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COL4A6 Gene

protein-coding   GIFtS: 65
GCID: GC0XM107386

Collagen, Type IV, Alpha 6

  See COL4A6-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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Collagen, Type IV, Alpha 61 2     Collagen IV, Alpha-6 Polypeptide2
CXDELq22.32 5     Collagen Of Basement Membrane, Alpha-62
DELXq22.32 5     DJ889N15.4 (Collagen Alpha 6(IV))2
DFNX62 5     EC 2.7.7.88
Collagen Alpha-6(IV) Chain2     

External Ids:    HGNC: 22081   Entrez Gene: 12882   Ensembl: ENSG000001975657   OMIM: 3036315   UniProtKB: Q140313   
ORGUL members:         

Export aliases for COL4A6 gene to outside databases

Previous GC identifers: GC0XM102806 GC0XM104474 GC0XM105431 GC0XM106170 GC0XM107204 GC0XM107285 GC0XM097021


(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 COL4A6 Gene:
This gene encodes one of the six subunits of type IV collagen, the major structural component of basement
membranes. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head
conformation with another type IV collagen gene, alpha 5 type IV collagen, so that the gene pair shares a common
promoter. Deletions in the alpha 5 gene that extend into the alpha 6 gene result in diffuse leiomyomatosis
accompanying the X-linked Alport syndrome caused by the deletion in the alpha 5 gene. Alternative splicing
results in multiple transcript variants encoding different isoforms. (provided by RefSeq, Dec 2013)

GeneCards Summary for COL4A6 Gene:
COL4A6 (collagen, type IV, alpha 6) is a protein-coding gene. Diseases associated with COL4A6 include leiomyomatosis, and deafness, x-linked 6. GO annotations related to this gene include extracellular matrix structural constituent. An important paralog of this gene is COL11A2.

UniProtKB/Swiss-Prot: CO4A6_HUMAN, Q14031
Function: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a
'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen

Gene Wiki entry for COL4A6 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_000023.10  NT_011651.18  NC_018934.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL4A6 gene promoter:
         NF-AT4   NF-AT2   HOXA5   NF-AT3   NF-AT1   NF-AT   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): COL4A6 promoter sequence
   Search Chromatin IP Primers for COL4A6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL4A6


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

Entrez Gene cytogenetic band: Xq22   Ensembl cytogenetic band:  Xq22.3   HGNC cytogenetic band: Xq22

COL4A6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL4A6 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM107386:  view genomic region     (about GC identifiers)

Start:
107,386,780 bp from pter      End:
107,682,727 bp from pter
Size:
295,948 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., 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: CO4A6_HUMAN, Q14031 (See protein sequence)
Recommended Name: Collagen alpha-6(IV) chain precursor  
Size: 1691 amino acids; 163807 Da
Subunit: There are six type IV collagen isoforms, alpha 1(IV)-alpha 6(IV), each of which can form a triple helix
structure with 2 other chains to generate type IV collagen network
Secondary accessions: Q12823 Q14053 Q5JYH6 Q5JYH8 Q9NQM5 Q9NTX3 Q9UJ76 Q9UMG6 Q9Y4L4
Alternative splicing: 2 isoforms:  Q14031-1   Q14031-2   

Explore the universe of human proteins at neXtProt for COL4A6: NX_Q14031

Explore proteomics data for COL4A6 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
  • Type IV collagens contain numerous cysteine residues which are involved in inter- and intramolecular disulfide
    bonding. 12 of these, located in the NC1 domain, are conserved in all known type IV collagens1
  • The trimeric structure of the NC1 domains is stabilized by covalent bonds between Lys and Met residues (By
    similarity)1
  • Glycosylation2 at Asn127
  • 2 DME Specific Peptides for COL4A6 (Q14031)
     LPGRDGL  LPGKDGL 


    See COL4A6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_001274687.1  NP_001274688.1  NP_001274689.1  NP_001838.2  NP_378667.1  

    ENSEMBL proteins: 
     ENSP00000334733   ENSP00000361290   ENSP00000406002   ENSP00000378340   ENSP00000443707  
     ENSP00000445236  
    Reactome Protein details: Q14031

    COL4A6 Human Recombinant Protein Products:

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

     
    Search eBioscience for Proteins for COL4A6 

     
    antibodies-online proteins for COL4A6 (4 products) 

     
    antibodies-online peptides for COL4A6

    COL4A6 Antibody Products:

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    antibodies-online antibodies for COL4A6 (19 products) 

    COL4A6 Assay Products:

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    Search eBioscience for ELISAs for COL4A6 
    antibodies-online kits for COL4A6 (2 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

    3 InterPro protein domains:
     IPR016187 C-type_lectin_fold
     IPR001442 Collagen_VI_NC
     IPR008160 Collagen

    Graphical View of Domain Structure for InterPro Entry Q14031

    ProtoNet protein and cluster: Q14031

    3 Blocks protein domains:
    IPB001442 Type 4 procollagen
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: CO4A6_HUMAN, Q14031
    Domain: Alpha chains of type IV collagen have a non-collagenous domain (NC1) at their C-terminus, frequent
    interruptions of the G-X-Y repeats in the long central triple-helical domain (which may cause flexibility in the
    triple helix), and a short N-terminal triple-helical 7S domain
    Similarity: Belongs to the type IV collagen family
    Similarity: Contains 1 collagen IV NC1 (C-terminal non-collagenous) domain


    Find genes that share domains with COL4A6           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: CO4A6_HUMAN, Q14031
    Function: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a
    'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen

         Genatlas biochemistry entry for COL4A6:
    collagen type IV,alpha 6,basement membrane,expressed in kidney renal tubules,not located in glomerular BM,also
    expressed in esophagus and lung and in the dermoepidermal junction during fetal skin development

         Enzyme Number (IUBMB): EC 2.7.7.82

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005198structural molecule activity ----
    GO:0005201extracellular matrix structural constituent IEA--
         
    Find genes that share ontologies with COL4A6           About GenesLikeMe


    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Col4a6):
     normal 

    Find genes that share phenotypes with COL4A6           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Col4a6tm1Jrs for COL4A6

       genOway: Develop your customized and physiologically relevant rodent model for COL4A6

    miRNA
    Products:
        
    miRTarBase miRNAs that target COL4A6:
    hsa-mir-197-3p (MIRT048147)

    Block miRNA regulation of human, mouse, rat COL4A6 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate COL4A6 (see all 32):
    hsa-miR-4254 hsa-miR-4251 hsa-let-7d hsa-miR-200a hsa-miR-29a hsa-miR-29c hsa-let-7c hsa-miR-29b-1*
    SwitchGear 3'UTR luciferase reporter plasmidCOL4A6 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for COL4A6
    Predesigned siRNA for gene silencing in human, mouse, rat COL4A6

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    GenScript: all cDNA clones in your preferred vector (see all 2): COL4A6 (NM_033641)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL4A6
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL4A6

    Cell Line
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL4A6


    (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
    CO4A6_HUMAN, Q14031: Secreted, extracellular space, extracellular matrix, basement membrane
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    plasma membrane2
    cytosol1
    lysosome1
    mitochondrion1
    nucleus1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005581collagen ----
    GO:0005587collagen type IV NAS8125972
    GO:0005604basement membrane ----
    GO:0005788endoplasmic reticulum lumen TAS--

    Find genes that share ontologies with COL4A6           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 COL4A6 About   (see all 16)  
    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
    3Cell adhesion ECM remodeling
    Metalloproteases in connective tissue degradation0.31
    Cell adhesion ECM remodeling0.31
    4Integrin 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
    5ERK Signaling
    Rho Family GTPases0.61
    Molecular Mechanisms of Cancer0.51
    ERK Signaling0.61
    ILK Signaling0.49
    MAPK Signaling0.58


    Find genes that share SuperPaths with COL4A6           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL4A6 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    5 GeneGo (Thomson Reuters) Pathways for COL4A6
        Cell adhesion Endothelial cell contacts by non-junctional mechanisms
    Cytoskeleton remodeling Integrin outside-in signaling
    Cell adhesion Integrin-mediated cell adhesion and migration
    Cell adhesion ECM remodeling
    Cell adhesion Plasmin signaling

    1 BioSystems Pathway for COL4A6
        Focal Adhesion

    Selected Reactome Pathways for COL4A6 (see all 9)
        Laminin interactions
    Integrin cell surface interactions
    Assembly of collagen fibrils and other multimeric structures
    Collagen degradation
    Anchoring fibril formation

    1 PharmGKB Pathway for COL4A6
        Platelet Aggregation Inhibitor Pathway, Pharmacodynamics

    Selected Kegg Pathways  (Kegg details for COL4A6) (see all 7):
        PI3K-Akt signaling pathway
    Focal adhesion
    ECM-receptor interaction
    Protein digestion and absorption
    Amoebiasis

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for COL4A6
    Interactions:

        Search GeneGlobe Interaction Network for COL4A6

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

    Selected Interacting proteins for COL4A6 (Q140313 ENSP000003612904) via UniProtKB, MINT, STRING, and/or I2D (see all 86)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    APPP050673, ENSP000002849814I2D: score=1 STRING: ENSP00000284981
    CD93Q9NPY33, ENSP000002460064I2D: score=1 STRING: ENSP00000246006
    DCNP075853, ENSP000000527544I2D: score=1 STRING: ENSP00000052754
    FN1P027513, ENSP000003468394I2D: score=1 STRING: ENSP00000346839
    HABP2Q145203, ENSP000002779034I2D: score=1 STRING: ENSP00000277903
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion IEA--
    GO:0022617extracellular matrix disassembly TAS--
    GO:0030198extracellular matrix organization TAS--
    GO:0030574collagen catabolic process TAS--
    GO:0071230cellular response to amino acid stimulus IEA--

    Find genes that share ontologies with COL4A6           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 COL4A6 (CO4A6)



    (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 COL4A6 gene (5 alternative transcripts): 
    NM_001287758.1  NM_001287759.1  NM_001287760.1  NM_001847.3  NM_033641.3  

    Unigene Cluster for COL4A6:

    Collagen, type IV, alpha 6
    Hs.145586  [show with all ESTs]
    Unigene Representative Sequence: NM_033641
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000334504(uc004env.4 uc011msn.2 uc010npk.3) ENST00000372216(uc004enw.4)
    ENST00000487645 ENST00000468338 ENST00000461897(uc004enx.2) ENST00000477085(uc004eny.2)
    ENST00000418180(uc011msm.1) ENST00000394872 ENST00000545689 ENST00000538570

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    hsa-miR-4254 hsa-miR-4251 hsa-let-7d hsa-miR-200a hsa-miR-29a hsa-miR-29c hsa-let-7c hsa-miR-29b-1*
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      QuantiFast Probe-based Assays in human, mouse, rat COL4A6

    Additional mRNA sequence: 

    AK098221.1 AK300502.1 AK302734.1 BC000874.1 BC005305.1 BC070203.1 BC140855.1 BC144669.1 
    BT007228.1 D21337.1 EU182215.1 L22763.1 U04845.1 

    7 DOTS entries:

    DT.100022166  DT.97797434  DT.91903198  DT.443940  DT.91824900  DT.99934091  DT.95338592 

    Selected AceView cDNA sequences (see all 55):

    AA912712 BM699063 CD676232 CA488244 BG740770 AW627863 AI273913 CR605243 
    AA910008 AW082083 CA397764 BG680578 L22763 BQ941056 AI889941 U04845 
    NM_001847 AI890815 AW452474 AA193517 BM717791 CA312783 AI680557 BC070203 

    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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    COL4A6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGTCAGTTT
    COL4A6 Expression
    About this image


    COL4A6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Fibroblasts
             Dermal Fibroblasts Dorsal Dermis
     
     Dermis (Integumentary System)    fully expand to see all 3 entries
             Dermal Fibroblasts Dorsal Dermis
     
     Neural Crest (Gastrulation Derivatives)
             PureStem 7PEND24, NCr-fac & Meso-prx Progenitor
     
     Primitive Streak (Early Embryonic Tissues)
             Primitive streak-like cells
     
     Eye (Sensory Organs)
             Lens
    COL4A6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL4A6 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.145586
        Custom PCR Arrays for COL4A6
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL4A6

    (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 COL4A6 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col4a61 , 5 collagen, type IV, alpha 61, 5 81.99(n)1
    80.19(a)1
      X (61.80 cM)5
    942161  NM_053185.21  NP_444415.21 
     1411654035 
    chicken
    (Gallus gallus)
    Aves COL4A61 collagen, type IV, alpha 6 65.69(n)
    65.31(a)
      422350  XM_420322.4  XP_420322.4 
    lizard
    (Anolis carolinensis)
    Reptilia COL4A66
    collagen, type IV, alpha 6
    63(a)
    1 ↔ 1
    GL343202.1(3989034-4145144)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.36402 Xenopus laevis transcribed sequence with moderate similarity more 80(n)    BJ073613.1 
    zebrafish
    (Danio rerio)
    Actinopterygii col4a61 collagen, type IV, alpha 6 57.07(n)
    54.62(a)
      554268  XM_001921595.3  XP_001921630.3 


    ENSEMBL Gene Tree for COL4A6 (if available)
    TreeFam Gene Tree for COL4A6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL4A6 gene
    COL11A22  COL4A52  COL24A12  COL4A42  COL5A32  COL1A12  COL4A22  COL5A22  
    COL5A12  COL4A32  COL1A22  COL7A12  COL2A12  COL3A12  COL27A12  COL4A12  
    COL11A12  
    9 SIMAP similar genes for COL4A6 using alignment to 9 protein entries:     CO4A6_HUMAN (see all proteins):
    MSR1    COL4A5    C1QB    COL4A2    COL4A4    FCN2
    COL4A1    COLEC11    COL4A3

    Find genes that share paralogs with COL4A6           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 COL4A6 (see all 3756)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0357484
    A colorectal cancer sample4--see VAR_0357482 G E mis40--------
    rs2001320411,2
    --107398409(+) CACAC-/AACACA 2 -- ds50010--------
    rs2021734981,2
    --107398681(+) CAGCT-/CTTTGA
            
    CTTTG
    2 -- ds50010--------
    rs1426048231,2
    --107398967(+) TTTATA/GTAATA 2 -- ut310--------
    rs1509925171,2
    C--107399162(+) TTTTAA/TGAGGT 2 -- ut310--------
    rs1399524551,2
    --107399248(+) AACATA/CCTCAG 2 -- ut310--------
    rs1435051491,2
    --107399251(+) ATCCTC/GAGAAT 2 -- ut310--------
    rs1836434581,2
    --107399363(+) TACCTC/TTTTGT 2 -- ut310--------
    rs59738501,2
    C,F,A,H--107399421(+) CTACTT/CCTGGC 2 -- ut31 ese316Minor allele frequency- C:0.39NS EA NA WA 1974
    rs10420711,2
    C,F,A,H--107399513(-) GAGGAT/CGTGGC 2 -- ut31 ese320Minor allele frequency- C:0.37MN NA NS EA WA 2290

    HapMap Linkage Disequilibrium report for COL4A6 (107386780 - 107636780 bp, first 250kb of COL4A6)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for COL4A6:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv9265CNV Gain19470904

    Human Gene Mutation Database (HGMD): COL4A6
    Locus Specific Mutation Databases (LSDB): COL4A6

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL4A6
    DNA2.0 Custom Variant and Variant Library Synthesis for COL4A6

    (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: 303631   
    OMIM disorders: 300914  
    UniProtKB/Swiss-Prot: CO4A6_HUMAN, Q14031
  • Note=Deletions covering the N-terminal regions of COL4A5 and COL4A6, which are localized in a
    head-to-head manner, are found in the chromosome Xq22.3 centromeric deletion syndrome. This results in a
    phenotype with features of diffuse leiomyomatosis and Alport syndrome (DL-ATS)

  • 7 diseases for COL4A6:    
    About MalaCards
    leiomyomatosis    deafness, x-linked 6    deafness, x-linked 1    x-linked diffuse leiomyomatosis - alport syndrome
    retinitis pigmentosa 27    secretory meningioma    alport syndrome

    2 diseases from the University of Copenhagen DISEASES database for COL4A6:
    Alport syndrome     Leiomyoma

    Find genes that share disorders with COL4A6           About GenesLikeMe

    7 Novoseek inferred disease relationships for COL4A6 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    leiomyomatosis 94.6 17 16114791 (2), 7833948 (2), 9562604 (1), 8599366 (1) (see all 13)
    alport syndrome, x-linked 94.5 3 11096082 (1), 8587250 (1), 10499074 (1)
    alports syndrome 93.7 19 8599366 (3), 8738805 (2), 7833948 (2), 9562604 (1) (see all 13)
    leiomyoma 45.6 1 9502408 (1)
    renal failure 25.8 2 7706490 (1), 8738805 (1)
    cataract 9.44 1 16114791 (1)
    tumors 6.62 5 9042160 (3), 18074349 (1), 9915944 (1)

    Genetic Association Database (GAD): COL4A6
    Human Genome Epidemiology (HuGE) Navigator: COL4A6 (6 documents)

    Export disorders for COL4A6 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 COL4A6 gene, integrated from 10 sources (see all 83):
    (articles sorted by number of sources associating them with COL4A6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Deletion of the paired alpha 5(IV) and alpha 6(IV) collagen genes in inherited smooth muscle tumors. (PubMed id 8356449)1, 2, 3, 9 Zhou J.... Reeders S.T. (Science 1993)
    2. Structure of the human type IV collagen COL4A6 gene, which is mutated in Alport syndrome-associated leiomyomatosis. (PubMed id 8661006)1, 2, 9 Zhang X.... Tryggvason K. (Genomics 1996)
    3. Identification of fetal and maternal single nucleotide polymorphisms in candidate genes that predispose to spontaneous preterm labor with intact membranes. (PubMed id 20452482)1, 4 Romero R....Menon R. (Am. J. Obstet. Gynecol. 2010)
    4. A genetic association study of maternal and fetal candidate genes that predispose to preterm prelabor rupture of membranes (PROM). (PubMed id 20673868)1, 4 Romero R....Menon R. (Am. J. Obstet. Gynecol. 2010)
    5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    6. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    7. Complete primary structure of the sixth chain of human basement membrane collagen, alpha 6(IV). Isolation of the cDNAs for alpha 6(IV) and comparison with five other type IV collagen chains. (PubMed id 8175748)1, 2 Zhou J.... Reeders S.T. (J. Biol. Chem. 1994)
    8. Identification of a new collagen IV chain, alpha 6(IV), by cDNA isolation and assignment of the gene to chromosome Xq22, which is the same locus for COL4A5. (PubMed id 8125972)1, 2 Oohashi T.... Ninomiya Y. (J. Biol. Chem. 1994)
    9. The genes COL4A5 and COL4A6, coding for basement membrane collagen chains alpha 5(IV) and alpha 6(IV), are located head-to-head in close proximity on human chromosome Xq22 and COL4A6 is transcribed from two alternative promoters. (PubMed id 7972123)1, 9 Sugimoto M....Ninomiya Y. (Proc. Natl. Acad. Sci. U.S.A. 1994)
    10. Isolation and structure of the COL4A6 gene encoding the human alpha 6(IV) collagen chain and comparison with other type IV collagen genes. (PubMed id 7592929)1, 9 Oohashi T.... Ninomiya Y. (J. Biol. Chem. 1995)

    (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: 1288 HGNC: 2208 AceView: COL4A6 Ensembl:ENSG00000197565 euGenes: HUgn1288
    ECgene: COL4A6 Kegg: 1288 H-InvDB: COL4A6

    (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 COL4A6 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for COL4A6 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for COL4A6 gene:
    Search GeneIP for patents involving COL4A6

    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, eBioscience, antibodies-online, 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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