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COL11A1 Gene

protein-coding   GIFtS: 62
GCID: GC01M103342

Collagen, Type XI, Alpha 1


(Previous symbol: COLL6)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Collagen, Type XI, Alpha 11 2     Collagen XI1
COLL61 2 3     CO11A12
STL22 5     Collagen Alpha-1(XI) Chain2
Alpha-1 Polypeptide1     Collagen XI, Alpha-1 Polypeptide2

External Ids:    HGNC: 21861   Entrez Gene: 13012   Ensembl: ENSG000000607187   OMIM: 1202805   UniProtKB: P121073   

Export aliases for COL11A1 gene to outside databases

Previous GC identifers: GC01M104172 GC01M102524 GC01M102633 GC01M102805 GC01M103055 GC01M101474


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for COL11A1 Gene:
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)

GeneCards Summary for COL11A1 Gene:
COL11A1 (collagen, type XI, alpha 1) is a protein-coding gene. Diseases associated with COL11A1 include lumbar disc herniation, and marshall syndrome. GO annotations related to this gene include extracellular matrix structural constituent and extracellular matrix binding. An important paralog of this gene is COL4A6.

UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107
Function: May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils

Gene Wiki entry for COL11A1 (Collagen, type XI, alpha 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL11A1 gene promoter:
         Spz1   GCNF   Nkx2-5   PPAR-gamma1   POU2F1   GCNF-1   HSF2   POU2F1a   PPAR-gamma2   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL11A1 promoter sequence
   Search Chromatin IP Primers for COL11A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL11A1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p21   Ensembl cytogenetic band:  1p21.1   HGNC cytogenetic band: 1p21

COL11A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL11A1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M103342:  view genomic region     (about GC identifiers)

Start:
103,342,023 bp from pter      End:
103,574,052 bp from pter
Size:
232,030 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107 (See protein sequence)
Recommended Name: Collagen alpha-1(XI) chain precursor  
Size: 1806 amino acids; 181065 Da
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)
Secondary accessions: B1ASK7 D3DT73 E9PCU0 Q14034 Q149N0 Q9UIT4 Q9UIT5 Q9UIT6
Alternative splicing: 4 isoforms:  P12107-1   P12107-2   P12107-3   P12107-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL11A1: NX_P12107

Explore proteomics data for COL11A1 at MOPED

Post-translational modifications: 

  • Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the
    chains1
  • N-glycosylated (By similarity)1
  • Glycosylation2 at Asn1640
  • Modification sites at PhosphoSitePlus

  • See COL11A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001177638.1  NP_001845.3  NP_542196.2  NP_542197.3  

    ENSEMBL proteins: 
     ENSP00000359114   ENSP00000426533   ENSP00000408640   ENSP00000410177   ENSP00000351163  
     ENSP00000302551  
    Reactome Protein details: P12107

    COL11A1 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    COLLAGEN: Collagens

    5 InterPro protein domains:
     IPR013320 ConA-like_subgrp
     IPR001791 Laminin_G
     IPR000885 Fib_collagen_C
     IPR008160 Collagen
     IPR008985 ConA-like_lec_gl_sf

    Graphical View of Domain Structure for InterPro Entry P12107

    ProtoNet protein and cluster: P12107

    5 Blocks protein domains:
    IPB000885 Fibrillar collagen
    IPB001791 Laminin G
    IPB003129 Thrombospondin
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107
    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)
    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


    COL11A1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: COBA1_HUMAN, P12107
    Function: May play an important role in fibrillogenesis by controlling lateral growth of collagen II fibrils

         Genatlas biochemistry entry for COL11A1:
    collagen type XI,alpha 1,fibril forming,expressed in hyaline cartilage,in the ocular vitreous, in the nucleus
    pulposus of the intervertebral disc and in the inner ear,playing an essential role in skeletal morphogenesis and
    in maitaining the interfibrillar spacing and fibril diameter of type II collagen

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005201extracellular matrix structural constituent NAS10486316
    GO:0030674protein binding, bridging NAS10486316
    GO:0046872metal ion binding IEA--
    GO:0050840extracellular matrix binding NAS3182841
         
    COL11A1 for ontologies           About GeneDecksing


    Phenotypes:
         5 GenomeRNAi human phenotypes for COL11A1:
     Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e  Increased gamma-H2AX phosphory 
     Synthetic lethal with Ras 

         9 MGI mutant phenotypes (inferred from 1 allele(MGI details for Col11a1):
     craniofacial  digestive/alimentary  hearing/vestibular/ear  immune system  limbs/digits/tail 
     mortality/aging  nervous system  respiratory system  skeleton 

    COL11A1 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL11A1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for COL11A1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL11A1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL11A1

    miRNA
    Products:
        
    miRTarBase miRNAs that target COL11A1:
    hsa-mir-335-5p (MIRT017414)

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    Selected qRT-PCR Assays for microRNAs that regulate COL11A1 (see all 36):
    hsa-let-7d hsa-miR-300 hsa-miR-29a hsa-miR-550a* hsa-let-7g hsa-let-7a hsa-miR-98 hsa-miR-200c*
    SwitchGear 3'UTR luciferase reporter plasmidCOL11A1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for COL11A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL11A1

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 4): COL11A1 (NM_080629)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL11A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL11A1

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    PureStem SK11, NCr-fac & Meso-prx Progenitor, PureStem SM30, NCr-fac & Meso-latp Progenitor,
    PureStem Z11, Meso Progenitor
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL11A1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    COBA1_HUMAN, P12107: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    cytosol2
    mitochondrion2
    golgi apparatus1
    nucleus1
    plasma membrane1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005581collagen ----
    GO:0005592collagen type XI NAS10486316
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0031012extracellular matrix ----

    COL11A1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for COL11A1 About   (see all 9)  
    See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.75
    Intrinsic Prothrombin Activation Pathway0.39
    Collagen formation0.75
    Blood Coagulation Cascade0.38
    Assembly of collagen fibrils and other multimeric structures0.62
    2Focal adhesion
    Focal adhesion0.65
    ECM-receptor interaction0.31
    Focal Adhesion0.65
    3Integrin Pathway
    FAK1 Signaling0.67
    UPA-UPAR Pathway0.56
    Integrin Pathway0.67
    Inhibition of Angiogenesis by TSP10.50
    GnRH Signaling0.56
    Transendothelial Migration of Leukocytes0.38
    4ERK Signaling
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58
    5Phospholipase-C Pathway
    Phospholipase-C Pathway0.56
    PTEN Pathway0.56

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL11A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    1 BioSystems Pathway for COL11A1
        Focal Adhesion

    4 Reactome Pathways for COL11A1
        Collagen biosynthesis and modifying enzymes
    Assembly of collagen fibrils and other multimeric structures
    Non-integrin membrane-ECM interactions
    Collagen degradation


    5 Kegg Pathways  (Kegg details for COL11A1):
        PI3K-Akt signaling pathway
    Focal adhesion
    ECM-receptor interaction
    Protein digestion and absorption
    Amoebiasis


    COL11A1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL11A1: 
              Lung Cancer in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for COL11A1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for COL11A1 (P121073 ENSP000003511634) via UniProtKB, MINT, STRING, and/or I2D (see all 96)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DDR1Q083453, ENSP000004060914I2D: score=1 STRING: ENSP00000406091
    ENSG00000137332Q083453I2D: score=1 
    ENSG00000215522Q083453I2D: score=1 
    ENSG00000230456Q083453I2D: score=1 
    ENSG00000234078Q083453I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 17):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001502cartilage condensation IEA--
    GO:0002063chondrocyte development IEA--
    GO:0003007heart morphogenesis ----
    GO:0006029proteoglycan metabolic process IEA--
    GO:0007601visual perception IMP10573014

    COL11A1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for COL11A1 (COBA1)

    1 Novoseek inferred chemical compound relationship for COL11A1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    oligonucleotide 24.7 1 17016581 (1)



    COL11A1 for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for COL11A1 gene (4 alternative transcripts): 
    NM_001190709.1  NM_001854.3  NM_080629.2  NM_080630.3  

    Unigene Cluster for COL11A1:

    Collagen, type XI, alpha 1
    Hs.523446  [show with all ESTs]
    Unigene Representative Sequence: NM_080629
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370096(uc001duk.3 uc001dul.3 uc009weh.3) ENST00000470170
    ENST00000512756 ENST00000465209 ENST00000461720 ENST00000475980 ENST00000427239
    ENST00000447608 ENST00000358392(uc001dum.3) ENST00000353414(uc001dun.3)

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    hsa-let-7d hsa-miR-300 hsa-miR-29a hsa-miR-550a* hsa-let-7g hsa-let-7a hsa-miR-98 hsa-miR-200c*
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      QuantiTect SYBR Green Assays in human, mouse, rat COL11A1
      QuantiFast Probe-based Assays in human, mouse, rat COL11A1

    Additional mRNA sequence: 

    AB208844.1 AK299025.1 BC117697.1 J04177.1 

    10 DOTS entries:

    DT.315738  DT.92423416  DT.100752223  DT.100029041  DT.75103415  DT.97831784  DT.315740  DT.92423418 
    DT.97812254  DT.91740538 

    Selected AceView cDNA sequences (see all 186):

    AA331862 AI753167 AW771186 BQ574107 BE011999 BM782714 BM721717 BU179650 
    BX476821 BQ007639 T28202 H89045 BQ681463 BU159588 BM832836 BQ007974 
    BQ574826 CA414254 BU196843 BQ774443 CA414600 CA419181 AA883622 CF529910 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    COL11A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCAAAAGCTT
    COL11A1 Expression
    About this image


    COL11A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 16) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 25 entries
             Prechondrocytes Autopod Epiphyseal End
             Stylopod Long Bone
             HyStem+BMP4-induced MEL2 cells
     
     Cartilage (Muscoskeletal System)    fully expand to see all 24 entries
             Chondrocytes Synchondroses
             Juvenile neocartilage (RevaFlex)
             Micromass-induced chondrocytes
     
     Limb (Muscoskeletal System)    fully expand to see all 3 entries
             Mesenchymal Condensate Cells Zeugopod
     
     Tendon & Ligament (Muscoskeletal System)    fully expand to see all 2 entries
             Tenocytes Limb Tendons and Ligaments
     
     Adipose (Muscoskeletal System)    fully expand to see all 2 entries
             HyStem+BMP4-induced E15 cells
    COL11A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL11A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.523446

    UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107
    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

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL11A1: 
              Lung Cancer in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat

    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for COL11A1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL11A1
    QuantiTect SYBR Green Assays in human, mouse, rat COL11A1
    QuantiFast Probe-based Assays in human, mouse, rat COL11A1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL11A1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for COL11A1 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col11a11 , 5 collagen, type XI, alpha 11, 5 87.29(n)1
    92.24(a)1
      3 (49.35 cM)5
    128141  NM_007729.21  NP_031755.21 
     1140305405 
    chicken
    (Gallus gallus)
    Aves COL11A11 collagen, type XI, alpha 1 81.8(n)
    89.15(a)
      374046  XM_001231623.3  XP_001231624.2 
    lizard
    (Anolis carolinensis)
    Reptilia COL11A16
    collagen, type XI, alpha 1
    88(a)
    1 ↔ 1
    4(85919156-86232782)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.138512 Transcribed sequence with moderate similarity to protein pirCGHU1E (H.sapiens) CGHU1E collagen alpha 1(XI) chain precursor - human less 79.65(n)    BX714579.1 
    zebrafish
    (Danio rerio)
    Actinopterygii col11a1a1 collagen, type XI, alpha 1a 72.43(n)
    81.31(a)
      565402  NM_001083844.1  NP_001077313.1 


    ENSEMBL Gene Tree for COL11A1 (if available)
    TreeFam Gene Tree for COL11A1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL11A1 gene
    COL4A62  COL11A22  COL4A52  COL24A12  COL4A42  COL5A32  COL1A12  COL4A22  
    COL5A22  COL5A12  COL4A32  COL1A22  COL7A12  COL2A12  COL3A12  COL27A12  
    COL4A12  
    13 SIMAP similar genes for COL11A1 using alignment to 10 protein entries:     COBA1_HUMAN (see all proteins):
    COL5A1    COL11A2    COL5A3    C1QTNF9    COL2A1    C1QTNF9B
    COL5A2    COL1A1    COL10A1    COL23A1    SFTPD    COL3A1
    COL1A2

    COL11A1 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for COL11A1
    PGOHUM00000262881


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for COL11A1 (see all 5519)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0135874
    Stickler syndrome 2 (STL2)4--see VAR_0135872 G V mis40--------
    VAR_0659054
    Fibrochondrogenesis 1 (FBCG1)4--see VAR_0659052 G R mis40--------
    VAR_0636754
    Stickler syndrome 2 (STL2)4--see VAR_0636752 G V mis40--------
    VAR_0357454
    A breast cancer sample4--see VAR_0357452 Q L mis40--------
    VAR_0659044
    Fibrochondrogenesis 1 (FBCG1)4--see VAR_0659042 G R mis40--------
    VAR_0636784
    Stickler syndrome 2 (STL2)4--see VAR_0636782 G D mis40--------
    VAR_0357444
    A breast cancer sample4--see VAR_0357442 Q K mis40--------
    VAR_0135834
    Stickler syndrome 2 (STL2)4--see VAR_0135832 G V mis40--------
    VAR_0135844
    Stickler syndrome 2 (STL2)4--see VAR_0135842 G R mis40--------
    VAR_0636764
    Stickler syndrome 2 (STL2)4--see VAR_0636762 G R mis40--------

    HapMap Linkage Disequilibrium report for COL11A1 (103342023 - 103574052 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for COL11A1 (see all 27):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2670279CNV Deletion23128226
    esv2323749CNV Deletion18987734
    nsv506951CNV Insertion20534489
    nsv462739CNV Loss19166990
    nsv870821CNV Loss21882294
    dgv285n71CNV Loss21882294
    dgv282n71CNV Loss21882294
    nsv871198CNV Loss21882294
    dgv284n71CNV Loss21882294
    nsv870521CNV Loss21882294

    Human Gene Mutation Database (HGMD): COL11A1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL11A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL11A1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 120280   
    OMIM disorders: 604841  154780  603932  228520  
    UniProtKB/Swiss-Prot: COBA1_HUMAN, P12107
  • Stickler syndrome 2 (STL2) [MIM:604841]: 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. Note=The disease is caused by mutations affecting the gene
    represented in this entry
  • Marshall syndrome (MRSHS) [MIM:154780]: 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. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Fibrochondrogenesis 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. Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for COL11A1 (see all 55):    
    About MalaCards
    lumbar disc herniation    marshall syndrome    fibrochondrogenesis 1    fibrochondrogenesis
    col11a1-related stickler syndrome    stickler syndrome, type 2    stickler syndrome type 1    vitreoretinal dystrophy
    stickler syndrome    stickler syndrome, type iv    snowflake vitreoretinal degeneration    wagner syndrome
    vitreoretinal degeneration    dihydropyrimidine dehydrogenase deficiency    pierre robin sequence    macroglossia
    multiple epiphyseal dysplasia    primary angle-closure glaucoma    spinal stenosis    chorioretinitis

    6 diseases from the University of Copenhagen DISEASES database for COL11A1:
    Stickler syndrome     Myopia     Vitreoretinal dystrophy     Retinal detachment
    Vitreous syneresis     Sensorineural hearing loss

    COL11A1 for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for COL11A1 gene (see all 12)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    myopia 71.4 2 10889003 (1), 18280717 (1)
    collagen fibril 53.5 2 17062562 (1), 16752401 (1)
    hearing loss sensorineural 48.6 1 10889003 (1)
    micrognathia 46.9 2 12673280 (2)
    cleft palate 37.3 1 12673280 (1)
    cataract 33.7 1 10889003 (1)
    colorectal carcinoma 13.9 2 11707154 (2)
    metastasis 8.45 3 17123152 (1), 16159426 (1), 17016581 (1)
    nsclc 3.15 2 17016581 (2)
    colorectal cancer 2.93 2 11707154 (1), 11375892 (1)

    GeneTests: COL11A1
    GeneReviews: COL11A1
    Genetic Association Database (GAD): COL11A1
    Human Genome Epidemiology (HuGE) Navigator: COL11A1 (11 documents)

    Export disorders for COL11A1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for COL11A1 gene, integrated from 10 sources (see all 111):
    (articles sorted by number of sources associating them with COL11A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and sequencing of pro-alpha 1 (XI) collagen cDNA demonstrates that type XI belongs to the fibrillar class of collagens and reveals that the expression of the gene is not restricted to cartilagenous tissue. (PubMed id 3182841)1, 2, 3 Bernard M.... Ramirez F. (J. Biol. Chem. 1988)
    2. Stickler syndrome and the vitreous phenotype: mutations in COL2A1 and COL11A1. (PubMed id 20513134)1, 2, 9 Richards A.J.... Snead M.P. (Hum. Mutat. 2010)
    3. Splicing mutations of 54-bp exons in the COL11A1 gene cause Marshall syndrome, but other mutations cause overlapping Marshall/Stickler phenotypes. (PubMed id 10486316)1, 2, 9 Annunen S.... Ala-Kokko L. (Am. J. Hum. Genet. 1999)
    4. A functional polymorphism in COL11A1, which encodes the alpha 1 chain of type XI collagen, is associated with susceptibility to lumbar disc herniation. (PubMed id 17999364)1, 4, 9 Mio F....Ikegawa S. (Am. J. Hum. Genet. 2007)
    5. A family with Stickler syndrome type 2 has a mutation in the COL11A1 gene resulting in the substitution of glycine 97 by valine in alpha- 1(XI) collagen. (PubMed id 8872475)1, 2, 9 Richards A.J.... Snead M.P. (Hum. Mol. Genet. 1996)
    6. Introduction of cytogenetic tests in colorectal cancer screening. (PubMed id 19337631)1, 4, 9 Suceveanu A.I....Adam T. (J Gastrointestin Liver Dis 2009)
    7. The role of sequence variations within the genes encoding collagen II, IX and XI in non-syndromic, early-onset osteoarthritis. (PubMed id 15922184)1, 4, 9 Jakkula E....Ala-Kokko L. (Osteoarthr. Cartil. 2005)
    8. Associations of 25 structural, degradative, and inflammatory candidate genes with lumbar disc desiccation, bulging, and height narrowing. (PubMed id 19180518)1, 4, 9 Videman T....BattiAc M.C. (Arthritis Rheum. 2009)
    9. Genetic variants in COL2A1, COL11A2, and IRF6 contribute risk to nonsyndromic cleft palate. (PubMed id 20672350)1, 4 Nikopensius T....Metspalu A. (Birth Defects Res. Part A Clin. Mol. Teratol. 2010)
    10. Fibrochondrogenesis results from mutations in the COL11A1 type XI collagen gene. (PubMed id 21035103)1, 2 Tompson S.W.... Cohn D.H. (Am. J. Hum. Genet. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1301 HGNC: 2186 AceView: COL11A1 Ensembl:ENSG00000060718 euGenes: HUgn1301
    ECgene: COL11A1 Kegg: 1301 H-InvDB: COL11A1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for COL11A1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=COL11A1[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for COL11A1 gene:
    Search GeneIP for patents involving COL11A1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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