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COL6A3 Gene

protein-coding   GIFtS: 64
GCID: GC02M238233

Collagen, Type VI, Alpha 3

  See COL6A3-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 VI, Alpha 31 2
Collagen Alpha-3(VI) Chain2
Collagen VI, Alpha-3 Polypeptide2

External Ids:    HGNC: 22131   Entrez Gene: 12932   Ensembl: ENSG000001633597   OMIM: 1202505   UniProtKB: P121113   

Export aliases for COL6A3 gene to outside databases

Previous GC identifers: GC02M236270 GC02M236914 GC02M238248 GC02M238519 GC02M238014 GC02M237897 GC02M230024


(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 COL6A3 Gene:
This gene encodes the alpha-3 chain, one of the three alpha chains of type VI collagen, a beaded filament collagen
found in most connective tissues. The alpha-3 chain of type VI collagen is much larger than the alpha-1 and -2
chains. This difference in size is largely due to an increase in the number of subdomains, similar to von
Willebrand Factor type A domains, that are found in the amino terminal globular domain of all the alpha chains.
These domains have been shown to bind extracellular matrix proteins, an interaction that explains the importance
of this collagen in organizing matrix components. Mutations in the type VI collagen genes are associated with
Bethlem myopathy, a rare autosomal dominant proximal myopathy with early childhood onset. Mutations in this gene
are also a cause of Ullrich congenital muscular dystrophy, also referred to as Ullrich scleroatonic muscular
dystrophy, an autosomal recessive congenital myopathy that is more severe than Bethlem myopathy. Multiple
transcript variants have been identified, but the full-length nature of only some of these variants has been
described. (provided by RefSeq, Jun 2009)

GeneCards Summary for COL6A3 Gene:
COL6A3 (collagen, type VI, alpha 3) is a protein-coding gene. Diseases associated with COL6A3 include bethlem myopathy, and ullrich congenital muscular dystrophy. GO annotations related to this gene include serine-type endopeptidase inhibitor activity. An important paralog of this gene is COL28A1.

UniProtKB/Swiss-Prot: CO6A3_HUMAN, P12111
Function: Collagen VI acts as a cell-binding protein

Gene Wiki entry for COL6A3 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 at NCBI GenBank:
NC_000002.11  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL6A3 gene promoter:
         LHX3b/Lhx3b   AML1a   RelA   NF-kappaB   POU2F1   POU2F1a   LHX3a/Lhx3a   NF-kappaB1   Pax-4a   RSRFC4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL6A3 promoter sequence
   Search Chromatin IP Primers for COL6A3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL6A3


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

Entrez Gene cytogenetic band: 2q37   Ensembl cytogenetic band:  2q37.3   HGNC cytogenetic band: 2q37

COL6A3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL6A3 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M238233:  view genomic region     (about GC identifiers)

Start:
238,232,646 bp from pter      End:
238,323,018 bp from pter
Size:
90,373 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: CO6A3_HUMAN, P12111 (See protein sequence)
Recommended Name: Collagen alpha-3(VI) chain precursor  
Size: 3177 amino acids; 343669 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)
4 PDB 3D structures from and Proteopedia for COL6A3:
1KNT (3D)        1KTH (3D)        1KUN (3D)        2KNT (3D)    
Secondary accessions: A8MT30 B4E3U5 B7ZMJ7 E9PFQ6 E9PGQ9 Q16501 Q53QF4 Q53QF6
Alternative splicing: 5 isoforms:  P12111-1   P12111-2   P12111-3   P12111-4   P12111-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL6A3: NX_P12111

Explore proteomics data for COL6A3 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
  • The N-terminus is blocked1
  • Glycosylation2 at Asn108, Asn116, Asn202, Asn251, Asn2079, Lys2103, Lys2209, Lys2212, Lys2322, Asn2331,
                                 Lys2337, Asn2558, Asn2677, Asn2861, Asn3037
  • Modification sites at PhosphoSitePlus

  • See COL6A3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_004360.2  NP_476505.3  NP_476506.3  NP_476507.3  NP_476508.2  

    ENSEMBL proteins: 
     ENSP00000295550   ENSP00000418285   ENSP00000386844   ENSP00000375861   ENSP00000375860  
     ENSP00000389539   ENSP00000460277   ENSP00000315609   ENSP00000315873   ENSP00000295546  
    Reactome Protein details: P12111

    COL6A3 Human Recombinant Protein Products:

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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for COL6A3 

    COL6A3 Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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    Novus Biologicals COL6A3 Antibodies
    Abcam antibodies for COL6A3 (P12110, P12109, P12111)
    Browse Antibodies at Cloud-Clone Corp.
    Search ThermoFisher Antibodies for COL6A3
    LSBio Antibodies in human, mouse, rat for COL6A3

    COL6A3 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse ELISAs at Cloud-Clone Corp.
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    Search eBioscience for ELISAs for COL6A3 


    (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

    Selected InterPro protein domains (see all 6):
     IPR003961 Fibronectin_type3
     IPR002223 Prot_inh_Kunz-m
     IPR013783 Ig-like_fold
     IPR020901 Prtase_inh_Kunz-CS
     IPR008160 Collagen

    Graphical View of Domain Structure for InterPro Entry P12111

    ProtoNet protein and cluster: P12111

    4 Blocks protein domains:
    IPB002035 Von Willebrand factor type A domain signature
    IPB002223 Pancreatic trypsin inhibitor (Kunitz)
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: CO6A3_HUMAN, P12111
    Similarity: Belongs to the type VI collagen family
    Similarity: Contains 1 BPTI/Kunitz inhibitor domain
    Similarity: Contains 5 collagen-like domains
    Similarity: Contains 1 fibronectin type-III domain
    Similarity: Contains 12 VWFA domains


    Find genes that share domains with COL6A3           About GenesLikeMe


    (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, 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: CO6A3_HUMAN, P12111
    Function: Collagen VI acts as a cell-binding protein

         Genatlas biochemistry entry for COL6A3:
    collagen type VI,alpha 3 (300kDa),microfibrillar,putative down-regulated c-Myc target gene,

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004867serine-type endopeptidase inhibitor activity IEA--
    GO:0005515protein binding ----
         
    Find genes that share ontologies with COL6A3           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for COL6A3:
     Decreased viability with pacli  Increased gamma-H2AX phosphory 

         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Col6a3):
     growth/size/body  muscle  skeleton  vision/eye 

    Find genes that share phenotypes with COL6A3           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL6A3
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for COL6A3

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL6A3
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL6A3

    miRNA
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    Block miRNA regulation of human, mouse, rat COL6A3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate COL6A3 (see all 28):
    hsa-miR-3149 hsa-miR-3685 hsa-miR-148b hsa-miR-202 hsa-miR-29c hsa-miR-29a hsa-miR-767-5p hsa-miR-301a
    SwitchGear 3'UTR luciferase reporter plasmidCOL6A3 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for COL6A3
    Predesigned siRNA for gene silencing in human, mouse, rat COL6A3

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for COL6A3

    Clone
    Products:
         
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 5): COL6A3 (NM_004369)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL6A3
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat COL6A3

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for COL6A3
    ESI BIO PureStem Progenitors for COL6A3: 
    PureStem 7PEND24, NCr-fac & Meso-prx Progenitor, PureStem SK11, NCr-fac & Meso-prx Progenitor
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A3


    (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
    CO6A3_HUMAN, P12111: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum4
    extracellular4
    plasma membrane3
    cytosol1
    golgi apparatus1
    mitochondrion1
    nucleus1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005589collagen type VI TAS8782832
    GO:0005615extracellular space IDA--
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0031012colocalizes with extracellular matrix ISS--

    Find genes that share ontologies with COL6A3           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 COL6A3 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 COL6A3           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL6A3 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    Selected Reactome Pathways for COL6A3 (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 COL6A3):
        PI3K-Akt signaling pathway
    Focal adhesion
    ECM-receptor interaction
    Protein digestion and absorption

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for COL6A3
    Interactions:

        Search GeneGlobe Interaction Network for COL6A3

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

    Selected Interacting proteins for COL6A3 (P121112, 3 ENSP000002955504) via UniProtKB, MINT, STRING, and/or I2D (see all 69)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PDIA3P301012, 3MINT-4301382 I2D: score=1 
    COL6A1P121093, ENSP000003551804I2D: score=1 STRING: ENSP00000355180
    MMP2P082533, ENSP000002190704I2D: score=1 STRING: ENSP00000219070
    PLCG1P191743I2D: score=2 
    COL10A1ENSP000002432224STRING: ENSP00000243222
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion IEA--
    GO:0007411axon guidance TAS--
    GO:0007517muscle organ development TAS8782832
    GO:0022617extracellular matrix disassembly TAS--
    GO:0030198extracellular matrix organization TAS--

    Find genes that share ontologies with COL6A3           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 COL6A3 (CO6A3)



    (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 COL6A3 gene (5 alternative transcripts): 
    NM_004369.3  NM_057164.4  NM_057165.4  NM_057166.4  NM_057167.3  

    Unigene Cluster for COL6A3:

    Collagen, type VI, alpha 3
    Hs.233240  [show with all ESTs]
    Unigene Representative Sequence: NM_004369
    15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000473258 ENST00000295550(uc002vwl.2) ENST00000491769(uc002vwj.2 uc002vwp.1)
    ENST00000472056 ENST00000409809 ENST00000493608 ENST00000468792 ENST00000493475
    ENST00000392004(uc002vwq.3) ENST00000392003(uc002vwr.3) ENST00000433762
    ENST00000491233 ENST00000347401 ENST00000353578(uc002vwo.2 uc010znj.1)
    ENST00000346358(uc010znk.1)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate COL6A3 (see all 28):
    hsa-miR-3149 hsa-miR-3685 hsa-miR-148b hsa-miR-202 hsa-miR-29c hsa-miR-29a hsa-miR-767-5p hsa-miR-301a
    SwitchGear 3'UTR luciferase reporter plasmidCOL6A3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat COL6A3
    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 5): COL6A3 (NM_004369)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL6A3
    Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat COL6A3
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for COL6A3
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL6A3
      QuantiTect SYBR Green Assays in human, mouse, rat COL6A3
      QuantiFast Probe-based Assays in human, mouse, rat COL6A3

    Additional mRNA sequence: 

    AB209636.1 AK092021.1 AK303290.1 AK304870.1 AK308451.1 BC033174.1 BC144595.1 BC150625.1 
    BC171790.1 BX647500.1 M20778.1 M27449.1 S49432.1 X06196.1 X52022.1 

    21 DOTS entries:

    DT.100882577  DT.418842  DT.95238570  DT.92397224  DT.95235064  DT.100031701  DT.91656644  DT.120942440 
    DT.100882571  DT.95212872  DT.91822008  DT.95169383  DT.121633820  DT.121635786  DT.91929100  DT.97823823 
    DT.120942507  DT.92455503  DT.95141963  DT.86848393  DT.99934594 

    Selected AceView cDNA sequences (see all 611):

    BX506215 BQ695331 CA417547 BQ773075 AK092021 CA414964 BF224027 AI589733 
    BQ183932 AW473611 H61492 CA420801 AW263673 BX481428 BQ332262 AI270009 
    BX472445 BX489281 AI890914 AA598999 AI421369 AI701238 AI270348 AI582564 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for COL6A3 (see all 18)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b ^ 15 ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                -     -                                                                                                                     
    SP5:                                                                                                                                                            

    ExUns: 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41a ·
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:  -     -     -     -     -     -     -     -     -     -     -     -                                                                                       

    ExUns: 41b ^ 42 ^ 43 ^ 44a · 44b ^ 45a · 45b ^ 46
    SP1:                                                
    SP2:                                                
    SP3:                                                
    SP4:                                                
    SP5:                                                


    ECgene alternative splicing isoforms for COL6A3

    (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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    COL6A3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTTTAGATG
    COL6A3 Expression
    About this image


    COL6A3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 19) fully expand
     
     Cartilage (Muscoskeletal System)    fully expand to see all 2 entries
             Intervertebral Disc Annulus Fibrosus Cells Annulus Fibrosus
     
     Bone (Muscoskeletal System)    fully expand to see all 4 entries
             Chondrocytes Zeugopod Epiphyseal End
             Bone Marrow
             Notch-transfected mesenchymal stromal cells (SB623)
             HyStem+TGFbeta3+GDF5-induced 7PEND24 cells
     
     Mesenchymal Stem Cells
             Umbilical cord-derived mesenchymal stem cells (family)
     
     Blood (Cardiovascular System)    fully expand to see all 2 entries
             Double Positive Thymocytes Thymus
             Umbilical cord blood-derived mesenchymal stem cells
     
     Neural Crest (Gastrulation Derivatives)    fully expand to see all 2 entries
             PureStem SK11, NCr-fac & Meso-prx Progenitor
    COL6A3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL6A3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.233240
        Custom PCR Arrays for COL6A3
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for COL6A3
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL6A3
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    QuantiFast Probe-based Assays in human, mouse, rat COL6A3
    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL6A3

    (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 COL6A3 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col6a31 , 5 collagen, type VI, alpha 31, 5 83.46(n)1
    84.61(a)1
      1 (45.53 cM)5
    128351  NM_001243008.11  NP_001229937.11 
     907668605 
    chicken
    (Gallus gallus)
    Aves COL6A31 collagen, type VI, alpha 3 68.94(n)
    65.79(a)
      396548  NM_205534.1  NP_990865.1 
    lizard
    (Anolis carolinensis)
    Reptilia COL6A36
    collagen, type VI, alpha 3
    61(a)
    1 ↔ 1
    1(123668004-123792068)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia col6a31 collagen, type VI, alpha 3 55.98(n)
    50.45(a)
      100488707  XM_002932021.2  XP_002932067.2 
    zebrafish
    (Danio rerio)
    Actinopterygii col6a31 collagen, type VI, alpha 3 52.06(n)
    44.68(a)
      556874  XM_002663369.3  XP_002663415.3 


    ENSEMBL Gene Tree for COL6A3 (if available)
    TreeFam Gene Tree for COL6A3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL6A3 gene
    COL28A12  COL6A12  COLEC122  COL6A52  COLQ2  COL6A62  COL6A22  SCARA32  
    COL17A12  
    17 SIMAP similar genes for COL6A3 using alignment to 7 protein entries:     CO6A3_HUMAN (see all proteins):
    DKFZp686D23123    DKFZp686K04147    EPPIN    SPINT3    COL21A1    ITIL
    TFPI2    COL6A6    COL6A5    C1QTNF9    C1QTNF9B    SPINT4
    ITGA2    SFTPD    COL6A1    COL9A2    DKFZp434L081

    Find genes that share paralogs with COL6A3           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 COL6A3 (see all 2711)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs119032061,2,,4
    C,F,HBethlem myopathy (BM)4 --237615321(+) TCGCTG/ACCGTT 6 /A /V mis1 ese37Minor allele frequency- A:0.02NA CSA NS WA 4946
    rs802727231,2,,4
    C,FUllrich congenital muscular dystrophy (UCMD)4 --237650889(+) GCTCCC/TGGAAG 10 Q R mis15Minor allele frequency- T:0.01EA NA 5274
    rs1460925011,2,,4
    C,FBethlem myopathy (BM)4 --237650917(+) ATATTC/TGGGGC 10 K E mis12Minor allele frequency- T:0.00NA EU 5875
    rs1126383911,2,,4
    C,FUllrich congenital muscular dystrophy (UCMD)4 --237653956(-) GGACCG/AGGTCC 10 /Q /R mis12Minor allele frequency- A:0.00NS NA 5090
    VAR_0582484
    Bethlem myopathy (BM)4--see VAR_0582482 K E mis40--------
    VAR_0582554
    Ullrich congenital muscular dystrophy (UCMD)4--see VAR_0582552 D N mis40--------
    VAR_0582614
    Bethlem myopathy (BM)4--see VAR_0582612 G D mis40--------
    VAR_0582574
    Bethlem myopathy (BM)4--see VAR_0582572 L R mis40--------
    VAR_0582584
    Bethlem myopathy (BM)4--see VAR_0582582 V M mis40--------
    VAR_0582524
    Bethlem myopathy (BM)4--see VAR_0582522 N D mis40--------

    HapMap Linkage Disequilibrium report for COL6A3 (238232646 - 238323018 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for COL6A3:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2665065CNV Deletion23128226
    nsv3226CNV Insertion18451855
    nsv520263CNV Loss19592680
    nsv876049CNV Gain21882294
    nsv876050CNV Gain21882294
    nsv876051CNV Gain21882294

    Human Gene Mutation Database (HGMD): COL6A3
    Locus Specific Mutation Databases (LSDB): COL6A3

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL6A3
    DNA2.0 Custom Variant and Variant Library Synthesis for COL6A3

    (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: 120250   
    OMIM disorders: 158810  254090  
    UniProtKB/Swiss-Prot: CO6A3_HUMAN, P12111
  • 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

  • 8 diseases for COL6A3:    
    About MalaCards
    bethlem myopathy    ullrich congenital muscular dystrophy    tenosynovial giant cell tumor    collagen type vi-related disorders
    congenital muscular dystrophy    giant cell tumor    myopathy    muscular dystrophy

    1 disease from the University of Copenhagen DISEASES database for COL6A3:
    Muscular dystrophy

    Find genes that share disorders with COL6A3           About GenesLikeMe

    6 Novoseek inferred disease relationships for COL6A3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ullrich congenital muscular dystrophy 97.5 10 16447767 (1), 18761340 (1), 15563506 (1), 15689448 (1) (see all 10)
    bethlem myopathy 97.2 12 15563506 (2), 10399756 (1), 16447767 (1), 18366090 (1) (see all 10)
    contracture 68.1 2 15563506 (1), 12840783 (1)
    myopathy 46.6 1 18761340 (1)
    down syndrome 20.7 5 9491853 (3), 9497154 (2)
    tumors 0 3 17601708 (1), 15949695 (1)

    GeneTests: COL6A3
    GeneReviews: COL6A3
    Genetic Association Database (GAD): COL6A3
    Human Genome Epidemiology (HuGE) Navigator: COL6A3 (4 documents)

    Export disorders for COL6A3 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 COL6A3 gene, integrated from 10 sources (see all 72):
    (articles sorted by number of sources associating them with COL6A3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations in COL6A3 cause severe and mild phenotypes of Ullrich congenital muscular dystrophy. (PubMed id 11992252)1, 2, 3 Demir E.... Guicheney P. (Am. J. Hum. Genet. 2002)
    2. The human type VI collagen gene. mRNA and protein variants of the alpha 3 chain generated by alternative splicing of an additional 5-end exon. (PubMed id 1339440)1, 2, 3 Zanussi S.... Colombatti A. (J. Biol. Chem. 1992)
    3. Missense mutation in a von Willebrand factor type A domain of the alpha 3(VI) collagen gene (COL6A3) in a family with Bethlem myopathy. (PubMed id 9536084)1, 2, 9 Pan T.-C.... Speer M.C. (Hum. Mol. Genet. 1998)
    4. Mosaic structure of globular domains in the human type VI collagen alpha 3 chain: similarity to von Willebrand factor, fibronectin, actin, salivary proteins and aprotinin type protease inhibitors. (PubMed id 1689238)1, 2, 9 Chu M.-L.... Timpl R. (EMBO J. 1990)
    5. A genome-wide association study of aging. (PubMed id 21782286)1, 4 Walter S....Franceschini N. (Neurobiol. Aging 2011)
    6. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PubMed id 20198315)1, 4 Yoshida T....Yamada Y. (Int. J. Mol. Med. 2010)
    7. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PubMed id 19851296)1, 4 Oguri M....Yamada Y. (Am. J. Hypertens. 2010)
    8. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    9. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. (PubMed id 19834535)1, 4 Wheeler H.E....Kim S.K. (PLoS Genet. 2009)
    10. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PubMed id 16335952)1, 2 Liu T.... Smith R.D. (J. Proteome Res. 2005)

    (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: 1293 HGNC: 2213 AceView: COL6A3 Ensembl:ENSG00000163359 euGenes: HUgn1293
    ECgene: COL6A3 Kegg: 1293 H-InvDB: COL6A3

    (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 COL6A3 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=COL6A3[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 COL6A3 gene:
    Search GeneIP for patents involving COL6A3

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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