Human Gene COL11A2 (uc011hgj.1) Description and Page Index
  Description: Homo sapiens collagen, type XI, alpha 2 (COL11A2), transcript variant 1, mRNA.
RefSeq Summary (NM_080680): This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. It is located on chromosome 6 very close to but separate from the gene for retinoid X receptor beta. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Proteolytic processing of this type XI chain produces PARP, a proline/arginine-rich protein that is an amino terminal domain. Mutations in this gene are associated with type III Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED syndrome), Weissenbacher-Zweymuller syndrome, autosomal dominant non-syndromic sensorineural type 13 deafness (DFNA13), and autosomal recessive non-syndromic sensorineural type 53 deafness (DFNB53). Alternative splicing results in multiple transcript variants. A related pseudogene is located nearby on chromosome 6. [provided by RefSeq, Jul 2009].
Transcript (Including UTRs)
   Position: chr6_mann_hap4:4,587,785-4,617,560 Size: 29,776 Total Exon Count: 66 Strand: -
Coding Region
   Position: chr6_mann_hap4:4,588,771-4,617,332 Size: 28,562 Coding Exon Count: 66 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDMicroarray
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
GeneReviewsModel InformationMethods
Data last updated: 2013-06-14

+  Sequence and Links to Tools and Databases
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-  Comments and Description Text from UniProtKB
  ID: COBA2_HUMAN
DESCRIPTION: RecName: Full=Collagen alpha-2(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).
INTERACTION: Q16832:DDR2; NbExp=2; IntAct=EBI-2515504, EBI-1381484;
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix (By similarity).
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: A disulfide-bonded peptide called proline/arginine-rich protein or PARP is released from the N-terminus during extracellular processing and is subsequently retained in the cartilage matrix from which it can be isolated in significant amounts.
DISEASE: Stickler syndrome 3 (STL3) [MIM:184840]: An autosomal dominant non-ocular form of Stickler syndrome. Classical Stickler syndrome associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural deafness. Ocular symptoms are absent. 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. Note=The disease is caused by mutations affecting the gene represented in this entry.
DISEASE: Otospondylomegaepiphyseal dysplasia (OSMED) [MIM:215150]: A skeletal dysplasia characterized by enlarged epiphyses, disproportionate shortness of the limbs, abnormalities in vertebral bodies, and sensorineural hearing loss. Patients have typical facial features, including mid-face hypoplasia with a short upturned nose and depressed nasal bridge. Cleft palate and a small mandible are also common findings. Note=The disease is caused by mutations affecting the gene represented in this entry.
DISEASE: Weissenbacher-Zweymueller syndrome (WZS) [MIM:277610]: An autosomal dominant disorder characterized by neonatal micrognathia and rhizomelic chondrodysplasia with dumbbell-shaped femora and humeri, and regression of bone changes and normal growth in later years. WZS is also referred to as heterozygous OSMED. Note=The disease is caused by mutations affecting the gene represented in this entry.
DISEASE: Deafness, autosomal dominant, 13 (DFNA13) [MIM:601868]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. Note=The disease is caused by mutations affecting the gene represented in this entry.
DISEASE: Deafness, autosomal recessive, 53 (DFNB53) [MIM:609706]: A form of non-syndromic sensorineural deafness characterized by prelingual, profound, non-progressive hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. Note=The disease is caused by mutations affecting the gene represented in this entry.
DISEASE: Fibrochondrogenesis 2 (FBCG2) [MIM:614524]: A severe skeletal dysplasia characterized by a flat midface, short long bones, short ribs with broad metaphyses, and vertebral bodies that show distinctive hypoplastic posterior ends and rounded anterior ends, giving the vertebral bodies a pinched appearance on lateral radiographic views. The chest is small, causing perinatal respiratory problems which usually, but not always, result in lethality. Affected individuals who survive the neonatal period have high myopia, mild to moderate hearing loss, and severe skeletal dysplasia. Note=The disease is caused by mutations affecting the gene represented in this entry.
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=Hereditary hearing loss homepage; Note=Gene page; URL="http://webhost.ua.ac.be/hhh/";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL11A2";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database: COL11A2
CDC HuGE Published Literature: COL11A2
Positive Disease Associations: Cholesterol, LDL , Creatinine , ossification of the posterior longitudinal ligament of the spine , osteochondrodysplasias
Related Studies:
  1. Cholesterol, LDL
    Cristen J Willer et al. Nature genetics 2008, Newly identified loci that influence lipid concentrations and risk of coronary artery disease., Nature genetics. [PubMed 18193043]
  2. Creatinine
    , , . [PubMed 0]
  3. Creatinine
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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GNF Expression Atlas 1 Human Data on Affy U95 Chips

      
    
     
      
    
    
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -104.40228-0.458 Picture PostScript Text
3' UTR -380.06986-0.385 Picture PostScript Text

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.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008160 - Collagen
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR000885 - Fib_collagen_C
IPR001791 - Laminin_G

Pfam Domains:
PF01391 - Collagen triple helix repeat (20 copies)
PF01410 - Fibrillar collagen C-terminal domain
PF02210 - Laminin G domain

SCOP Domains:
49899 - Concanavalin A-like lectins/glucanases

ModBase Predicted Comparative 3D Structure on P13942
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
Jackson LabRGD    
Protein Sequence     
Alignment     

-  Descriptions from all associated GenBank mRNAs
  AK130938 - Homo sapiens cDNA FLJ27428 fis, clone WMD05691, highly similar to Collagen alpha 2(XI) chain precursor.
J04974 - Human alpha-2 type XI collagen mRNA (COL11A2).
L18987 - Human alpha-2 type XI collagen mRNA, partial cds.
BC053886 - Homo sapiens collagen, type XI, alpha 2, mRNA (cDNA clone IMAGE:6051150), complete cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04510 - Focal adhesion
hsa04512 - ECM-receptor interaction

-  Other Names for This Gene
  Alternate Gene Symbols: A6NLX2, COBA2_HUMAN, E7ER90, NM_080680, NP_542411, P13942, Q07751, Q13271, Q13272, Q13273, Q5JP94, Q5SUI8, Q7Z6C3, Q99866, Q9UIP9
UCSC ID: uc011hgj.1
RefSeq Accession: NM_080680
Protein: P13942 (aka COBA2_HUMAN