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COL6A1 Gene

protein-coding   GIFtS: 70
GCID: GC21P047401

Collagen, Type VI, Alpha 1

  See COL6A1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, 15RNAdb, and/or 11Nature:405,311-319 and CroW21)
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Aliases
Collagen, Type VI, Alpha 11 2
OPLL2 5
Human MRNA For Collagen VI Alpha-1 C-Terminal Globular Domain11
Alpha 1 (VI) Chain (61 AA)2
Collagen Alpha-1(VI) Chain2
Collagen VI, Alpha-1 Polypeptide2

External Ids:    HGNC: 22111   Entrez Gene: 12912   Ensembl: ENSG000001421567   OMIM: 1202205   UniProtKB: P121093   

Export aliases for COL6A1 gene to outside databases

Previous GC identifers: GC21P043908 GC21P046259 GC21P046260 GC21P046261 GC21P046226 GC21P032782


(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 COL6A1 Gene:
The collagens are a superfamily of proteins that play a role in maintaining the integrity of various tissues.
Collagens are extracellular matrix proteins and have a triple-helical domain as their common structural element.
Collagen VI is a major structural component of microfibrils. The basic structural unit of collagen VI is a
heterotrimer of the alpha1(VI), alpha2(VI), and alpha3(VI) chains. The alpha2(VI) and alpha3(VI) chains are
encoded by the COL6A2 and COL6A3 genes, respectively. The protein encoded by this gene is the alpha 1 subunit of
type VI collagen (alpha1(VI) chain). Mutations in the genes that code for the collagen VI subunits result in the
autosomal dominant disorder, Bethlem myopathy. (provided by RefSeq, Jul 2008)

GeneCards Summary for COL6A1 Gene:
COL6A1 (collagen, type VI, alpha 1) is a protein-coding gene. Diseases associated with COL6A1 include collagen type vi-related disorders, and spinal cord disease. GO annotations related to this gene include platelet-derived growth factor binding. An important paralog of this gene is COL28A1.

UniProtKB/Swiss-Prot: CO6A1_HUMAN, P12109
Function: Collagen VI acts as a cell-binding protein

Gene Wiki entry for COL6A1 (Collagen, type VI, 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, Whole Chromsome Sequence According to Nature (Cited Here with Permission):405,311-319 and CroW21)
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RefSeq DNA sequence at NCBI GenBank:
NC_000021.8  NT_011512.12  NC_018932.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL6A1 gene promoter:
         Max1   AML1a   AP-1   ATF-2   RelA   NF-kappaB   c-Jun   NF-kappaB1   c-Myc   Ik-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL6A1 promoter sequence

   Search Chromatin IP Primers for COL6A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL6A1


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

Entrez Gene cytogenetic band: 21q22.3   Ensembl cytogenetic band:  21q22.3   HGNC cytogenetic band: 21q22.3
Nature(405: 311-319) cytogenetic band:   21q22.3
COL6A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL6A1 gene location
GeneLoc information about chromosome 21         GeneLoc Exon Structure

(about GC identifiers)
GC21P047401:   GeneLoc Nature:405,311-319
Start:
47,401,651 bp from pter       32,926,714 bp from centromere
End:
47,424,964 bp from pter 32,931,431 bp from centromere
Size:
23,314 bases 4,718 bases
Orientation:
plus strand plus strand

Whole chromosome sequencing:
cDNA sequence: X15880
genomic clones: f94F12


(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CO6A1_HUMAN, P12109 (See protein sequence)
Recommended Name: Collagen alpha-1(VI) chain precursor  
Size: 1028 amino acids; 108529 Da
Subunit: Trimers composed of three different chains: alpha-1(VI), alpha-2(VI), and alpha-3(VI) or alpha-5(VI) or
alpha-6(VI)
Secondary accessions: O00117 O00118 Q14040 Q14041 Q16258 Q7Z645 Q9BSA8

Explore the universe of human proteins at neXtProt for COL6A1: NX_P12109

Explore proteomics data for COL6A1 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
  • Glycosylation2 at Asn212, Asn516, Asn537, Asn804, Asn896
  • Modification sites at PhosphoSitePlus

  • See COL6A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001839.2  
    ENSEMBL proteins: 
     ENSP00000355180  
    Reactome Protein details: P12109

    COL6A1 Human Recombinant Protein Products:

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    Novus Biologicals COL6A1 Proteins
    Novus Biologicals COL6A1 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for COL6A1
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for COL6A1 

     
    antibodies-online proteins for COL6A1 (17 products) 

     
    antibodies-online peptides for COL6A1

    COL6A1 Antibody Products:

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    antibodies-online antibodies for COL6A1 (23 products) 

    COL6A1 Assay Products:

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    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for COL6A1 
    antibodies-online kits for COL6A1 (27 products) 


    (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

    2 InterPro protein domains:
     IPR008160 Collagen
     IPR002035 VWF_A

    Graphical View of Domain Structure for InterPro Entry P12109

    ProtoNet protein and cluster: P12109

    3 Blocks protein domains:
    IPB002035 Von Willebrand factor type A domain signature
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: CO6A1_HUMAN, P12109
    Similarity: Belongs to the type VI collagen family
    Similarity: Contains 3 VWFA domains


    Find genes that share domains with COL6A1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CO6A1_HUMAN, P12109
    Function: Collagen VI acts as a cell-binding protein

         Genatlas biochemistry entry for COL6A1:
    collagen type VI,alpha 1 (150kDa),microfibrillar

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0048407platelet-derived growth factor binding IDA8900172
         
    Find genes that share ontologies with COL6A1           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for COL6A1:
     Elongated cells with protrusio  Increased gamma-H2AX phosphory 

         3 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Col6a1):
     cellular  muscle  no phenotypic analysis 

    Find genes that share phenotypes with COL6A1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Col6a1tm1Gmb for COL6A1

       genOway: Develop your customized and physiologically relevant rodent model for COL6A1

    miRNA
    Products:
        
    miRTarBase miRNAs that target COL6A1:
    hsa-mir-324-5p (MIRT043222), hsa-mir-1301-3p (MIRT035972), hsa-mir-877-3p (MIRT037192), hsa-let-7e-5p (MIRT051548), hsa-mir-615-3p (MIRT039896), hsa-mir-335-5p (MIRT018149)

    Block miRNA regulation of human, mouse, rat COL6A1 using miScript Target Protectors
    Search for qRT-PCR Assays for microRNAs that regulate COL6A1
    SwitchGear 3'UTR luciferase reporter plasmidCOL6A1 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Predesigned siRNA for gene silencing in human, mouse, rat COL6A1

    Gene Editing
    Products:
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    Clone
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    OriGene clones in human, mouse for COL6A1 (see all 6)
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    GenScript: all cDNA clones in your preferred vector: COL6A1 (NM_001848)
    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL6A1

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for COL6A1
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A1


    (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
    CO6A1_HUMAN, P12109: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    mitochondrion2
    plasma membrane2
    cytosol1
    nucleus1

    Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005589collagen type VI NAS2551668
    GO:0005765lysosomal membrane IDA17897319
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0031012colocalizes with extracellular matrix ISS--

    Find genes that share ontologies with COL6A1           About GenesLikeMe


    (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 COL6A1 About   (see all 12)  
    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
    2Integrin 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
    3ERK Signaling
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58
    4Focal adhesion
    Focal adhesion0.65
    ECM-receptor interaction0.31
    5L1CAM interactions
    Axon guidance0.63
    Developmental Biology0.63


    Find genes that share SuperPaths with COL6A1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL6A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    Selected Reactome Pathways for COL6A1 (see all 7)
        ECM proteoglycans
    Integrin cell surface interactions
    NCAM1 interactions
    Collagen biosynthesis and modifying enzymes
    Assembly of collagen fibrils and other multimeric structures


    4 Kegg Pathways  (Kegg details for COL6A1):
        PI3K-Akt signaling pathway
    Focal adhesion
    ECM-receptor interaction
    Protein digestion and absorption

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL6A1: 
              Osteogenesis in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for COL6A1

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

    Selected Interacting proteins for COL6A1 (P121092, 3 ENSP000003551804) via UniProtKB, MINT, STRING, and/or I2D (see all 75)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DNAJB11Q9UBS42, 3, ENSP000002650284MINT-8254188 I2D: score=2 STRING: ENSP00000265028
    LGALS3BPQ083803, ENSP000002627764I2D: score=2 STRING: ENSP00000262776
    COL6A3P121113, ENSP000002955504I2D: score=1 STRING: ENSP00000295550
    DCNP075853, ENSP000000527544I2D: score=1 STRING: ENSP00000052754
    LAMB1P079423, ENSP000002223994I2D: score=1 STRING: ENSP00000222399
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion IEA--
    GO:0007411axon guidance TAS--
    GO:0022617extracellular matrix disassembly TAS--
    GO:0030198extracellular matrix organization TAS--
    GO:0030574collagen catabolic process TAS--

    Find genes that share ontologies with COL6A1           About GenesLikeMe



    (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 COL6A1 (CO6A1)

    1 Novoseek inferred chemical compound relationship for COL6A1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cysteine 9.14 1 17785673 (1)



    Find genes that share compounds with COL6A1           About GenesLikeMe



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for COL6A1 gene: 
    NM_001848.2  

    Unigene Cluster for COL6A1:

    Collagen, type VI, alpha 1
    Hs.474053  [show with all ESTs]
    Unigene Representative Sequence: NM_001848
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000361866(uc002zhu.1) ENST00000492851 ENST00000466285 ENST00000463060
    ENST00000498614(uc002zhv.1) ENST00000486023
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat COL6A1
      QuantiFast Probe-based Assays in human, mouse, rat COL6A1

    Additional mRNA sequence: 

    AK298968.1 AK299396.1 AK307989.1 BC005159.2 BC022236.1 BC032821.1 BC052575.1 M20776.1 
    M27447.1 X06194.1 X15879.1 X15880.1 

    23 DOTS entries:

    DT.119974  DT.91759556  DT.95166523  DT.92385835  DT.87017577  DT.100808150  DT.95180211  DT.95166529 
    DT.100043697  DT.100808153  DT.121136561  DT.121136591  DT.95166534  DT.100808151  DT.100808154  DT.119975 
    DT.121136541  DT.91729933  DT.91985112  DT.92442314  DT.95166533  DT.120695386  DT.121136549 

    Selected AceView cDNA sequences (see all 700):

    AI139683 AI754604 AI472874 BM555982 BQ924339 CF243115 BU733239 W63771 
    AI755192 CA414899 CA421550 AI814481 CB268159 AW069326 AI753544 AI380650 
    AI186401 BE272538 W72946 CA392328 AA953231 BM722310 AI263220 CA416995 

    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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    COL6A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTGCTGACTT
    COL6A1 Expression
    About this image


    COL6A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 26) fully expand
     
     Cartilage (Muscoskeletal System)    fully expand to see all 2 entries
             Intervertebral Disc Annulus Fibrosus Cells Annulus Fibrosus
             Juvenile neocartilage (RevaFlex)
     
     Neural Crest (Gastrulation Derivatives)    fully expand to see all 2 entries
             PureStem SK11, NCr-fac & Meso-prx Progenitor
     
     Paraxial Mesoderm (Gastrulation Derivatives)    fully expand to see all 2 entries
             PureStem SK11, NCr-fac & Meso-prx Progenitor
     
     Ovary (Reproductive System)    fully expand to see all 4 entries
             Secondary Follicle
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
    COL6A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL6A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.474053
        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL6A1: 
              Osteogenesis in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat

    Primer
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    OriGene qPCR primer pairs and template standards for COL6A1
    OriGene qSTAR qPCR primer pairs in human, mouse for COL6A1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL6A1
    QuantiTect SYBR Green Assays in human, mouse, rat COL6A1
    QuantiFast Probe-based Assays in human, mouse, rat COL6A1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A1

    (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 animals.

    Orthologs for COL6A1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col6a11 , 5 collagen, type VI, alpha 11, 5 83.15(n)1
    90.31(a)1
      10 (39.71 cM)5
    128331  NM_009933.41  NP_034063.11 
     767087925 
    chicken
    (Gallus gallus)
    Aves COL6A11 collagen, type VI, alpha 1 70.63(n)
    70.3(a)
      396000  NM_205107.1  NP_990438.1 
    lizard
    (Anolis carolinensis)
    Reptilia COL6A16
    collagen, type VI, alpha 1
    69(a)
    1 ↔ 1
    1(123275685-123333127)
    African clawed frog
    (Xenopus laevis)
    Amphibia col6a1-prov2 procollagen, type VI, alpha 1 74.12(n)    BC047255.1 
    zebrafish
    (Danio rerio)
    Actinopterygii col6a11 collagen, type VI, alpha 1 59.8(n)
    56.97(a)
      569755  XM_693161.5  XP_698253.3 
    worm
    (Caenorhabditis elegans)
    Secernentea mec-56
    Protein MEC-5 (mec-5) mRNA, complete cds
    39(a)
    1 → many
    X(15944009-15948951) WBGene00003169


    ENSEMBL Gene Tree for COL6A1 (if available)
    TreeFam Gene Tree for COL6A1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL6A1 gene
    COL28A12  COLEC122  COL6A52  COLQ2  COL6A62  COL6A22  SCARA32  COL17A12  
    COL6A32  
    7 SIMAP similar genes for COL6A1 using alignment to 3 protein entries:     CO6A1_HUMAN (see all proteins):
    COL6A2    COL7A1    COL1A1    DKFZp434L081    C1QTNF9    C1QTNF9B
    COL6A3

    Find genes that share paralogs with COL6A1           About GenesLikeMe



    (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 COL6A1 (see all 1218)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 21 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs115535191,2,,4
    C,FBethlem myopathy (BM)4 --47404302(+) AAGCAG/ACGTGG 2 /N /S mis1 ese35Minor allele frequency- A:0.04NA CSA EU 5893
    VAR_0135824
    Bethlem myopathy (BM)4--see VAR_0135822 G D mis40--------
    VAR_0582214
    Bethlem myopathy (BM)4--see VAR_0582212 G V mis40--------
    VAR_0135814
    Bethlem myopathy (BM)4--see VAR_0135812 G V mis40--------
    VAR_0582194
    Ullrich congenital muscular dystrophy (UCMD)4--see VAR_0582192 G R mis40--------
    VAR_0582164
    Bethlem myopathy (BM)4--see VAR_0582162 G R mis40--------
    VAR_0135804
    Bethlem myopathy (BM)4--see VAR_0135802 K R mis40--------
    VAR_0582174
    Ullrich congenital muscular dystrophy (UCMD)4--see VAR_0582172 G R mis40--------
    VAR_0582184
    Ullrich congenital muscular dystrophy (UCMD)4--see VAR_0582182 G R mis40--------
    VAR_0582154
    Bethlem myopathy (BM)4--see VAR_0582152 P L mis40--------

    HapMap Linkage Disequilibrium report for COL6A1 (47401651 - 47424964 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for COL6A1 (see all 20):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2723849CNV Deletion23290073
    esv2723852CNV Deletion23290073
    esv2723853CNV Deletion23290073
    esv2723851CNV Deletion23290073
    esv1409667CNV Insertion17803354
    esv1025241CNV Insertion17803354
    esv1396032CNV Insertion17803354
    nsv513579CNV Insertion21212237
    esv1561412CNV Insertion17803354
    nsv509804CNV Insertion20534489

    Human Gene Mutation Database (HGMD): COL6A1
    Locus Specific Mutation Databases (LSDB): COL6A1

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL6A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL6A1

    (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: 120220   
    OMIM disorders: 158810  254090  602475  
    UniProtKB/Swiss-Prot: CO6A1_HUMAN, P12109
  • Bethlem myopathy (BM) [MIM:158810]: A benign autosomal dominant proximal myopathy characterized by early
    childhood onset and joint contractures most frequently affecting the elbows and ankles. Note=The disease is
    caused by mutations affecting the gene represented in this entry
  • Ullrich congenital muscular dystrophy (UCMD) [MIM:254090]: UCMD is a congenital myopathy characterized by
    muscle weakness and multiple joint contractures, generally noted at birth or early infancy. The clinical course
    is more severe than in Bethlem myopathy. Note=The disease is caused by mutations affecting the gene represented
    in this entry

  • 11 diseases for COL6A1:    
    About MalaCards
    collagen type vi-related disorders    spinal cord disease    bethlem myopathy    diffuse idiopathic skeletal hyperostosis
    ullrich congenital muscular dystrophy    adult spinal muscular atrophy    ossification of the posterior longitudinal ligament of the spine    spondylosis
    quadriplegia    radiculopathy    spinal stenosis

    9 diseases from the University of Copenhagen DISEASES database for COL6A1:
    Spinal cord disease     Spondylosis     Diffuse idiopathic skeletal hyperostosis     Radiculopathy
    Spinal stenosis     Muscular dystrophy     Adult spinal muscular atrophy     Quadriplegia
    Hyperostosis

    Find genes that share disorders with COL6A1           About GenesLikeMe

    6 Novoseek inferred disease relationships for COL6A1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    bethlem myopathy 97.8 20 11932968 (2), 15563506 (2), 15955946 (2), 12401455 (1) (see all 16)
    ullrich congenital muscular dystrophy 97.6 15 16130093 (3), 16447767 (1), 18761340 (1), 17537636 (1) (see all 10)
    contracture 71.8 2 11865138 (1), 8817344 (1)
    myopathy 63.7 2 18761340 (1), 8817344 (1)
    down syndrome 61.3 18 7909528 (3), 9491853 (3), 8094066 (2), 17334655 (2) (see all 8)
    heart defects congenital 31.8 7 8094066 (2), 7909528 (2), 7486833 (2)

    GeneTests: COL6A1
    GeneReviews: COL6A1
    Genetic Association Database (GAD): COL6A1
    Human Genome Epidemiology (HuGE) Navigator: COL6A1 (5 documents)

    Export disorders for COL6A1 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 COL6A1 gene, integrated from 10 sources (see all 107):
    (articles sorted by number of sources associating them with COL6A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. COL6A1 polymorphisms associated with ossification of the ligamentum flavum and ossification of the posterior longitudinal ligament. (PubMed id 18246005)1, 4, 9 Kong Q....Chen Z. (Spine 2007)
    2. COL6A1, the candidate gene for ossification of the posterior longitudinal ligament, is associated with diffuse idiopathic skeletal hyperostosis in Japanese. (PubMed id 16227896)1, 4, 9 Tsukahara S....Inoue I. (Spine 2005)
    3. Single nucleotide polymorphism of COL6A1 in patients with ankylosing spondylitis. (PubMed id 18634150)1, 4, 9 Kim T.H....Jun J.B. (J. Rheumatol. 2008)
    4. Dominant and recessive COL6A1 mutations in Ullrich scleroatonic muscular dystrophy. (PubMed id 16130093)1, 2, 9 Giusti B....Pepe G. (Ann. Neurol. 2005)
    5. Human COL6A1: genomic characterization of the globular domains, structural and evolutionary comparison with COL6A2. (PubMed id 9107679)1, 2, 9 Trikka D.... Kessling A.M. (Mamm. Genome 1997)
    6. New molecular mechanism for Ullrich congenital muscular dystrophy: a heterozygous in-frame deletion in the COL6A1 gene causes a severe phenotype. (PubMed id 12840783)1, 4, 9 Pan T.C....Chu M.L. (Am. J. Hum. Genet. 2003)
    7. Genomewide linkage and linkage disequilibrium analyses identify COL6A1, on chromosome 21, as the locus for ossification of the posterior longitudinal ligament of the spine. (PubMed id 12958705)1, 4, 9 Tanaka T....Inoue I. (Am. J. Hum. Genet. 2003)
    8. Novel mutations in collagen VI genes: expansion of the Bethlem myopathy phenotype. (PubMed id 11865138)1, 2, 9 Scacheri P.C.... Hoffman E.P. (Neurology 2002)
    9. RUNX2 polymorphisms associated with OPLL and OLF in the Han population. (PubMed id 20721706)1, 4 Liu Y....Yuan W. (Clin. Orthop. Relat. Res. 2010)
    10. Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease. (PubMed id 19204726)1, 4 Chapuis J....Lambert J.C. (Mol. Psychiatry 2009)

    (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: 1291 HGNC: 2211 AceView: COL6A1 Ensembl:ENSG00000142156 euGenes: HUgn1291
    ECgene: COL6A1 Kegg: 1291 H-InvDB: COL6A1

    (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)
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    NameDescription
    PharmGKB entry for COL6A1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for COL6A1 Genetics and Cytogenetics in Oncology and Haematology
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=COL6A1[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 COL6A1 gene:
    Search GeneIP for patents involving COL6A1

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



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