

Interactioni

Subunit structurei

Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain.

Protein-protein interaction databases

BioGridi107696. 1 interaction.
IntActiQ14050. 1 interaction.
STRINGi9606.ENSP00000341640.

Structurei

3D structure databases

ProteinModelPortaliQ14050.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni29 – 519491Triple-helical region 3 (COL3)Add
BLAST
Regioni520 – 55031Nonhelical region 3 (NC3)Add
BLAST
Regioni551 – 63080Triple-helical region 2 (COL2)Add
BLAST
Regioni631 – 6322Nonhelical region 2 (NC2)
Regioni633 – 66129Triple-helical region 1 (COL1)Add
BLAST
Regioni662 – 68423Nonhelical region 1 (NC1)Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi423 – 4253Cell attachment siteSequence Analysis
Motifi601 – 6033Cell attachment siteSequence Analysis

Sequence similaritiesi

Keywords - Domaini

Collagen, Repeat, Signal

Phylogenomic databases

eggNOGiNOG297550.
GeneTreeiENSGT00780000121854.
HOGENOMiHOG000085653.
HOVERGENiHBG004933.
InParanoidiQ14050.
KOiK08131.
OMAiQKVGPQG.
OrthoDBiEOG7J180G.
PhylomeDBiQ14050.

Family and domain databases

InterProiIPR008160. Collagen.
[Graphical view]
PfamiPF01391. Collagen. 9 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q14050-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGPRACAPL LLLLLLGELL AAAGAQRVGL PGPPGPPGPP GKPGQDGIDG
60 70 80 90 100
EAGPPGLPGP PGPKGAPGKP GKPGEAGLPG LPGVDGLTGR DGPPGPKGAP
110 120 130 140 150
GERGSLGPPG PPGLGGKGLP GPPGEAGVSG PPGGIGLRGP PGPSGLPGLP
160 170 180 190 200
GPPGPPGPPG HPGVLPEGAT DLQCPSICPP GPPGPPGMPG FKGPTGYKGE
210 220 230 240 250
QGEVGKDGEK GDPGPPGPAG LPGSVGLQGP RGLRGLPGPL GPPGDRGPIG
260 270 280 290 300
FRGPPGIPGA PGKAGDRGER GPEGFRGPKG DLGRPGPKGT PGVAGPSGEP
310 320 330 340 350
GMPGKDGQNG VPGLDGQKGE AGRNGAPGEK GPNGLPGLPG RAGSKGEKGE
360 370 380 390 400
RGRAGELGEA GPSGEPGVPG DAGMPGERGE AGHRGSAGAL GPQGPPGAPG
410 420 430 440 450
VRGFQGQKGS MGDPGLPGPQ GLRGDVGDRG PGGAAGPKGD QGIAGSDGLP
460 470 480 490 500
GDKGELGPSG LVGPKGESGS RGELGPKGTQ GPNGTSGVQG VPGPPGPLGL
510 520 530 540 550
QGVPGVPGIT GKPGVPGKEA SEQRIRELCG GMISEQIAQL AAHLRKPLAP
560 570 580 590 600
GSIGRPGPAG PPGPPGPPGS IGHPGARGPP GYRGPTGELG DPGPRGNQGD
610 620 630 640 650
RGDKGAAGAG LDGPEGDQGP QGPQGVPGTS KDGQDGAPGE PGPPGDPGLP
660 670 680
GAIGAQGTPG ICDTSACQGA VLGGVGEKSG SRSS
Length:684
Mass (Da):63,616
Last modified:January 23, 2002 - v2
Checksum:i892F035CF6E06733
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti18 – 181E → Q in AAC41947 (PubMed:8586434).Curated
Sequence conflicti18 – 181E → Q in AAD47357 (PubMed:10428822).Curated
Sequence conflicti39 – 391P → R in AAC41947 (PubMed:8586434).Curated
Sequence conflicti144 – 1441S → P in AAC41947 (PubMed:8586434).Curated
Sequence conflicti524 – 5241R → H in CAA62495 (PubMed:9164858).Curated
Sequence conflicti576 – 5761A → T in CAA62495 (PubMed:9164858).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti94 – 941P → S.
Corresponds to variant rs35908728 [ dbSNP | Ensembl ].
VAR_048808
Natural varianti103 – 1031R → Q.1 Publication
Corresponds to variant rs142639450 [ dbSNP | Ensembl ].
VAR_026467
Natural varianti103 – 1031R → W Associated with an increased risk for intervertebral disk disease. 1 Publication
Corresponds to variant rs61734651 [ dbSNP | Ensembl ].
VAR_026468
Natural varianti296 – 2961P → L.1 Publication
Corresponds to variant rs45628843 [ dbSNP | Ensembl ].
VAR_026469
Natural varianti402 – 4021R → Q.1 Publication
VAR_026470
Natural varianti435 – 4351A → E.2 Publications
Corresponds to variant rs751557 [ dbSNP | Ensembl ].
VAR_026471
Natural varianti563 – 5653Missing .1 Publication
VAR_012660
Natural varianti564 – 5663Missing .1 Publication
VAR_012661

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS13505.1.
RefSeqiNP_001844.3. NM_001853.3.
UniGeneiHs.716639.

Genome annotation databases

EnsembliENST00000343916; ENSP00000341640; ENSG00000092758.
GeneIDi1299.
KEGGihsa:1299.
UCSCiuc002ydm.3. human.

Polymorphism databases

DMDMi20137327.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS13505.1.
RefSeqiNP_001844.3. NM_001853.3.
UniGeneiHs.716639.

3D structure databases

ProteinModelPortaliQ14050.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi107696. 1 interaction.
IntActiQ14050. 1 interaction.
STRINGi9606.ENSP00000341640.

PTM databases

PhosphoSiteiQ14050.

Polymorphism databases

DMDMi20137327.

Proteomic databases

MaxQBiQ14050.
PaxDbiQ14050.
PRIDEiQ14050.

Protocols and materials databases

DNASUi1299.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000343916; ENSP00000341640; ENSG00000092758.
GeneIDi1299.
KEGGihsa:1299.
UCSCiuc002ydm.3. human.

Organism-specific databases

CTDi1299.
GeneCardsiGC20P061447.
GeneReviewsiCOL9A3.
HGNCiHGNC:2219. COL9A3.
HPAiHPA040125.
HPA058323.
MIMi120270. gene.
600969. phenotype.
603932. phenotype.
neXtProtiNX_Q14050.
Orphaneti250984. Autosomal recessive Stickler syndrome.
166002. Multiple epiphyseal dysplasia due to collagen 9 anomaly.
PharmGKBiPA26735.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG297550.
GeneTreeiENSGT00780000121854.
HOGENOMiHOG000085653.
HOVERGENiHBG004933.
InParanoidiQ14050.
KOiK08131.
OMAiQKVGPQG.
OrthoDBiEOG7J180G.
PhylomeDBiQ14050.

Enzyme and pathway databases

ReactomeiREACT_121139. Collagen biosynthesis and modifying enzymes.
REACT_13552. Integrin cell surface interactions.
REACT_150401. Collagen degradation.
REACT_163906. ECM proteoglycans.
REACT_16888. Signaling by PDGF.
REACT_18312. NCAM1 interactions.

Miscellaneous databases

ChiTaRSiCOL9A3. human.
GeneWikiiCOL9A3.
GenomeRNAii1299.
NextBioi5275.
PROiQ14050.
SOURCEiSearch...

Gene expression databases

BgeeiQ14050.
CleanExiHS_COL9A3.
ExpressionAtlasiQ14050. baseline and differential.
GenevestigatoriQ14050.

Family and domain databases

InterProiIPR008160. Collagen.
[Graphical view]
PfamiPF01391. Collagen. 9 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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. Cited for: INVOLVEMENT IN SUSCEPTIBILITY TO IDD.
  9. Cited for: VARIANTS GLN-103; TRP-103; LEU-296; GLN-402 AND GLU-435.

Entry informationi

Entry nameiCO9A3_HUMAN
AccessioniPrimary (citable) accession number: Q14050
Secondary accession number(s): Q13681, Q9H4G9, Q9UPE2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: January 23, 2002
Last modified: March 4, 2015
This is version 149 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.