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Aliases for COL9A1 Gene

Aliases for COL9A1 Gene

  • Collagen, Type IX, Alpha 1 2 3
  • EDM6 3 6
  • STL4 3 6
  • Cartilage-Specific Short Collagen 3
  • Collagen IX, Alpha-1 Polypeptide 3
  • Alpha-1(IX) Collagen Chain 3
  • Collagen Alpha-1(IX) Chain 3
  • DJ149L1.1.2 3
  • MED 3

External Ids for COL9A1 Gene

Previous GeneCards Identifiers for COL9A1 Gene

  • GC06M070884
  • GC06M070921
  • GC06M070982
  • GC06M068124
  • GC06M070924

Summaries for COL9A1 Gene

Entrez Gene Summary for COL9A1 Gene

  • This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL9A1 Gene

COL9A1 (Collagen, Type IX, Alpha 1) is a Protein Coding gene. Diseases associated with COL9A1 include epiphyseal dysplasia, multiple, 6 and stickler syndrome, type iv. Among its related pathways are Signaling by FGFR and Signaling by GPCR. GO annotations related to this gene include extracellular matrix structural constituent conferring tensile strength. An important paralog of this gene is COL21A1.

UniProtKB/Swiss-Prot for COL9A1 Gene

  • Structural component of hyaline cartilage and vitreous of the eye

Gene Wiki entry for COL9A1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL9A1 Gene

Genomics for COL9A1 Gene

Regulatory Elements for COL9A1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for COL9A1 Gene

70,215,061 bp from pter
70,303,083 bp from pter
88,023 bases
Minus strand

Genomic View for COL9A1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL9A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL9A1 Gene

Proteins for COL9A1 Gene

  • Protein details for COL9A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-1(IX) chain
    Protein Accession:
    Secondary Accessions:
    • Q13699
    • Q13700
    • Q5TF52
    • Q6P467
    • Q96BM8
    • Q99225
    • Q9H151
    • Q9H152
    • Q9Y6P2
    • Q9Y6P3

    Protein attributes for COL9A1 Gene

    921 amino acids
    Molecular mass:
    91869 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 COL9A1 Gene

    Alternative splice isoforms for COL9A1 Gene


neXtProt entry for COL9A1 Gene

Proteomics data for COL9A1 Gene at MOPED

Post-translational modifications for COL9A1 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 Asn171
  • Modification sites at PhosphoSitePlus

Other Protein References for COL9A1 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for COL9A1 Gene

Domains for COL9A1 Gene

Gene Families for COL9A1 Gene

  • COLLAGEN :Collagens
  • COLPG :Proteoglycans / Extracellular Matrix : Collagen proteoglycans

Suggested Antigen Peptide Sequences for COL9A1 Gene

Graphical View of Domain Structure for InterPro Entry



  • P20849
  • 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
  • Contains 10 collagen-like domains.
  • Contains 1 laminin G-like domain.
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
genes like me logo Genes that share domains with COL9A1: view

Function for COL9A1 Gene

Molecular function for COL9A1 Gene

GENATLAS Biochemistry:
collagen,type IX,alpha 1,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 COL9A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030020 extracellular matrix structural constituent conferring tensile strength IC 8660302
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with COL9A1: view
genes like me logo Genes that share phenotypes with COL9A1: view

Animal Models for COL9A1 Gene

MGI Knock Outs for COL9A1:

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL9A1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for COL9A1 Gene

Localization for COL9A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL9A1 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

Jensen Localization Image for COL9A1 Gene COMPARTMENTS Subcellular localization image for COL9A1 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
plasma membrane 2
golgi apparatus 1
lysosome 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for COL9A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005578 proteinaceous extracellular matrix IEA --
GO:0005594 collagen type IX trimer TAS 9707347
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL9A1: view

Pathways for COL9A1 Gene

genes like me logo Genes that share pathways with COL9A1: view

Pathways by source for COL9A1 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for COL9A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001894 tissue homeostasis IEA --
GO:0003417 growth plate cartilage development IEA --
GO:0007411 axon guidance TAS --
GO:0009887 organ morphogenesis TAS 3473493
GO:0022617 extracellular matrix disassembly TAS --
genes like me logo Genes that share ontologies with COL9A1: view

Transcripts for COL9A1 Gene

Unigene Clusters for COL9A1 Gene

Collagen, type IX, alpha 1:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL9A1

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL9A1 Gene

No ASD Table

Relevant External Links for COL9A1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL9A1 Gene

mRNA expression in normal human tissues for COL9A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL9A1 Gene

This gene is overexpressed in Brain - Substantia nigra (4.9), Prostate (4.8), and Brain - Putamen (basal ganglia) (4.1).

Protein differential expression in normal tissues for COL9A1 Gene

This gene is overexpressed in Vitreous humor (53.8) and Pancreatic juice (10.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for COL9A1 Gene

SOURCE GeneReport for Unigene cluster for COL9A1 Gene Hs.590892

genes like me logo Genes that share expressions with COL9A1: view

Expression partners for COL9A1 Gene

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for COL9A1 Gene

Orthologs for COL9A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL9A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia COL9A1 35
  • 90.69 (n)
  • 93.04 (a)
COL9A1 36
  • 91 (a)
(Mus musculus)
Mammalia Col9a1 35
  • 86.78 (n)
  • 90.11 (a)
Col9a1 16
Col9a1 36
  • 90 (a)
(Pan troglodytes)
Mammalia COL9A1 35
  • 99.53 (n)
  • 99.13 (a)
COL9A1 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Col9a1 35
  • 86.16 (n)
  • 90.22 (a)
(Bos Taurus)
Mammalia COL9A1 36
  • 84 (a)
(Monodelphis domestica)
Mammalia COL9A1 36
  • 86 (a)
(Ornithorhynchus anatinus)
Mammalia COL9A1 36
  • 84 (a)
(Gallus gallus)
Aves COL9A1 35
  • 73.41 (n)
  • 74.43 (a)
COL9A1 36
  • 74 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 73 (a)
-- 36
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col9a1 35
  • 66.74 (n)
  • 67.92 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16042 35
(Danio rerio)
Actinopterygii -- 35
zgc:194937 35
  • 64.68 (n)
  • 66.72 (a)
col9a1 36
  • 63 (a)
COL9A1 (2 of 2) 36
  • 64 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG42342 36
  • 28 (a)
(Caenorhabditis elegans)
Secernentea col-99 36
  • 31 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4013 36
  • 45 (a)
Species with no ortholog for COL9A1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 COL9A1 Gene

Gene Tree for COL9A1 (if available)
Gene Tree for COL9A1 (if available)

Paralogs for COL9A1 Gene

Paralogs for COL9A1 Gene

Selected SIMAP similar genes for COL9A1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with COL9A1: view

Variants for COL9A1 Gene

Sequence variations from dbSNP and Humsavar for COL9A1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs25570 -- 70,290,638(-) GCTAA(-/AA)GAGTC intron-variant
rs113979 -- 70,259,250(+) TACAA(C/T)GTACA intron-variant
rs474856 -- 70,268,041(+) GTTTG(C/T)ATGGA intron-variant
rs476863 -- 70,218,264(-) TGAAA(A/T)TTTGT intron-variant
rs477680 -- 70,215,584(-) TAATC(A/G)TATTG downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for COL9A1 Gene

Variant ID Type Subtype PubMed ID
nsv886142 CNV Gain 21882294
nsv830683 CNV Gain 17160897
esv271252 CNV Insertion 20981092
nsv524328 CNV Gain 19592680
nsv886143 CNV Gain 21882294

Relevant External Links for COL9A1 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL9A1 Gene

Disorders for COL9A1 Gene

(2) OMIM Diseases for COL9A1 Gene (120210)


  • 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. {ECO:0000269 PubMed:11565064}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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. 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. {ECO:0000269 PubMed:16909383}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(4) Novoseek inferred disease relationships for COL9A1 Gene

Disease -log(P) Hits PubMed IDs
multiple epiphyseal dysplasia 93 1
psach 73 1
osteoarthritis 55.9 2
collagen fibril 53.6 2

Relevant External Links for COL9A1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with COL9A1: view

No data available for Genatlas for COL9A1 Gene

Publications for COL9A1 Gene

  1. Human COL9A1 and COL9A2 genes. Two genes of 90 and 15 kb code for similar polypeptides of the same collagen molecule. (PMID: 9707347) Pihlajamaa T. … Ala-Kokko L. (Matrix Biol. 1998) 3 4 23
  2. 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 23 48
  3. A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity. (PMID: 11565064) Czarny-Ratajczak M. … Ala-Kokko L. (Am. J. Hum. Genet. 2001) 3 4 23
  4. [Analysis of association between COL9A1 gene and idiopathic congenital talipes equinovarus]. (PMID: 17548304) Liu L.Y. … Sun K.L. (Yi Chuan 2007) 3 23 48
  5. Evidence for a role of the genomic region of the gene encoding for the alpha1 chain of type IX collagen (COL9A1) in hip osteoarthritis: A population-based study. (PMID: 15880806) Alizadeh B.Z. … Duijn C.M. (Arthritis Rheum. 2005) 3 23 48

Products for COL9A1 Gene

Sources for COL9A1 Gene

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