Free for academic non-profit institutions. Other users need a Commercial license

Aliases for COL9A2 Gene

Aliases for COL9A2 Gene

  • Collagen, Type IX, Alpha 2 2 3
  • STL5 3 6
  • EDM2 3 6
  • Collagen IX, Alpha-2 Polypeptide 3
  • Collagen Alpha-2(IX) Chain 3
  • Alpha 2 Type IX Collagen 3
  • DJ39G22.4 3
  • MED 3

External Ids for COL9A2 Gene

Previous HGNC Symbols for COL9A2 Gene

  • EDM2

Previous GeneCards Identifiers for COL9A2 Gene

  • GC01M040801
  • GC01M039769
  • GC01M040228
  • GC01M040179
  • GC01M040435
  • GC01M040538
  • GC01M040766
  • GC01M038884

Summaries for COL9A2 Gene

Entrez Gene Summary for COL9A2 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. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]

GeneCards Summary for COL9A2 Gene

COL9A2 (Collagen, Type IX, Alpha 2) is a Protein Coding gene. Diseases associated with COL9A2 include epiphyseal dysplasia, multiple, 2 and intervertebral disc disease. 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 COL9A2 Gene

  • Structural component of hyaline cartilage and vitreous of the eye

Gene Wiki entry for COL9A2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL9A2 Gene

Genomics for COL9A2 Gene

Regulatory Elements for COL9A2 Gene

Epigenetics Products

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

Genomic Location for COL9A2 Gene

40,300,487 bp from pter
40,317,816 bp from pter
17,330 bases
Minus strand

Genomic View for COL9A2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for COL9A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL9A2 Gene

Proteins for COL9A2 Gene

  • Protein details for COL9A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Collagen alpha-2(IX) chain
    Protein Accession:
    Secondary Accessions:
    • B2RMP9

    Protein attributes for COL9A2 Gene

    689 amino acids
    Molecular mass:
    65131 Da
    Quaternary structure:
    • Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain

neXtProt entry for COL9A2 Gene

Proteomics data for COL9A2 Gene at MOPED

Post-translational modifications for COL9A2 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 Ser169
  • Modification sites at PhosphoSitePlus

Other Protein References for COL9A2 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for COL9A2 Gene

Domains for COL9A2 Gene

Gene Families for COL9A2 Gene

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

Protein Domains for COL9A2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Q14055
  • Belongs to the fibril-associated collagens with interrupted helices (FACIT) family.
genes like me logo Genes that share domains with COL9A2: view

Function for COL9A2 Gene

Molecular function for COL9A2 Gene

GENATLAS Biochemistry:
collagen,type IX,alpha 2,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 COL9A2 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 COL9A2: view
genes like me logo Genes that share phenotypes with COL9A2: view

Animal Model Products

miRNA for COL9A2 Gene

miRTarBase miRNAs that target COL9A2

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL9A2

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for COL9A2 Gene

Localization for COL9A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL9A2 Gene

Secreted, extracellular space, extracellular matrix.

Subcellular locations from

Jensen Localization Image for COL9A2 Gene COMPARTMENTS Subcellular localization image for COL9A2 gene
Compartment Confidence
endoplasmic reticulum 4
extracellular 4
golgi apparatus 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for COL9A2 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 IDA 8660302
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COL9A2: view

Pathways for COL9A2 Gene

genes like me logo Genes that share pathways with COL9A2: view

Gene Ontology (GO) - Biological Process for COL9A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development TAS 10364514
GO:0007411 axon guidance TAS --
GO:0022617 extracellular matrix disassembly TAS --
GO:0030198 extracellular matrix organization TAS --
GO:0030574 collagen catabolic process TAS --
genes like me logo Genes that share ontologies with COL9A2: view

Compounds for COL9A2 Gene

(2) Novoseek inferred chemical compound relationships for COL9A2 Gene

Compound -log(P) Hits PubMed IDs
col 3 86.5 1
glutamine 7.77 1
genes like me logo Genes that share compounds with COL9A2: view

Transcripts for COL9A2 Gene

Unigene Clusters for COL9A2 Gene

Collagen, type IX, alpha 2:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for COL9A2

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL9A2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
SP3: - - - - -
SP4: -
SP8: - - - - - - - - - -
SP10: -

ExUns: 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31

Relevant External Links for COL9A2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for COL9A2 Gene

mRNA expression in normal human tissues for COL9A2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL9A2 Gene

This gene is overexpressed in Pituitary (7.4), Brain - Spinal cord (cervical c-1) (6.3), and Brain - Substantia nigra (4.7).

Protein differential expression in normal tissues for COL9A2 Gene

This gene is overexpressed in Vitreous humor (58.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for COL9A2 Gene

SOURCE GeneReport for Unigene cluster for COL9A2 Gene Hs.418012

genes like me logo Genes that share expressions with COL9A2: view

Expression partners for COL9A2 Gene

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for COL9A2 Gene

Orthologs for COL9A2 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL9A2 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia COL9A2 35
  • 86.38 (n)
  • 88.43 (a)
COL9A2 36
  • 89 (a)
(Canis familiaris)
Mammalia COL9A2 35
  • 88.77 (n)
  • 92.24 (a)
COL9A2 36
  • 90 (a)
(Mus musculus)
Mammalia Col9a2 35
  • 87.27 (n)
  • 91.93 (a)
Col9a2 16
Col9a2 36
  • 91 (a)
(Pan troglodytes)
Mammalia COL9A2 35
  • 96.6 (n)
  • 95.33 (a)
(Rattus norvegicus)
Mammalia Col9a2 35
  • 87.16 (n)
  • 91.46 (a)
(Monodelphis domestica)
Mammalia COL9A2 36
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia COL9A2 36
  • 75 (a)
(Gallus gallus)
Aves COL9A2 35
  • 71.95 (n)
  • 79.04 (a)
COL9A2 36
  • 74 (a)
(Anolis carolinensis)
Reptilia COL9A2 36
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia col9a2 35
  • 66.46 (n)
  • 74.14 (a)
(Danio rerio)
Actinopterygii col9a2 35
  • 62.42 (n)
  • 67.55 (a)
col9a2 36
  • 67 (a)
(Caenorhabditis elegans)
Secernentea col-135 36
  • 37 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 22 (a)
Species with no ortholog for COL9A2:
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 COL9A2 Gene

Gene Tree for COL9A2 (if available)
Gene Tree for COL9A2 (if available)

Paralogs for COL9A2 Gene

Paralogs for COL9A2 Gene

Selected SIMAP similar genes for COL9A2 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with COL9A2: view

Variants for COL9A2 Gene

Sequence variations from dbSNP and Humsavar for COL9A2 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs176684 -- 40,315,153(-) ATTTA(A/G)AATCA intron-variant
rs176685 -- 40,315,855(-) cggtt(C/T)tgagt intron-variant, upstream-variant-2KB
rs176686 -- 40,315,912(-) acgtt(C/T)tgagc intron-variant, upstream-variant-2KB
rs176687 -- 40,303,995(+) GGTCA(A/G)ACGCG intron-variant
rs182359 -- 40,305,193(+) ctcca(A/G)agtag intron-variant

Relevant External Links for COL9A2 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for COL9A2 Gene

Disorders for COL9A2 Gene

(3) OMIM Diseases for COL9A2 Gene (120260)


  • Multiple epiphyseal dysplasia 2 (EDM2) [MIM:600204]: 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:10364514}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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:10411504}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Stickler syndrome 5 (STL5) [MIM:614284]: 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. 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. {ECO:0000269 PubMed:21671392}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(5) Novoseek inferred disease relationships for COL9A2 Gene

Disease -log(P) Hits PubMed IDs
multiple epiphyseal dysplasia 97 6
intervertebral disc disease 87.9 6
psach 85.9 1
lumbar disc disease 81.3 3
rheumatoid arthritis 0 1

Relevant External Links for COL9A2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with COL9A2: view

No data available for Genatlas for COL9A2 Gene

Publications for COL9A2 Gene

  1. Molecular cloning of the human alpha 2(IX) collagen cDNA and assignment of the human COL9A2 gene to chromosome 1. (PMID: 8454052) Peraelae M. … Vuorio E. (FEBS Lett. 1993) 2 3 4 23
  2. An allele of COL9A2 associated with intervertebral disc disease. (PMID: 10411504) Annunen S. … Ala-Kokko L. (Science 1999) 3 4 23 48
  3. Identification of novel pro-alpha2(IX) collagen gene mutations in two families with distinctive oligo-epiphyseal forms of multiple epiphyseal dysplasia. (PMID: 10364514) Holden P. … Briggs M.D. (Am. J. Hum. Genet. 1999) 3 4 23
  4. Identification of a novel common genetic risk factor for lumbar disk disease. (PMID: 11308397) Paassilta P. … Ala-Kokko L. (JAMA 2001) 3 23 48
  5. A mutation in the gene encoding the alpha 2 chain of the fibril-associated collagen IX, COL9A2, causes multiple epiphyseal dysplasia (EDM2). (PMID: 8528240) Muragaki Y. … Hamel B.C. (Nat. Genet. 1996) 2 3 23

Products for COL9A2 Gene

Sources for COL9A2 Gene

Back to Top