Description: Homo sapiens collagen, type IX, alpha 1 (COL9A1), transcript variant 1, mRNA. RefSeq Summary (NM_001851): 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]. Transcript (Including UTRs) Position: hg19 chr6:70,925,743-71,012,786 Size: 87,044 Total Exon Count: 38 Strand: - Coding Region Position: hg19 chr6:70,926,600-71,012,627 Size: 86,028 Coding Exon Count: 38
ID:CO9A1_HUMAN DESCRIPTION: RecName: Full=Collagen alpha-1(IX) chain; Flags: Precursor; FUNCTION: Structural component of hyaline cartilage and vitreous of the eye. SUBUNIT: Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain. SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular 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. PTM: Covalently linked to the telopeptides of type II collagen by lysine-derived cross-links. PTM: Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains. DISEASE: Defects in COL9A1 are the cause of multiple epiphyseal dysplasia type 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. DISEASE: Defects in COL9A1 are the cause of Stickler syndrome type 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. SIMILARITY: Belongs to the fibril-associated collagens with interrupted helices (FACIT) family. SIMILARITY: Contains 10 collagen-like domains. SIMILARITY: Contains 1 laminin G-like domain. WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL9A1";
To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3
Genetic Association Studies of Complex Diseases and Disorders
Genetic Association Database (archive): COL9A1 CDC HuGE Published Literature: COL9A1 Positive Disease Associations: club foot
, osteoarthritis
, Sleep Related Studies:
club foot Liu, L. Y. et al. 2007, Analysis of association between COL9A1 gene and idiopathic congenital talipes equinovarus, Yi Chuan 2007 29(4) 427-32.
[PubMed 17548304]
osteoarthritis Alizadeh, B. Z. et al. 2005, Evidence for a role of the genomic region of the gene encoding for the alpha1 chain of type IX collagen (COL9A1) in hip osteoarthritis: Apopulation-based study., Arthritis and rheumatism. 2005 May;52(5):1437-42.
[PubMed 15880806]
Our data suggest that susceptibility for hip OA is conferred within or close to the COL9A1 gene in linkage disequilibrium with the COL9A1 509-8B2 marker.
Sleep Daniel J Gottlieb et al. BMC medical genetics 2007, Genome-wide association of sleep and circadian phenotypes., BMC medical genetics.
[PubMed 17903308]
This analysis confirms prior reports of significant heritability of sleepiness, usual bedtime, and usual sleep duration. Several genetic loci with suggestive linkage to these traits are identified, including linkage peaks containing circadian clock-related genes. Association tests identify NPSR1 and PDE4D as possible mediators of bedtime and sleepiness.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on P20849
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
US Server
Sequence and Links to Tools and Databases 
Common Gene Haplotype Alleles 
