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 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:102,876,473-103,108,522)mRNA (may differ from genome)Protein (1806 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGImyGene2neXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  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";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

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


-  MalaCards Disease Associations
  MalaCards Gene Search: COL11A1
Diseases sorted by gene-association score: stickler syndrome, type ii* (1550), marshall syndrome* (1414), fibrochondrogenesis 1* (1353), fibrochondrogenesis* (820), col11a1-related stickler syndrome* (500), periodic fever, aphthous stomatitis, pharyngitis and adenitis* (400), autosomal dominant myopia-midfacial retrusion-sensorineural hearing loss-rhizomelic dysplasia syndrome* (350), intervertebral disc disease* (246), autosomal recessive stickler syndrome* (175), stickler syndrome (35), retinal detachment (17), primary angle-closure glaucoma (15), myopia (14), macroglossia (13), esotropia (13), deafness, autosomal recessive 32 (12), retinal perforation (11), dihydropyrimidine dehydrogenase deficiency (11), otospondylomegaepiphyseal dysplasia (9), snowflake vitreoretinal degeneration (9), hypochondrogenesis (9), vitreous syneresis (8), achondrogenesis, type ii or hypochondrogenesis (8), vitreoretinal degeneration (7), multiple epiphyseal dysplasia (7), kniest dysplasia (6), vitreoretinal dystrophy (6), sed congenita (5), strabismus (4), cleft palate, isolated (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D004997 Ethinyl Estradiol
  • D013749 Tetrachlorodibenzodioxin
  • D015056 1-Methyl-3-isobutylxanthine
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C023514 2,6-dinitrotoluene
  • C573693 2-(4-((4-(6-methoxy-3-pyridinyl)-5-(4-(trifluoromethoxy)phenyl)-2-thiazolyl)methoxy)-2-methylphenoxy)acetic acid
  • D015122 6-Mercaptopurine
  • D015127 9,10-Dimethyl-1,2-benzanthracene
  • D019386 Alendronate
  • D000537 Aluminum Oxide
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.71 RPKM in Cells - Cultured fibroblasts
Total median expression: 59.29 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -128.90344-0.375 Picture PostScript Text
3' UTR -306.941546-0.199 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:
PF01410 - Fibrillar collagen C-terminal domain
PF01391 - Collagen triple helix repeat (20 copies)
PF02210 - Laminin G domain

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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005201 extracellular matrix structural constituent
GO:0030674 protein binding, bridging
GO:0046872 metal ion binding
GO:0050840 extracellular matrix binding

Biological Process:
GO:0001502 cartilage condensation
GO:0001503 ossification
GO:0002063 chondrocyte development
GO:0003007 heart morphogenesis
GO:0006029 proteoglycan metabolic process
GO:0007601 visual perception
GO:0007605 sensory perception of sound
GO:0030198 extracellular matrix organization
GO:0030199 collagen fibril organization
GO:0035987 endodermal cell differentiation
GO:0035989 tendon development
GO:0042472 inner ear morphogenesis
GO:0048704 embryonic skeletal system morphogenesis
GO:0048705 skeletal system morphogenesis
GO:0050910 detection of mechanical stimulus involved in sensory perception of sound
GO:0051216 cartilage development
GO:0055010 ventricular cardiac muscle tissue morphogenesis

Cellular Component:
GO:0005576 extracellular region
GO:0005581 collagen trimer
GO:0005592 collagen type XI trimer
GO:0005788 endoplasmic reticulum lumen
GO:0031012 extracellular matrix


-  Descriptions from all associated GenBank mRNAs
  J04177 - Human alpha-1 type XI collagen (COL11A1) mRNA, complete cds.
AB208844 - Homo sapiens mRNA for alpha 1 type XI collagen isoform C preproprotein variant protein.
BC117697 - Homo sapiens collagen, type XI, alpha 1, mRNA (cDNA clone MGC:134933 IMAGE:40073305), complete cds.
LF206313 - JP 2014500723-A/13816: Polycomb-Associated Non-Coding RNAs.
MA441890 - JP 2018138019-A/13816: Polycomb-Associated Non-Coding RNAs.
LF353121 - JP 2014500723-A/160624: Polycomb-Associated Non-Coding RNAs.
MA588698 - JP 2018138019-A/160624: Polycomb-Associated Non-Coding RNAs.
JD058406 - Sequence 39430 from Patent EP1572962.
JD428011 - Sequence 409035 from Patent EP1572962.
AK299025 - Homo sapiens cDNA FLJ57066 complete cds, highly similar to Collagen alpha-1(XI) chain precursor.
JD555423 - Sequence 536447 from Patent EP1572962.
JD513191 - Sequence 494215 from Patent EP1572962.
LF353120 - JP 2014500723-A/160623: Polycomb-Associated Non-Coding RNAs.
MA588697 - JP 2018138019-A/160623: Polycomb-Associated Non-Coding RNAs.
LF353119 - JP 2014500723-A/160622: Polycomb-Associated Non-Coding RNAs.
MA588696 - JP 2018138019-A/160622: Polycomb-Associated Non-Coding RNAs.
LF353118 - JP 2014500723-A/160621: Polycomb-Associated Non-Coding RNAs.
MA588695 - JP 2018138019-A/160621: Polycomb-Associated Non-Coding RNAs.
E03362 - DNA sequence of Insulin binding site of human collagen 11.
JD554782 - Sequence 535806 from Patent EP1572962.
JD265641 - Sequence 246665 from Patent EP1572962.
JD302226 - Sequence 283250 from Patent EP1572962.
JD125247 - Sequence 106271 from Patent EP1572962.
JD290521 - Sequence 271545 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein P12107 (Reactome details) participates in the following event(s):

R-HSA-8944266 Association of procollagen type XI
R-HSA-2002460 P4HB binds Collagen chains
R-HSA-8948230 P3HB binds 4-Hyp-collagen propeptides
R-HSA-1650808 Prolyl 4-hydroxylase converts collagen prolines to 4-hydroxyprolines
R-HSA-1980233 Collagen prolyl 3-hydroxylase converts 4-Hyp collagen to 3,4-Hyp collagen
R-HSA-8948219 PLOD3 binds Lysyl hydroxylated collagen propeptides
R-HSA-8948228 COLGALT1,COLGALT2 bind Lysyl hydroxylated collagen propeptides
R-HSA-2002440 Removal of fibrillar collagen C-propeptides
R-HSA-2022073 Procollagen triple helix formation
R-HSA-1981104 Procollagen lysyl hydroxylases convert collagen lysines to 5-hydroxylysines
R-HSA-1981120 Galactosylation of collagen propeptide hydroxylysines by procollagen galactosyltransferases 1, 2.
R-HSA-1981128 Galactosylation of collagen propeptide hydroxylysines by PLOD3
R-HSA-1981157 Glucosylation of collagen propeptide hydroxylysines
R-HSA-2002428 Removal of fibrillar collagen N-propeptides
R-HSA-8948216 Collagen chain trimerization
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-1474290 Collagen formation
R-HSA-2022090 Assembly of collagen fibrils and other multimeric structures
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: B1ASK7, COBA1_HUMAN, COLL6, D3DT73, ENST00000370096.1, ENST00000370096.2, ENST00000370096.3, ENST00000370096.4, ENST00000370096.5, ENST00000370096.6, ENST00000370096.7, ENST00000370096.8, NR_134980, P12107, Q14034, Q9UIT4, Q9UIT5, Q9UIT6, uc001dul.1, uc001dul.2, uc001dul.3, uc001dul.4, uc001dul.5, uc001dul.6
UCSC ID: ENST00000370096.9
RefSeq Accession: NM_001854
Protein: P12107 (aka COBA1_HUMAN or CA1B_HUMAN)
CCDS: CCDS778.1, CCDS53348.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene COL11A1:
stickler (Stickler Syndrome)

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