Human Gene COL11A1 (ENST00000370096.9) from GENCODE V44
Description: Homo sapiens collagen type XI alpha 1 chain (COL11A1), transcript variant F, non-coding RNA. (from RefSeq NR_134980) RefSeq Summary (NM_001854): This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]. Gencode Transcript: ENST00000370096.9 Gencode Gene: ENSG00000060718.22 Transcript (Including UTRs) Position: hg38 chr1:102,876,473-103,108,522 Size: 232,050 Total Exon Count: 67 Strand: - Coding Region Position: hg38 chr1:102,878,019-103,108,178 Size: 230,160 Coding Exon Count: 67
ID:COBA1_HUMAN DESCRIPTION: RecName: Full=Collagen alpha-1(XI) chain; Flags: Precursor; FUNCTION: May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils. SUBUNIT: Trimers composed of three different chains: alpha 1(XI), alpha 2(XI), and alpha 3(XI). Alpha 3(XI) is a post-translational modification of alpha 1(II). Alpha 1(V) can also be found instead of alpha 3(XI)=1(II). SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix (By similarity). TISSUE SPECIFICITY: Cartilage, placenta and some tumor or virally transformed cell lines. Isoforms using exon IIA or IIB are found in the cartilage while isoforms using only exon IIB are found in the tendon. DOMAIN: The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity). PTM: Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains. PTM: N-glycosylated (By similarity). DISEASE: Defects in COL11A1 are the cause of Stickler syndrome type 2 (STL2) [MIM:604841]; also known as Stickler syndrome vitreous type 2. STL2 is an autosomal dominant 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. DISEASE: Defects in COL11A1 are the cause of Marshall syndrome (MRSHS) [MIM:154780]. It is an autosomal dominant disorder characterized by ocular abnormalities, deafness, craniofacial anomalies, and anhidrotic ectodermal dysplasia. Clinical features include short stature; flat or retruded midface with short, depressed nose, flat nasal bridge and anteverted nares; cleft palate with or without the Pierre Robin sequence; appearance of large eyes with ocular hypertelorism; cataracts, either congenital or juvenile; esotropia; high myopia; sensorineural hearing loss; spondyloepiphyseal abnormalities; calcification of the falx cerebri; ectodermal abnormalities, including defects in sweating and dental structures. DISEASE: Defects in COL11A1 are the cause of fibrochondrogenesis type 1 (FBCG1) [MIM:228520]. A severe short-limbed skeletal dysplasia characterized by broad long-bone metaphyses, pear-shaped vertebral bodies, and characteristic morphology of the growth plate, in which the chondrocytes have a fibroblastic appearance and there are regions of fibrous cartilage extracellular matrix. Clinical features include a flat midface with a small nose and anteverted nares, significant shortening of all limb segments but relatively normal hands and feet, and a small bell-shaped thorax with a protuberant abdomen. SIMILARITY: Belongs to the fibrillar collagen family. SIMILARITY: Contains 8 collagen-like domains. SIMILARITY: Contains 1 fibrillar collagen NC1 domain. SIMILARITY: Contains 1 laminin G-like domain. WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL11A1";
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 P12107
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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.