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Protein

Collagen alpha-2(IX) chain

Gene

COL9A2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein 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. skeletal system development Source: ProtInc
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-2(IX) chain
Gene namesi
Name:COL9A2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:2218. COL9A2.

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 21 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:600204
Intervertebral disc disease1 Publication

Disease susceptibility is associated with variations affecting the gene represented in this entry.

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
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti326 – 3261Q → W in IDD; requires 2 nucleotide substitutions. 1 Publication
VAR_012658
Stickler syndrome 51 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. STL5 is characterized by high myopia, vitreoretinal degeneration, retinal detachment, mild to moderate sensorineural hearing loss, short stature in childhood, and absence of cleft palate and Pierre Robin sequence.

See also OMIM:614284

Keywords - Diseasei

Deafness, Disease mutation, Dwarfism, Stickler syndrome

Organism-specific databases

MIMi600204. phenotype.
603932. phenotype.
614284. phenotype.
Orphaneti250984. Autosomal recessive Stickler syndrome.
166002. Multiple epiphyseal dysplasia due to collagen 9 anomaly.
PharmGKBiPA26734.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2323Sequence AnalysisAdd
BLAST
Chaini24 – 689666Collagen alpha-2(IX) chainPRO_0000005837Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi169 – 1691O-linked (Xyl...) (glycosaminoglycan)By similarity
Disulfide bondi174 – 174InterchainSequence Analysis
Disulfide bondi178 – 178InterchainSequence 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

Disulfide bond, Glycoprotein, Hydroxylation, Proteoglycan

Proteomic databases

PaxDbiQ14055.
PRIDEiQ14055.

PTM databases

PhosphoSiteiQ14055.

Expressioni

Gene expression databases

BgeeiQ14055.
CleanExiHS_COL9A2.
ExpressionAtlasiQ14055. baseline and differential.
GenevestigatoriQ14055.

Organism-specific databases

HPAiHPA056316.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi107695. 4 interactions.
IntActiQ14055. 3 interactions.
STRINGi9606.ENSP00000361834.

Structurei

3D structure databases

ProteinModelPortaliQ14055.
SMRiQ14055. Positions 22-60.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni27 – 163137Triple-helical region 4 (COL4)Add
BLAST
Regioni164 – 18017Nonhelical region 4 (NC4)Add
BLAST
Regioni181 – 519339Triple-helical region 3 (COL3)Add
BLAST
Regioni520 – 54930Nonhelical region 3 (NC3)Add
BLAST
Regioni550 – 63283Triple-helical region 2 (COL2)Add
BLAST
Regioni633 – 6342Nonhelical region 2 (NC2)
Regioni635 – 66430Triple-helical region 1 (COL1)Add
BLAST
Regioni665 – 68925Nonhelical region 1 (NC1)Add
BLAST

Sequence similaritiesi

Keywords - Domaini

Collagen, Repeat, Signal

Phylogenomic databases

eggNOGiNOG12793.
GeneTreeiENSGT00780000121854.
HOGENOMiHOG000085653.
HOVERGENiHBG004933.
InParanoidiQ14055.
KOiK08131.
OMAiANGGNET.
OrthoDBiEOG7XSTG3.
PhylomeDBiQ14055.

Family and domain databases

InterProiIPR008160. Collagen.
[Graphical view]
PfamiPF01391. Collagen. 10 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q14055-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAATASPRS LLVLLQVVVL ALAQIRGPPG ERGPPGPPGP PGVPGSDGID
60 70 80 90 100
GDNGPPGKAG PPGPKGEPGK AGPDGPDGKP GIDGLTGAKG EPGPMGIPGV
110 120 130 140 150
KGQPGLPGPP GLPGPGFAGP PGPPGPVGLP GEIGIRGPKG DPGPDGPSGP
160 170 180 190 200
PGPPGKPGRP GTIQGLEGSA DFLCPTNCPP GMKGPPGLQG VKGHAGKRGI
210 220 230 240 250
LGDPGHQGKP GPKGDVGASG EQGIPGPPGP QGIRGYPGMA GPKGETGPHG
260 270 280 290 300
YKGMVGAIGA TGPPGEEGPR GPPGRAGEKG DEGSPGIRGP QGITGPKGAT
310 320 330 340 350
GPPGINGKDG TPGTPGMKGS AGQAGQPGSP GHQGLAGVPG QPGTKGGPGD
360 370 380 390 400
QGEPGPQGLP GFSGPPGKEG EPGPRGEIGP QGIMGQKGDQ GERGPVGQPG
410 420 430 440 450
PQGRQGPKGE QGPPGIPGPQ GLPGVKGDKG SPGKTGPRGK VGDPGVAGLP
460 470 480 490 500
GEKGEKGESG EPGPKGQQGV RGEPGYPGPS GDAGAPGVQG YPGPPGPRGL
510 520 530 540 550
AGNRGVPGQP GRQGVEGRDA TDQHIVDVAL KMLQEQLAEV AVSAKREALG
560 570 580 590 600
AVGMMGPPGP PGPPGYPGKQ GPHGHPGPRG VPGIVGAVGQ IGNTGPKGKR
610 620 630 640 650
GEKGDPGEVG RGHPGMPGPP GIPGLPGRPG QAINGKDGDR GSPGAPGEAG
660 670 680
RPGLPGPVGL PGFCEPAACL GASAYASARL TEPGSIKGP
Length:689
Mass (Da):65,131
Last modified:May 1, 1999 - v2
Checksum:iEB6106E02F6FA862
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti246 – 2461T → M.1 Publication
Corresponds to variant rs2228565 [ dbSNP | Ensembl ].
VAR_026465
Natural varianti326 – 3261Q → R.2 Publications
Corresponds to variant rs2228564 [ dbSNP | Ensembl ].
VAR_012659
Natural varianti326 – 3261Q → W in IDD; requires 2 nucleotide substitutions. 1 Publication
VAR_012658
Natural varianti335 – 3351L → V.1 Publication
Corresponds to variant rs2228567 [ dbSNP | Ensembl ].
VAR_026466
Natural varianti581 – 5811V → I.
Corresponds to variant rs3737821 [ dbSNP | Ensembl ].
VAR_020014

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF019406 Genomic DNA. Translation: AAC33512.1.
AL050341 Genomic DNA. Translation: CAB81611.1.
CH471059 Genomic DNA. Translation: EAX07229.1.
BC136326 mRNA. Translation: AAI36327.1.
BC136327 mRNA. Translation: AAI36328.1.
M95610 mRNA. Translation: AAA80977.1.
CCDSiCCDS450.1.
PIRiS32436.
RefSeqiNP_001843.1. NM_001852.3.
XP_006710428.1. XM_006710365.1.
UniGeneiHs.418012.

Genome annotation databases

EnsembliENST00000372748; ENSP00000361834; ENSG00000049089.
GeneIDi1298.
KEGGihsa:1298.
UCSCiuc001cfh.1. human.

Polymorphism databases

DMDMi20137328.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF019406 Genomic DNA. Translation: AAC33512.1.
AL050341 Genomic DNA. Translation: CAB81611.1.
CH471059 Genomic DNA. Translation: EAX07229.1.
BC136326 mRNA. Translation: AAI36327.1.
BC136327 mRNA. Translation: AAI36328.1.
M95610 mRNA. Translation: AAA80977.1.
CCDSiCCDS450.1.
PIRiS32436.
RefSeqiNP_001843.1. NM_001852.3.
XP_006710428.1. XM_006710365.1.
UniGeneiHs.418012.

3D structure databases

ProteinModelPortaliQ14055.
SMRiQ14055. Positions 22-60.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi107695. 4 interactions.
IntActiQ14055. 3 interactions.
STRINGi9606.ENSP00000361834.

PTM databases

PhosphoSiteiQ14055.

Polymorphism databases

DMDMi20137328.

Proteomic databases

PaxDbiQ14055.
PRIDEiQ14055.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000372748; ENSP00000361834; ENSG00000049089.
GeneIDi1298.
KEGGihsa:1298.
UCSCiuc001cfh.1. human.

Organism-specific databases

CTDi1298.
GeneCardsiGC01M040766.
GeneReviewsiCOL9A2.
H-InvDBHIX0028759.
HGNCiHGNC:2218. COL9A2.
HPAiHPA056316.
MIMi120260. gene.
600204. phenotype.
603932. phenotype.
614284. phenotype.
neXtProtiNX_Q14055.
Orphaneti250984. Autosomal recessive Stickler syndrome.
166002. Multiple epiphyseal dysplasia due to collagen 9 anomaly.
PharmGKBiPA26734.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG12793.
GeneTreeiENSGT00780000121854.
HOGENOMiHOG000085653.
HOVERGENiHBG004933.
InParanoidiQ14055.
KOiK08131.
OMAiANGGNET.
OrthoDBiEOG7XSTG3.
PhylomeDBiQ14055.

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

GeneWikiiCOL9A2.
GenomeRNAii1298.
NextBioi5271.
PROiQ14055.
SOURCEiSearch...

Gene expression databases

BgeeiQ14055.
CleanExiHS_COL9A2.
ExpressionAtlasiQ14055. baseline and differential.
GenevestigatoriQ14055.

Family and domain databases

InterProiIPR008160. Collagen.
[Graphical view]
PfamiPF01391. Collagen. 10 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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 [GENOMIC DNA].
    Tissue: Foreskin.
  2. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. 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: Brain.
  5. "Molecular cloning of the human alpha 2(IX) collagen cDNA and assignment of the human COL9A2 gene to chromosome 1."
    Peraelae M., Haenninen M., Haestbacka J., Elima K., Vuorio E.
    FEBS Lett. 319:177-180(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 50-668.
    Tissue: Cartilage.
  6. "Identification of novel pro-alpha2(IX) collagen gene mutations in two families with distinctive oligo-epiphyseal forms of multiple epiphyseal dysplasia."
    Holden P., Canty E.G., Mortier G.R., Zabel B., Spranger J., Carr A., Grant M.E., Loughlin J.A., Briggs M.D.
    Am. J. Hum. Genet. 65:31-38(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN EDM2.
  7. "A loss of function mutation in the COL9A2 gene causes autosomal recessive Stickler syndrome."
    Baker S., Booth C., Fillman C., Shapiro M., Blair M.P., Hyland J.C., Ala-Kokko L.
    Am. J. Med. Genet. A 155:1668-1672(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN STL5.
  8. Cited for: VARIANT IDD TRP-326, VARIANT ARG-326.
  9. Cited for: VARIANTS MET-246; ARG-326 AND VAL-335.

Entry informationi

Entry nameiCO9A2_HUMAN
AccessioniPrimary (citable) accession number: Q14055
Secondary accession number(s): B2RMP9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2002
Last sequence update: May 1, 1999
Last modified: February 4, 2015
This is version 140 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 1
    Human chromosome 1: 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.