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Aliases for COL9A3 Gene

Aliases for COL9A3 Gene

  • Collagen Type IX Alpha 3 Chain 2 3 5
  • Collagen Type IX Proteoglycan 2 3
  • Collagen, Type IX, Alpha 3 2 3
  • Collagen IX, Alpha-3 Polypeptide 3
  • Collagen Alpha-3(IX) Chain 3
  • DJ885L7.4.1 3
  • EDM3 3
  • MED 3
  • IDD 3

External Ids for COL9A3 Gene

Previous GeneCards Identifiers for COL9A3 Gene

  • GC20P061325
  • GC20P062127
  • GC20P062174
  • GC20P060918
  • GC20P061447
  • GC20P058166

Summaries for COL9A3 Gene

Entrez Gene Summary for COL9A3 Gene

  • This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]

GeneCards Summary for COL9A3 Gene

COL9A3 (Collagen Type IX Alpha 3 Chain) is a Protein Coding gene. Diseases associated with COL9A3 include Epiphyseal Dysplasia, Multiple, 3 and Intervertebral Disc Disease. Among its related pathways are Collagen biosynthesis and modifying enzymes and RET signaling. GO annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is COL22A1.

UniProtKB/Swiss-Prot for COL9A3 Gene

  • Structural component of hyaline cartilage and vitreous of the eye.

Gene Wiki entry for COL9A3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL9A3 Gene

Genomics for COL9A3 Gene

Regulatory Elements for COL9A3 Gene

Enhancers for COL9A3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20F062831 1.1 Ensembl ENCODE 53.4 +16.4 16358 2.8 PKNOX1 SIN3A RAD21 YY1 RCOR1 KLF7 CEBPB GATAD2B REST SMARCB1 COL9A3 TCFL5 OGFR DPH3P1
GH20F062814 0.9 ENCODE 31.3 0.0 -29 2.6 ELF3 INSM2 ARID4B ZNF48 ZNF121 GLIS2 PAF1 ZNF263 KLF11 SP3 COL9A3 TCFL5 ENSG00000223669 OGFR OGFR-AS1
GH20F062922 1.5 FANTOM5 ENCODE 4.8 +110.2 110222 8.5 PKNOX1 CREB3L1 MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 DIDO1 SLC17A9 GID8 COL9A3 ENSG00000273759 ARF4P2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around COL9A3 on UCSC Golden Path with GeneCards custom track

Promoters for COL9A3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for COL9A3 Gene

62,816,244 bp from pter
62,841,159 bp from pter
24,916 bases
Plus strand

Genomic View for COL9A3 Gene

Genes around COL9A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL9A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL9A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL9A3 Gene

Proteins for COL9A3 Gene

  • Protein details for COL9A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-3(IX) chain
    Protein Accession:
    Secondary Accessions:
    • Q13681
    • Q9H4G9
    • Q9UPE2

    Protein attributes for COL9A3 Gene

    684 amino acids
    Molecular mass:
    63616 Da
    Quaternary structure:
    • Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain.

    Three dimensional structures from OCA and Proteopedia for COL9A3 Gene

neXtProt entry for COL9A3 Gene

Post-translational modifications for COL9A3 Gene

  • 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.
  • Glycosylation at Asn 483
  • Modification sites at PhosphoSitePlus

Other Protein References for COL9A3 Gene

No data available for DME Specific Peptides for COL9A3 Gene

Domains & Families for COL9A3 Gene

Gene Families for COL9A3 Gene

Protein Domains for COL9A3 Gene

Suggested Antigen Peptide Sequences for COL9A3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
genes like me logo Genes that share domains with COL9A3: view

Function for COL9A3 Gene

Molecular function for COL9A3 Gene

GENATLAS Biochemistry:
collagen,type IX,alpha 3,fibril associated collagen with interrupted triple helices (FACIT),expressed in cartilage
UniProtKB/Swiss-Prot Function:
Structural component of hyaline cartilage and vitreous of the eye.

Gene Ontology (GO) - Molecular Function for COL9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030020 extracellular matrix structural constituent conferring tensile strength IC 8660302
genes like me logo Genes that share ontologies with COL9A3: view
genes like me logo Genes that share phenotypes with COL9A3: view

Human Phenotype Ontology for COL9A3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for COL9A3 Gene

miRTarBase miRNAs that target COL9A3

Inhibitory RNA Products

Clone Products

Cell Line Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for COL9A3 Gene

Localization for COL9A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL9A3 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COL9A3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
cytoskeleton 2
nucleus 2
plasma membrane 1
lysosome 1

Gene Ontology (GO) - Cellular Components for COL9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005581 collagen trimer IEA --
GO:0005594 collagen type IX trimer IDA 8660302
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL9A3: view

Pathways & Interactions for COL9A3 Gene

genes like me logo Genes that share pathways with COL9A3: view

Gene Ontology (GO) - Biological Process for COL9A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008584 male gonad development IEA --
GO:0008585 female gonad development IEA --
GO:0030198 extracellular matrix organization TAS --
genes like me logo Genes that share ontologies with COL9A3: view

No data available for SIGNOR curated interactions for COL9A3 Gene

Transcripts for COL9A3 Gene

Unigene Clusters for COL9A3 Gene

Collagen, type IX, alpha 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL9A3 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9
SP1: -
SP2: -

Relevant External Links for COL9A3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL9A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COL9A3 Gene

mRNA differential expression in normal tissues according to GTEx for COL9A3 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x6.8) and Brain - Substantia nigra (x4.7).

Protein differential expression in normal tissues from HIPED for COL9A3 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for COL9A3 Gene

Protein tissue co-expression partners for COL9A3 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL9A3 Gene:


SOURCE GeneReport for Unigene cluster for COL9A3 Gene:

genes like me logo Genes that share expression patterns with COL9A3: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for COL9A3 Gene

Orthologs for COL9A3 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL9A3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia COL9A3 34 35
  • 98.98 (n)
(Monodelphis domestica)
Mammalia COL9A3 35
  • 87 (a)
(Canis familiaris)
Mammalia COL9A3 34 35
  • 85.37 (n)
(Bos Taurus)
Mammalia COL9A3 34 35
  • 84.69 (n)
(Mus musculus)
Mammalia Col9a3 34 16 35
  • 84.04 (n)
(Rattus norvegicus)
Mammalia Col9a3 34
  • 83.83 (n)
(Ornithorhynchus anatinus)
Mammalia COL9A3 35
  • 81 (a)
(Gallus gallus)
Aves COL9A3 34 35
  • 69.97 (n)
(Anolis carolinensis)
Reptilia COL9A3 35
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col9a3 34
  • 67.93 (n)
Str.11870 34
(Danio rerio)
Actinopterygii col9a3 34 35
  • 63.59 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG42342 35
  • 27 (a)
(Caenorhabditis elegans)
Secernentea col-99 35
  • 30 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 48 (a)
Species where no ortholog for COL9A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for COL9A3 Gene

Gene Tree for COL9A3 (if available)
Gene Tree for COL9A3 (if available)

Paralogs for COL9A3 Gene

(4) SIMAP similar genes for COL9A3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with COL9A3: view

Variants for COL9A3 Gene

Sequence variations from dbSNP and Humsavar for COL9A3 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
VAR_072736 Multiple epiphyseal dysplasia 3 (EDM3) [MIM:600969]
rs606231367 Pathogenic 62,818,517(+) TCACA(A/G)GGAGA splice-acceptor-variant
rs139573483 Likely benign 62,826,783(+) GTTCC(A/G)AGGGC reference, missense
rs143930593 Likely benign 62,836,270(+) CCCCC(C/T)GGTCC intron-variant, reference, synonymous-codon
rs188924459 Likely benign 62,827,907(+) TGTCA(C/T)TTGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL9A3 Gene

Variant ID Type Subtype PubMed ID
esv2722839 CNV deletion 23290073
nsv1131599 CNV deletion 24896259
nsv428380 CNV loss 18775914
nsv470558 CNV loss 18288195
nsv828794 CNV loss 20364138
nsv834027 CNV loss 17160897
nsv953302 CNV deletion 24416366
nsv9825 CNV gain 18304495
esv2722838 CNV deletion 23290073
esv2259099 CNV deletion 18987734
esv1317287 CNV deletion 17803354

Variation tolerance for COL9A3 Gene

Residual Variation Intolerance Score: 96.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.65; 89.16% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL9A3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL9A3 Gene

Disorders for COL9A3 Gene

MalaCards: The human disease database

(16) MalaCards diseases for COL9A3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • 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. {ECO:0000269 PubMed:11308397, ECO:0000269 PubMed:25381065}. 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 (PubMed:11308397). {ECO:0000269 PubMed:11308397}.
  • 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. {ECO:0000269 PubMed:10090888}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL9A3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with COL9A3: view

No data available for Genatlas for COL9A3 Gene

Publications for COL9A3 Gene

  1. Molecular cloning of the alpha 3 chain of human type IX collagen: linkage of the gene COL9A3 to chromosome 20q13.3. (PMID: 8586434) Brewton R.G. … Mayne R. (Genomics 1995) 2 3 4 22 64
  2. Occupational and genetic risk factors associated with intervertebral disc disease. (PMID: 17471097) Virtanen I.M. … Ala-Kokko L. (Spine 2007) 3 22 46 64
  3. Intervertebral disc degeneration in relation to the COL9A3 and the IL-1ss gene polymorphisms. (PMID: 16133074) Solovieva S. … RiihimAoki H. (Eur Spine J 2006) 3 22 46 64
  4. Mutations in the known genes are not the major cause of MED; distinctive phenotypic entities among patients with no identified mutations. (PMID: 15523498) Jakkula E. … Ala-Kokko L. (Eur. J. Hum. Genet. 2005) 3 22 46 64
  5. Mutation analysis of COL9A3, a gene highly expressed in the cochlea, in hearing loss patients. (PMID: 15917166) Asamura K. … Usami S. (Auris Nasus Larynx 2005) 3 22 46 64

Products for COL9A3 Gene

Sources for COL9A3 Gene

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