Human Gene COL11A2 (uc011hgi.1) Description and Page Index
  Description: Homo sapiens collagen, type XI, alpha 2 (COL11A2), transcript variant 3, mRNA.
RefSeq Summary (NM_080679): 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_hap4:4,587,785-4,602,986 Size: 15,202 Total Exon Count: 9 Strand: -
Coding Region
   Position: chr6_mann_hap4:4,588,771-4,602,906 Size: 14,136 Coding Exon Count: 9 

Page IndexSequence and LinksGenetic AssociationsCTDMicroarrayRNA Structure
Other SpeciesmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

+  Sequence and Links to Tools and Databases
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-  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 -27.7080-0.346 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.

-  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.

-  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: A2ABA7, A2ABA7_HUMAN, AK130938, DAQB-79P13.8-004
UCSC ID: uc011hgi.1
RefSeq Accession: NM_080679

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene COL11A2:
stickler (Stickler Syndrome)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK130938.1
exon count: 9CDS single in 3' UTR: no RNA size: 1985
ORF size: 921CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 1966.00frame shift in genome: no % Coverage: 99.95
has start codon: yes stop codon in genome: no # of Alignments: 7
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.