Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P20849 (CO9A1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 167. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Collagen alpha-1(IX) chain
Gene names
Name:COL9A1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length921 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein 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

Secretedextracellular spaceextracellular matrix By similarity.

Domain

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.

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 6 (EDM6) [MIM:614135]: 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.9

Stickler syndrome 4 (STL4) [MIM:614134]: An 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. 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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.10

Sequence similarities

Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.

Contains 10 collagen-like domains.

Contains 1 laminin G-like domain.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: P20849-1)

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.
Isoform 2 (identifier: P20849-2)

Also known as: Short;

The sequence of this isoform differs from the canonical sequence as follows:
     1-243: Missing.
     244-267: PLRPRRETCHELPARITPSQTTDE → MAWTARDRGALGLLLLGLCLCAAQ
Isoform 3 (identifier: P20849-3)

The sequence of this isoform differs from the canonical sequence as follows:
     326-328: GLT → TSP
     329-921: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2323
Chain24 – 921898Collagen alpha-1(IX) chain
PRO_0000005765

Regions

Domain50 – 244195Laminin G-like
Domain269 – 32456Collagen-like 1
Domain325 – 35632Collagen-like 2
Domain358 – 40346Collagen-like 3
Domain416 – 47257Collagen-like 4
Domain473 – 51644Collagen-like 5
Domain587 – 64357Collagen-like 6
Domain655 – 71258Collagen-like 7
Domain713 – 75543Collagen-like 8
Domain790 – 84758Collagen-like 9
Domain848 – 89952Collagen-like 10
Region24 – 268245Nonhelical region (NC4)
Region269 – 405137Triple-helical region (COL3)
Region406 – 41712Nonhelical region (NC3)
Region418 – 756339Triple-helical region (COL2)
Region757 – 78630Nonhelical region (NC2)
Region787 – 901115Triple-helical region (COL1)
Region902 – 92120Nonhelical region (NC1)

Sites

Metal binding2131Zinc
Metal binding2151Zinc
Metal binding2531Zinc

Amino acid modifications

Glycosylation1711N-linked (GlcNAc...) Potential
Disulfide bond44 ↔ 242 Ref.8
Disulfide bond198 ↔ 252 Ref.8
Disulfide bond411Interchain Ref.8
Disulfide bond415Interchain Ref.8

Natural variations

Alternative sequence1 – 243243Missing in isoform 2.
VSP_001141
Alternative sequence244 – 26724PLRPR…QTTDE → MAWTARDRGALGLLLLGLCL CAAQ in isoform 2.
VSP_001142
Alternative sequence326 – 3283GLT → TSP in isoform 3.
VSP_015250
Alternative sequence329 – 921593Missing in isoform 3.
VSP_015251
Natural variant3391S → P. Ref.9
Corresponds to variant rs592121 [ dbSNP | Ensembl ].
VAR_026463
Natural variant6211Q → R. Ref.2 Ref.9
Corresponds to variant rs1135056 [ dbSNP | Ensembl ].
VAR_026464
Natural variant6841E → K.
Corresponds to variant rs35470562 [ dbSNP | Ensembl ].
VAR_055668
Natural variant7671M → V.
Corresponds to variant rs6910140 [ dbSNP | Ensembl ].
VAR_055669
Natural variant8701R → K. Ref.1 Ref.2 Ref.6
Corresponds to variant rs1056921 [ dbSNP | Ensembl ].
VAR_023326
Natural variant8821V → L. Ref.1 Ref.2 Ref.6
Corresponds to variant rs1056923 [ dbSNP | Ensembl ].
VAR_023327

Experimental info

Sequence conflict279 – 2802PP → AS in CAA38276. Ref.1
Sequence conflict279 – 2802PP → AS in CAA38277. Ref.1
Sequence conflict4761I → L in CAA38276. Ref.1
Sequence conflict5701Q → H in AAC33527. Ref.2
Sequence conflict5701Q → H in AAC33528. Ref.2
Sequence conflict910 – 92112AGQRA…KGPDP → LVSEHLTKGLTLERLTAAWL SA in AAA53475. Ref.1

Secondary structure

........................................... 921
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Long) [UniParc].

Last modified May 18, 2010. Version 3.
Checksum: A69BF076127283D0

FASTA92191,869
        10         20         30         40         50         60 
MKTCWKIPVF FFVCSFLEPW ASAAVKRRPR FPVNSNSNGG NELCPKIRIG QDDLPGFDLI 

        70         80         90        100        110        120 
SQFQVDKAAS RRAIQRVVGS ATLQVAYKLG NNVDFRIPTR NLYPSGLPEE YSFLTTFRMT 

       130        140        150        160        170        180 
GSTLKKNWNI WQIQDSSGKE QVGIKINGQT QSVVFSYKGL DGSLQTAAFS NLSSLFDSQW 

       190        200        210        220        230        240 
HKIMIGVERS SATLFVDCNR IESLPIKPRG PIDIDGFAVL GKLADNPQVS VPFELQWMLI 

       250        260        270        280        290        300 
HCDPLRPRRE TCHELPARIT PSQTTDERGP PGEQGPPGPP GPPGVPGIDG IDGDRGPKGP 

       310        320        330        340        350        360 
PGPPGPAGEP GKPGAPGKPG TPGADGLTGP DGSPGSIGSK GQKGEPGVPG SRGFPGRGIP 

       370        380        390        400        410        420 
GPPGPPGTAG LPGELGRVGP VGDPGRRGPP GPPGPPGPRG TIGFHDGDPL CPNACPPGRS 

       430        440        450        460        470        480 
GYPGLPGMRG HKGAKGEIGE PGRQGHKGEE GDQGELGEVG AQGPPGAQGL RGITGIVGDK 

       490        500        510        520        530        540 
GEKGARGLDG EPGPQGLPGA PGDQGQRGPP GEAGPKGDRG AEGARGIPGL PGPKGDTGLP 

       550        560        570        580        590        600 
GVDGRDGIPG MPGTKGEPGK PGPPGDAGLQ GLPGVPGIPG AKGVAGEKGS TGAPGKPGQM 

       610        620        630        640        650        660 
GNSGKPGQQG PPGEVGPRGP QGLPGSRGEL GPVGSPGLPG KLGSLGSPGL PGLPGPPGLP 

       670        680        690        700        710        720 
GMKGDRGVVG EPGPKGEQGA SGEEGEAGER GELGDIGLPG PKGSAGNPGE PGLRGPEGSR 

       730        740        750        760        770        780 
GLPGVEGPRG PPGPRGVQGE QGATGLPGVQ GPPGRAPTDQ HIKQVCMRVI QEHFAEMAAS 

       790        800        810        820        830        840 
LKRPDSGATG LPGRPGPPGP PGPPGENGFP GQMGIRGLPG IKGPPGALGL RGPKGDLGEK 

       850        860        870        880        890        900 
GERGPPGRGP NGLPGAIGLP GDPGPASYGR NGRDGERGPP GVAGIPGVPG PPGPPGLPGF 

       910        920 
CEPASCTMQA GQRAFNKGPD P 

« Hide

Isoform 2 (Short) [UniParc].

Checksum: AD0E99997DF2896E
Show »

FASTA67864,372
Isoform 3 [UniParc].

Checksum: BDD662939FECAD21
Show »

FASTA32835,509

References

« Hide 'large scale' references
[1]"The complete primary structure of two distinct forms of human alpha 1 (IX) collagen chains."
Muragaki Y., Kimura T., Ninomiya Y., Olsen B.R.
Eur. J. Biochem. 192:703-708(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, VARIANTS LYS-870 AND LEU-882.
[2]"Human COL9A1 and COL9A2 genes. Two genes of 90 and 15 kb code for similar polypeptides of the same collagen molecule."
Pihlajamaa T., Vuoristo M.M., Annunen S., Peraelae M., Prockop D.J., Ala-Kokko L.
Matrix Biol. 17:237-241(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), ALTERNATIVE SPLICING, VARIANTS ARG-621; LYS-870 AND LEU-882.
[3]"The DNA sequence and analysis of human chromosome 6."
Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
Nature 425:805-811(2003) [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] (ISOFORMS 2 AND 3).
Tissue: Brain and Mammary gland.
[5]"Collagen type IX from human cartilage: a structural profile of intermolecular cross-linking sites."
Diab M., Wu J.J., Eyre D.R.
Biochem. J. 314:327-332(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 405-417 (ISOFORMS 1/2).
[6]"Molecular cloning of rat and human type IX collagen cDNA and localization of the alpha 1(IX) gene on the human chromosome 6."
Kimura T., Mattei M.-G., Stevens J.W., Goldring M.B., Ninomiya Y., Olsen B.R.
Eur. J. Biochem. 179:71-78(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 580-820 AND 835-884, VARIANTS LYS-870 AND LEU-882.
[7]"The alpha 1 (IX) collagen gene gives rise to two different transcripts in both mouse embryonic and human fetal RNA."
Muragaki Y., Nishimura I., Henney A., Ninomiya Y., Olsen B.R.
Proc. Natl. Acad. Sci. U.S.A. 87:2400-2404(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING.
[8]"Crystal structure of the N-terminal NC4 domain of collagen IX, a zinc binding member of the laminin-neurexin-sex hormone binding globulin (LNS) domain family."
Leppanen V.M., Tossavainen H., Permi P., Lehtio L., Ronnholm G., Goldman A., Kilpelainen I., Pihlajamaa T.
J. Biol. Chem. 282:23219-23230(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 24-268, DISULFIDE BONDS, ZINC-BINDING SITES.
[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 PRO-339 AND ARG-621, INVOLVEMENT IN EDM6.
[10]"A new autosomal recessive form of Stickler syndrome is caused by a mutation in the COL9A1 gene."
Van Camp G., Snoeckx R.L., Hilgert N., van den Ende J., Fukuoka H., Wagatsuma M., Suzuki H., Smets R.M., Vanhoenacker F., Declau F., Van de Heyning P., Usami S.
Am. J. Hum. Genet. 79:449-457(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN STL4.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X54412 mRNA. Translation: CAA38276.1.
X54413 mRNA. Translation: CAA38277.1.
AF036130 expand/collapse EMBL AC list , 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 expand/collapse EMBL AC list , AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA. Translation: AAC33528.1.
AL080275, AL160262 Genomic DNA. Translation: CAI19590.1.
AL080275 Genomic DNA. Translation: CAI19591.1.
AL160262, AL080275 Genomic DNA. Translation: CAI42321.1.
BC015409 mRNA. Translation: AAH15409.1.
BC063646 mRNA. Translation: AAH63646.1.
M32137, M32133 Genomic DNA. Translation: AAA53474.1.
M32137, M32135 Genomic DNA. Translation: AAA53475.1.
CCDSCCDS47447.1. [P20849-2]
CCDS4971.1. [P20849-1]
PIRS13580.
S13581.
RefSeqNP_001842.3. NM_001851.4. [P20849-1]
NP_511040.2. NM_078485.3. [P20849-2]
UniGeneHs.590892.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2UURX-ray1.80A24-268[»]
ProteinModelPortalP20849.
SMRP20849. Positions 42-256.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid107694. 2 interactions.

PTM databases

PhosphoSiteP20849.

Polymorphism databases

DMDM296439373.

Proteomic databases

PaxDbP20849.
PRIDEP20849.

Protocols and materials databases

DNASU1297.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000320755; ENSP00000315252; ENSG00000112280. [P20849-2]
ENST00000357250; ENSP00000349790; ENSG00000112280. [P20849-1]
ENST00000370496; ENSP00000359527; ENSG00000112280. [P20849-3]
GeneID1297.
KEGGhsa:1297.
UCSCuc003pff.4. human. [P20849-2]
uc003pfg.4. human. [P20849-1]

Organism-specific databases

CTD1297.
GeneCardsGC06M070924.
GeneReviewsCOL9A1.
HGNCHGNC:2217. COL9A1.
MIM120210. gene.
614134. phenotype.
614135. phenotype.
neXtProtNX_P20849.
Orphanet250984. Autosomal recessive Stickler syndrome.
166002. Multiple epiphyseal dysplasia due to collagen 9 anomaly.
PharmGKBPA26733.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG12793.
HOVERGENHBG004933.
InParanoidP20849.
KOK08131.
OMAGFCEPAS.
OrthoDBEOG7VHSXW.
PhylomeDBP20849.
TreeFamTF332900.

Enzyme and pathway databases

ReactomeREACT_111045. Developmental Biology.
REACT_111102. Signal Transduction.
REACT_118779. Extracellular matrix organization.

Gene expression databases

ArrayExpressP20849.
BgeeP20849.
GenevestigatorP20849.

Family and domain databases

Gene3D2.60.120.200. 1 hit.
InterProIPR008160. Collagen.
IPR008985. ConA-like_lec_gl_sf.
IPR013320. ConA-like_subgrp.
IPR001791. Laminin_G.
[Graphical view]
PfamPF01391. Collagen. 10 hits.
[Graphical view]
SMARTSM00210. TSPN. 1 hit.
[Graphical view]
SUPFAMSSF49899. SSF49899. 1 hit.
ProtoNetSearch...

Other

ChiTaRSCOL9A1. human.
EvolutionaryTraceP20849.
GeneWikiCollagen,_type_IX,_alpha_1.
GenomeRNAi1297.
NextBio5265.
PROP20849.
SOURCESearch...

Entry information

Entry nameCO9A1_HUMAN
AccessionPrimary (citable) accession number: P20849
Secondary accession number(s): Q13699 expand/collapse secondary AC list , Q13700, Q5TF52, Q6P467, Q96BM8, Q99225, Q9H151, Q9H152, Q9Y6P2, Q9Y6P3
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: May 18, 2010
Last modified: July 9, 2014
This is version 167 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM