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Protein

Collagen alpha-1(IX) chain

Gene

COL9A1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Structural component of hyaline cartilage and vitreous of the eye.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi213Zinc1
Metal bindingi215Zinc1
Metal bindingi253Zinc1

GO - Molecular functioni

  • extracellular matrix structural constituent Source: GO_Central
  • extracellular matrix structural constituent conferring tensile strength Source: BHF-UCL
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • animal organ morphogenesis Source: ProtInc
  • extracellular matrix organization Source: GO_Central

Keywordsi

LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-1442490 Collagen degradation
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-186797 Signaling by PDGF
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures
R-HSA-216083 Integrin cell surface interactions
R-HSA-3000178 ECM proteoglycans
R-HSA-419037 NCAM1 interactions
R-HSA-8948216 Collagen chain trimerization

Names & Taxonomyi

Protein namesi
Recommended name:
Collagen alpha-1(IX) chain
Gene namesi
Name:COL9A1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000112280.15
HGNCiHGNC:2217 COL9A1
MIMi120210 gene
neXtProtiNX_P20849

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Extracellular matrix, Secreted

Pathology & Biotechi

Involvement in diseasei

Multiple epiphyseal dysplasia 6 (EDM6)1 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:614135
Stickler syndrome 4 (STL4)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive form of Stickler syndrome, an inherited disorder that associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or chorioretinal degeneration, retinal detachment, and chronic uveitis. Pierre Robin sequence includes an opening in the roof of the mouth (a cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones are affected by slight platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed by early signs of arthrosis. The degree of hearing loss varies among affected individuals and may become more severe over time. Syndrome expressivity is variable.
See also OMIM:614134

Keywords - Diseasei

Deafness, Stickler syndrome

Organism-specific databases

DisGeNETi1297
GeneReviewsiCOL9A1
MalaCardsiCOL9A1
MIMi614134 phenotype
614135 phenotype
OpenTargetsiENSG00000112280
Orphaneti250984 Autosomal recessive Stickler syndrome
166002 Multiple epiphyseal dysplasia due to collagen 9 anomaly
PharmGKBiPA26733

Polymorphism and mutation databases

BioMutaiCOL9A1
DMDMi296439373

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Add BLAST23
ChainiPRO_000000576524 – 921Collagen alpha-1(IX) chainAdd BLAST898

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi44 ↔ 2421 Publication
Glycosylationi171N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi198 ↔ 2521 Publication
Disulfide bondi411Interchain1 Publication
Disulfide bondi415Interchain1 Publication

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

Disulfide bond, Glycoprotein, Hydroxylation

Proteomic databases

PaxDbiP20849
PeptideAtlasiP20849
PRIDEiP20849
ProteomicsDBi53816
53817 [P20849-2]
53818 [P20849-3]

PTM databases

iPTMnetiP20849
PhosphoSitePlusiP20849

Expressioni

Gene expression databases

BgeeiENSG00000112280 Expressed in 101 organ(s), highest expression level in tibia
GenevisibleiP20849 HS

Organism-specific databases

HPAiHPA074749

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi107694, 8 interactors
ComplexPortaliCPX-1748 Collagen type IX trimer
STRINGi9606.ENSP00000349790

Structurei

Secondary structure

1921
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP20849
SMRiP20849
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP20849

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini50 – 244Laminin G-likeAdd BLAST195
Domaini269 – 324Collagen-like 1Add BLAST56
Domaini325 – 356Collagen-like 2Add BLAST32
Domaini358 – 403Collagen-like 3Add BLAST46
Domaini416 – 472Collagen-like 4Add BLAST57
Domaini473 – 516Collagen-like 5Add BLAST44
Domaini587 – 643Collagen-like 6Add BLAST57
Domaini655 – 712Collagen-like 7Add BLAST58
Domaini713 – 755Collagen-like 8Add BLAST43
Domaini790 – 847Collagen-like 9Add BLAST58
Domaini848 – 899Collagen-like 10Add BLAST52

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni24 – 268Nonhelical region (NC4)Add BLAST245
Regioni269 – 405Triple-helical region (COL3)Add BLAST137
Regioni406 – 417Nonhelical region (NC3)Add BLAST12
Regioni418 – 756Triple-helical region (COL2)Add BLAST339
Regioni757 – 786Nonhelical region (NC2)Add BLAST30
Regioni787 – 901Triple-helical region (COL1)Add BLAST115
Regioni902 – 921Nonhelical region (NC1)Add BLAST20

Domaini

Each subunit is composed of three triple-helical domains interspersed with non-collagenous domains. The globular domain at the N-terminus of type IX collagen molecules represents the NC4 domain which may participate in electrostatic interactions with polyanionic glycosaminoglycans in cartilage.

Sequence similaritiesi

Keywords - Domaini

Collagen, Repeat, Signal

Phylogenomic databases

eggNOGiKOG3544 Eukaryota
ENOG410Y4B3 LUCA
GeneTreeiENSGT00900000140850
HOVERGENiHBG004933
InParanoidiP20849
KOiK08131
OMAiFPGQMGL
OrthoDBiEOG091G0ESN
PhylomeDBiP20849
TreeFamiTF332900

Family and domain databases

InterProiView protein in InterPro
IPR008160 Collagen
IPR013320 ConA-like_dom_sf
IPR001791 Laminin_G
PfamiView protein in Pfam
PF01391 Collagen, 8 hits
SMARTiView protein in SMART
SM00210 TSPN, 1 hit
SUPFAMiSSF49899 SSF49899, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket
Note: Additional isoforms seem to exist.

This entry has 3 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: P20849-1) [UniParc]FASTAAdd to basket
Also known as: Long

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MKTCWKIPVF FFVCSFLEPW ASAAVKRRPR FPVNSNSNGG NELCPKIRIG
60 70 80 90 100
QDDLPGFDLI SQFQVDKAAS RRAIQRVVGS ATLQVAYKLG NNVDFRIPTR
110 120 130 140 150
NLYPSGLPEE YSFLTTFRMT GSTLKKNWNI WQIQDSSGKE QVGIKINGQT
160 170 180 190 200
QSVVFSYKGL DGSLQTAAFS NLSSLFDSQW HKIMIGVERS SATLFVDCNR
210 220 230 240 250
IESLPIKPRG PIDIDGFAVL GKLADNPQVS VPFELQWMLI HCDPLRPRRE
260 270 280 290 300
TCHELPARIT PSQTTDERGP PGEQGPPGPP GPPGVPGIDG IDGDRGPKGP
310 320 330 340 350
PGPPGPAGEP GKPGAPGKPG TPGADGLTGP DGSPGSIGSK GQKGEPGVPG
360 370 380 390 400
SRGFPGRGIP GPPGPPGTAG LPGELGRVGP VGDPGRRGPP GPPGPPGPRG
410 420 430 440 450
TIGFHDGDPL CPNACPPGRS GYPGLPGMRG HKGAKGEIGE PGRQGHKGEE
460 470 480 490 500
GDQGELGEVG AQGPPGAQGL RGITGIVGDK GEKGARGLDG EPGPQGLPGA
510 520 530 540 550
PGDQGQRGPP GEAGPKGDRG AEGARGIPGL PGPKGDTGLP GVDGRDGIPG
560 570 580 590 600
MPGTKGEPGK PGPPGDAGLQ GLPGVPGIPG AKGVAGEKGS TGAPGKPGQM
610 620 630 640 650
GNSGKPGQQG PPGEVGPRGP QGLPGSRGEL GPVGSPGLPG KLGSLGSPGL
660 670 680 690 700
PGLPGPPGLP GMKGDRGVVG EPGPKGEQGA SGEEGEAGER GELGDIGLPG
710 720 730 740 750
PKGSAGNPGE PGLRGPEGSR GLPGVEGPRG PPGPRGVQGE QGATGLPGVQ
760 770 780 790 800
GPPGRAPTDQ HIKQVCMRVI QEHFAEMAAS LKRPDSGATG LPGRPGPPGP
810 820 830 840 850
PGPPGENGFP GQMGIRGLPG IKGPPGALGL RGPKGDLGEK GERGPPGRGP
860 870 880 890 900
NGLPGAIGLP GDPGPASYGR NGRDGERGPP GVAGIPGVPG PPGPPGLPGF
910 920
CEPASCTMQA GQRAFNKGPD P
Length:921
Mass (Da):91,869
Last modified:May 18, 2010 - v3
Checksum:iA69BF076127283D0
GO
Isoform 2 (identifier: P20849-2) [UniParc]FASTAAdd to basket
Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     1-243: Missing.
     244-267: PLRPRRETCHELPARITPSQTTDE → MAWTARDRGALGLLLLGLCLCAAQ

Show »
Length:678
Mass (Da):64,372
Checksum:iAD0E99997DF2896E
GO
Isoform 3 (identifier: P20849-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     326-328: GLT → TSP
     329-921: Missing.

Note: No experimental confirmation available.
Show »
Length:328
Mass (Da):35,509
Checksum:iBDD662939FECAD21
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A2R8YG47A0A2R8YG47_HUMAN
Collagen alpha-1(IX) chain
COL9A1
112Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti279 – 280PP → AS in CAA38276 (PubMed:2209617).Curated2
Sequence conflicti279 – 280PP → AS in CAA38277 (PubMed:2209617).Curated2
Sequence conflicti476I → L in CAA38276 (PubMed:2209617).Curated1
Sequence conflicti570Q → H in AAC33527 (PubMed:9707347).Curated1
Sequence conflicti570Q → H in AAC33528 (PubMed:9707347).Curated1
Sequence conflicti910 – 921AGQRA…KGPDP → LVSEHLTKGLTLERLTAAWL SA in AAA53475 (PubMed:2209617).CuratedAdd BLAST12

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_026463339S → P1 PublicationCorresponds to variant dbSNP:rs592121EnsemblClinVar.1
Natural variantiVAR_026464621Q → R2 PublicationsCorresponds to variant dbSNP:rs1135056EnsemblClinVar.1
Natural variantiVAR_055668684E → K. Corresponds to variant dbSNP:rs35470562Ensembl.1
Natural variantiVAR_055669767M → V. Corresponds to variant dbSNP:rs6910140EnsemblClinVar.1
Natural variantiVAR_023326870R → K3 PublicationsCorresponds to variant dbSNP:rs1056921Ensembl.1
Natural variantiVAR_023327882V → L3 PublicationsCorresponds to variant dbSNP:rs1056923Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0011411 – 243Missing in isoform 2. 2 PublicationsAdd BLAST243
Alternative sequenceiVSP_001142244 – 267PLRPR…QTTDE → MAWTARDRGALGLLLLGLCL CAAQ in isoform 2. 2 PublicationsAdd BLAST24
Alternative sequenceiVSP_015250326 – 328GLT → TSP in isoform 3. 1 Publication3
Alternative sequenceiVSP_015251329 – 921Missing in isoform 3. 1 PublicationAdd BLAST593

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54412 mRNA Translation: CAA38276.1
X54413 mRNA Translation: CAA38277.1
AF036130
, AF036110, AF036111, AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA Translation: AAC33527.1
AF036130
, AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA Translation: AAC33528.1
AL080275 Genomic DNA No translation available.
AL160262 Genomic DNA No translation available.
BC015409 mRNA Translation: AAH15409.1
BC063646 mRNA Translation: AAH63646.1
M32137, M32133 Genomic DNA Translation: AAA53474.1
M32137, M32135 Genomic DNA Translation: AAA53475.1
CCDSiCCDS47447.1 [P20849-2]
CCDS4971.1 [P20849-1]
PIRiS13580
S13581
RefSeqiNP_001842.3, NM_001851.4 [P20849-1]
NP_511040.2, NM_078485.3 [P20849-2]
UniGeneiHs.590892

Genome annotation databases

EnsembliENST00000320755; ENSP00000315252; ENSG00000112280 [P20849-2]
ENST00000357250; ENSP00000349790; ENSG00000112280 [P20849-1]
ENST00000370496; ENSP00000359527; ENSG00000112280 [P20849-3]
GeneIDi1297
KEGGihsa:1297
UCSCiuc003pff.5 human [P20849-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54412 mRNA Translation: CAA38276.1
X54413 mRNA Translation: CAA38277.1
AF036130
, AF036110, AF036111, AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA Translation: AAC33527.1
AF036130
, AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA Translation: AAC33528.1
AL080275 Genomic DNA No translation available.
AL160262 Genomic DNA No translation available.
BC015409 mRNA Translation: AAH15409.1
BC063646 mRNA Translation: AAH63646.1
M32137, M32133 Genomic DNA Translation: AAA53474.1
M32137, M32135 Genomic DNA Translation: AAA53475.1
CCDSiCCDS47447.1 [P20849-2]
CCDS4971.1 [P20849-1]
PIRiS13580
S13581
RefSeqiNP_001842.3, NM_001851.4 [P20849-1]
NP_511040.2, NM_078485.3 [P20849-2]
UniGeneiHs.590892

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2UURX-ray1.80A24-268[»]
5CTDX-ray1.60A754-789[»]
5CTIX-ray1.90A754-789[»]
5CVAX-ray2.10A/D754-789[»]
5CVBX-ray2.25A/D754-789[»]
ProteinModelPortaliP20849
SMRiP20849
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi107694, 8 interactors
ComplexPortaliCPX-1748 Collagen type IX trimer
STRINGi9606.ENSP00000349790

PTM databases

iPTMnetiP20849
PhosphoSitePlusiP20849

Polymorphism and mutation databases

BioMutaiCOL9A1
DMDMi296439373

Proteomic databases

PaxDbiP20849
PeptideAtlasiP20849
PRIDEiP20849
ProteomicsDBi53816
53817 [P20849-2]
53818 [P20849-3]

Protocols and materials databases

DNASUi1297
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000320755; ENSP00000315252; ENSG00000112280 [P20849-2]
ENST00000357250; ENSP00000349790; ENSG00000112280 [P20849-1]
ENST00000370496; ENSP00000359527; ENSG00000112280 [P20849-3]
GeneIDi1297
KEGGihsa:1297
UCSCiuc003pff.5 human [P20849-1]

Organism-specific databases

CTDi1297
DisGeNETi1297
EuPathDBiHostDB:ENSG00000112280.15
GeneCardsiCOL9A1
GeneReviewsiCOL9A1
HGNCiHGNC:2217 COL9A1
HPAiHPA074749
MalaCardsiCOL9A1
MIMi120210 gene
614134 phenotype
614135 phenotype
neXtProtiNX_P20849
OpenTargetsiENSG00000112280
Orphaneti250984 Autosomal recessive Stickler syndrome
166002 Multiple epiphyseal dysplasia due to collagen 9 anomaly
PharmGKBiPA26733
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3544 Eukaryota
ENOG410Y4B3 LUCA
GeneTreeiENSGT00900000140850
HOVERGENiHBG004933
InParanoidiP20849
KOiK08131
OMAiFPGQMGL
OrthoDBiEOG091G0ESN
PhylomeDBiP20849
TreeFamiTF332900

Enzyme and pathway databases

ReactomeiR-HSA-1442490 Collagen degradation
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-186797 Signaling by PDGF
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures
R-HSA-216083 Integrin cell surface interactions
R-HSA-3000178 ECM proteoglycans
R-HSA-419037 NCAM1 interactions
R-HSA-8948216 Collagen chain trimerization

Miscellaneous databases

ChiTaRSiCOL9A1 human
EvolutionaryTraceiP20849
GeneWikiiCollagen,_type_IX,_alpha_1
GenomeRNAii1297
PROiPR:P20849
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000112280 Expressed in 101 organ(s), highest expression level in tibia
GenevisibleiP20849 HS

Family and domain databases

InterProiView protein in InterPro
IPR008160 Collagen
IPR013320 ConA-like_dom_sf
IPR001791 Laminin_G
PfamiView protein in Pfam
PF01391 Collagen, 8 hits
SMARTiView protein in SMART
SM00210 TSPN, 1 hit
SUPFAMiSSF49899 SSF49899, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiCO9A1_HUMAN
AccessioniPrimary (citable) accession number: P20849
Secondary accession number(s): Q13699
, Q13700, Q5TF52, Q6P467, Q96BM8, Q99225, Q9H151, Q9H152, Q9Y6P2, Q9Y6P3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: May 18, 2010
Last modified: November 7, 2018
This is version 202 of the entry and version 3 of the sequence. See 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
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