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COL4A1 Gene

protein-coding   GIFtS: 70
GCID: GC13M110801

Collagen, Type IV, Alpha 1

  See COL4A1-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 IV, Alpha 11 2     Collagen Alpha-1(IV) Chain2
HANAC2 5     Collagen IV, Alpha-1 Polypeptide2
ICH2 5     Collagen Of Basement Membrane, Alpha-1 Chain2
POREN12 5     EC 3.4.238
arresten2     EC 6.3.1.28
COL4A1 NC1 Domain2     

External Ids:    HGNC: 22021   Entrez Gene: 12822   Ensembl: ENSG000001874987   OMIM: 1201305   UniProtKB: P024623   

Export aliases for COL4A1 gene to outside databases

Previous GC identifers: GC13M109161 GC13M105188 GC13M109638 GC13M108499 GC13M109599 GC13M091400


(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 COL4A1 Gene:
This gene encodes the major type IV alpha collagen chain 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
so that each gene pair shares a common promoter. (provided by RefSeq, Jul 2008)

GeneCards Summary for COL4A1 Gene:
COL4A1 (collagen, type IV, alpha 1) is a protein-coding gene. Diseases associated with COL4A1 include hemorrhage, intracerebral, and col4a1-related brain small-vessel disease. GO annotations related to this gene include platelet-derived growth factor binding and extracellular matrix structural constituent. An important paralog of this gene is COL4A6.

UniProtKB/Swiss-Prot: CO4A1_HUMAN, P02462
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
Function: Arresten, comprising the C-terminal NC1 domain, inhibits angiogenesis and tumor formation. The
C-terminal half is found to possess the anti-angiogenic activity. Specifically inhibits endothelial cell
proliferation, migration and tube formation. Inhibits expression of hypoxia-inducible factor 1alpha and ERK1/2
and p38 MAPK activation. Ligand for alpha1/beta1 integrin

Gene Wiki entry for COL4A1 (Collagen, type IV, alpha 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000013.10  NC_018924.2  NT_009952.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL4A1 gene promoter:
         HOXA9B   HOXA9   AREB6   SREBP-1c   Sox9   Meis-1a   MIF-1   LyF-1   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL4A1 promoter sequence
   Search Chromatin IP Primers for COL4A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL4A1


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

Entrez Gene cytogenetic band: 13q34   Ensembl cytogenetic band:  13q34   HGNC cytogenetic band: 13q34

COL4A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL4A1 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M110801:  view genomic region     (about GC identifiers)

Start:
110,801,310 bp from pter      End:
110,959,496 bp from pter
Size:
158,187 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: CO4A1_HUMAN, P02462 (See protein sequence)
Recommended Name: Collagen alpha-1(IV) chain precursor  
Size: 1669 amino acids; 160615 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
1 PDB 3D structure from and Proteopedia for COL4A1:
1LI1 (3D)    
Secondary accessions: A7E2W4 B1AM70 Q1P9S9 Q5VWF6 Q86X41 Q8NF88 Q9NYC5
Alternative splicing: 2 isoforms:  P02462-1   P02462-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL4A1: NX_P02462

Explore proteomics data for COL4A1 at MOPED

Post-translational modifications: 

  • Lysines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in all cases and bind
    carbohydrates1
  • 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 residues1
  • Proteolytic processing produces the C-terminal NC1 peptide, arresten1
  • Glycosylation2 at Asn126
  • Modification sites at PhosphoSitePlus
  • 2 DME Specific Peptides for COL4A1 (P02462)
     VTGLVGI  GFPGPQG 


    See COL4A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001836.2  
    ENSEMBL proteins: 
     ENSP00000364979   ENSP00000443348  
    Reactome Protein details: P02462

    COL4A1 Human Recombinant Protein Products:

    EMD Millipore Purified and/or Recombinant COL4A1 Protein
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    Novus Biologicals COL4A1 Proteins
    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 COL4A1 

    COL4A1 Antibody Products:

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    Novus Biologicals COL4A1 Antibodies
    Abcam antibodies for COL4A1 (Q01955, P08572, P02462, P29400, P20908, P53420)
    Browse Antibodies at Cloud-Clone Corp.
    ThermoFisher Antibody for COL4A1
    LSBio Antibodies in human, mouse, rat for COL4A1

    COL4A1 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 COL4A1 


    (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 P02462

    ProtoNet protein and cluster: P02462

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


    UniProtKB/Swiss-Prot: CO4A1_HUMAN, P02462
    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 COL4A1           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: CO4A1_HUMAN, P02462
    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
    Function: Arresten, comprising the C-terminal NC1 domain, inhibits angiogenesis and tumor formation. The
    C-terminal half is found to possess the anti-angiogenic activity. Specifically inhibits endothelial cell
    proliferation, migration and tube formation. Inhibits expression of hypoxia-inducible factor 1alpha and ERK1/2
    and p38 MAPK activation. Ligand for alpha1/beta1 integrin

         Genatlas biochemistry entry for COL4A1:
    collagen type IV,alpha 1,basement membrane,all tissues,expressed in the dermoepidermal junction during fetal skin
    development

         Enzyme Numbers (IUBMB): EC 3.4.232 EC 6.3.1.22

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005201extracellular matrix structural constituent IMP16107487
    GO:0005515protein binding IPI12011424
    GO:0030023extracellular matrix constituent conferring elasticity IC16107487
    GO:0048407platelet-derived growth factor binding IDA8900172
         
    Find genes that share ontologies with COL4A1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for COL4A1:
     Increased cell death HMECs cel 

         14 MGI mutant phenotypes (inferred from 14 alleles(MGI details for Col4a1):
     behavior/neurological  cardiovascular system  cellular  embryogenesis  growth/size/body 
     hematopoietic system  homeostasis/metabolism  mortality/aging  muscle  nervous system 
     other  renal/urinary system  reproductive system  vision/eye 

    Find genes that share phenotypes with COL4A1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Col4a1/Col4a2Col4a1/tm1Epo for COL4A1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL4A1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for COL4A1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL4A1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL4A1

    miRNA
    Products:
        
    miRTarBase miRNAs that target COL4A1:
    hsa-mir-29a-3p (MIRT003221), hsa-mir-16-5p (MIRT051073), hsa-mir-125a-5p (MIRT045748), hsa-mir-769-3p (MIRT039089), hsa-mir-99a-5p (MIRT048676), hsa-mir-18a-3p (MIRT040877), hsa-mir-29b-3p (MIRT005568), hsa-mir-124-3p (MIRT022172), hsa-mir-218-5p (MIRT024242), hsa-mir-100-5p (MIRT048584), hsa-mir-92a-3p (MIRT049483), hsa-mir-29c-3p (MIRT001927), hsa-mir-193b-3p (MIRT041389)

    Block miRNA regulation of human, mouse, rat COL4A1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate COL4A1 (see all 68):
    hsa-miR-100* hsa-miR-3152-3p hsa-miR-106a hsa-miR-3653 hsa-miR-3142 hsa-miR-93 hsa-miR-556-3p hsa-miR-490-3p
    SwitchGear 3'UTR luciferase reporter plasmidCOL4A1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for COL4A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL4A1

    Gene Editing
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    Clone
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    OriGene ORF clones in mouse, rat for COL4A1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: COL4A1 (NM_001845)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL4A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL4A1

    Cell Line
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    ESI BIO PureStem Progenitor for COL4A1: 
    PureStem ES-210, Ecto-ntu Progenitor
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL4A1

    Flow Cytometry
    Products:
       

     
    eBioscience FlowRNA Probe Sets ( VA1-10870) for COL4A1 


    (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
    CO4A1_HUMAN, P02462: Secreted, extracellular space, extracellular matrix, basement membrane
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    mitochondrion1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005581collagen ----
    GO:0005587collagen type IV IMP16107487
    GO:0005604basement membrane IC--
    GO:0005788endoplasmic reticulum lumen TAS--

    Find genes that share ontologies with COL4A1           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 COL4A1 About   (see all 24)  
    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 COL4A1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 R&D Systems Pathway for COL4A1
        Blood Coagulation Signaling Pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL4A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    5 GeneGo (Thomson Reuters) Pathways for COL4A1
        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

    2 BioSystems Pathways for COL4A1
        Focal Adhesion
    Spinal Cord Injury

    Selected Reactome Pathways for COL4A1 (see all 12)
        Laminin interactions
    Integrin cell surface interactions
    NCAM1 interactions
    Assembly of collagen fibrils and other multimeric structures
    Collagen degradation

    1 PharmGKB Pathway for COL4A1
        Platelet Aggregation Inhibitor Pathway, Pharmacodynamics

    Selected Kegg Pathways  (Kegg details for COL4A1) (see all 7):
        PI3K-Akt signaling pathway
    Focal adhesion
    ECM-receptor interaction
    Protein digestion and absorption
    Amoebiasis

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL4A1: 
              Osteogenesis in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Wound Healing in human mouse rat
              Hepatotoxicity in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for COL4A1

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

    Selected Interacting proteins for COL4A1 (P024621, 2, 3 ENSP000003649794) via UniProtKB, MINT, STRING, and/or I2D (see all 107)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    COL4A2P085721, 3, ENSP000003536544EBI-2432478,EBI-2432506 I2D: score=5 STRING: ENSP00000353654
    COCHO434052, 3, ENSP000002163614MINT-6796166 I2D: score=1 STRING: ENSP00000216361
    ACHEP223033, ENSP000003032114I2D: score=2 STRING: ENSP00000303211
    APPP050673, ENSP000002849814I2D: score=2 STRING: ENSP00000284981
    FBLN2P980953, ENSP000003841694I2D: score=2 STRING: ENSP00000384169
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 14):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001525angiogenesis ----
    GO:0001569patterning of blood vessels IMP--
    GO:0007411axon guidance TAS--
    GO:0007420brain development IMP16107487
    GO:0007528neuromuscular junction development IEA--

    Find genes that share ontologies with COL4A1           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 COL4A1 (CO4A1)

    2 Novoseek inferred chemical compound relationships for COL4A1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    arresten 93.3 6 10811134 (4), 18775695 (1), 16151532 (1)
    tyrosine 0 2 17638901 (1), 9027485 (1)



    Find genes that share compounds with COL4A1           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 COL4A1 gene: 
    NM_001845.4  

    Unigene Cluster for COL4A1:

    Collagen, type IV, alpha 1
    Hs.17441  [show with all ESTs]
    Unigene Representative Sequence: NM_001845
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000375820(uc001vqw.4) ENST00000467182 ENST00000474391 ENST00000543140

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate COL4A1 (see all 68):
    hsa-miR-100* hsa-miR-3152-3p hsa-miR-106a hsa-miR-3653 hsa-miR-3142 hsa-miR-93 hsa-miR-556-3p hsa-miR-490-3p
    SwitchGear 3'UTR luciferase reporter plasmidCOL4A1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat COL4A1
    Clone
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    GenScript: all cDNA clones in your preferred vector: COL4A1 (NM_001845)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL4A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL4A1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for COL4A1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL4A1
      QuantiTect SYBR Green Assays in human, mouse, rat COL4A1
      QuantiFast Probe-based Assays in human, mouse, rat COL4A1
    Flow Cytometry
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    eBioscience FlowRNA Probe Sets ( VA1-10870) for COL4A1 

    Additional mRNA sequence: 

    AB209646.1 AF258349.1 AF363672.1 AF400431.1 AF536207.1 AY285780.1 BC047305.1 BC142626.1 
    BC151220.1 DQ464183.1 EU260121.1 M10940.1 M10941.1 M11315.1 X03963.1 X05561.1 
    Y00706.1 

    23 DOTS entries:

    DT.452612  DT.100686990  DT.100796389  DT.100796397  DT.95242820  DT.402672  DT.95242796  DT.100796390 
    DT.120766951  DT.100030647  DT.100796398  DT.102838671  DT.121627343  DT.85104942  DT.86855614  DT.95185880 
    DT.95258962  DT.97784947  DT.99958932  DT.40123811  DT.91759496  DT.95177824  DT.97809583 

    Selected AceView cDNA sequences (see all 685):

    M11315 AI753948 AA494330 AW273468 AA579667 AI572565 BQ711352 H60111 
    BQ774173 AW087920 CA431427 AI922296 AA167181 AI167909 BU782831 BG939825 
    AI951133 AI619601 AI753366 AI685091 AW513908 BU689514 AI033360 AF363672 

    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)
    About This Section

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    COL4A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GACCGCAGGA
    COL4A1 Expression
    About this image


    COL4A1 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
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 14 entries
             Multinuclear Myocytes Lumbar Back Muscles
     
     Fibroblasts
             Dermal Fibroblasts Dorsal Dermis
     
     Dermis (Integumentary System)    fully expand to see all 3 entries
             Dermal Fibroblasts Dorsal Dermis
     
     Heart (Cardiovascular System)    fully expand to see all 4 entries
             Subepicardial Cells Epicardium
             Coronary Vessels
     
     Hypoblast (Extraembryonic Tissues)
             Extraembryonic endoderm-like cells
    COL4A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL4A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.17441

    UniProtKB/Swiss-Prot: CO4A1_HUMAN, P02462
    Tissue specificity: Highly expressed in placenta

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL4A1: 
              Osteogenesis in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Wound Healing in human mouse rat
              Hepatotoxicity in human mouse rat

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    (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 COL4A1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col4a11 , 5 collagen, type IV, alpha 11, 5 83.48(n)1
    90.71(a)1
      8 (5.53 cM)5
    128261  NM_009931.21  NP_034061.21 
     111984235 
    chicken
    (Gallus gallus)
    Aves COL4A11 collagen, type IV, alpha 1 69.83(n)
    74.64(a)
      395530  NM_001162399.1  NP_001155871.1 
    lizard
    (Anolis carolinensis)
    Reptilia COL4A16
    collagen, type IV, alpha 1
    71(a)
    1 ↔ 1
    1(137145643-137277961)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia col4a11 collagen alpha-1(IV) chain 64.36(n)
    66.06(a)
      100124870  XM_002933018.2  XP_002933064.2 
    zebrafish
    (Danio rerio)
    Actinopterygii col4a11 collagen, type IV, alpha 1 61.26(n)
    63.33(a)
      554269  XM_688948.6  XP_694040.5 
    fruit fly
    (Drosophila melanogaster)
    Insecta Cg25C3 dorsal closure 41(a)   25C1   --
    worm
    (Caenorhabditis elegans)
    Secernentea let-23 alpha-2 type IV collagen 66(a)   X(16411823-16420128)   --


    ENSEMBL Gene Tree for COL4A1 (if available)
    TreeFam Gene Tree for COL4A1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL4A1 gene
    COL4A62  COL11A22  COL4A52  COL24A12  COL4A42  COL5A32  COL1A12  COL4A22  
    COL5A22  COL5A12  COL4A32  COL1A22  COL7A12  COL2A12  COL3A12  COL27A12  
    COL11A12  
    8 SIMAP similar genes for COL4A1 using alignment to 3 protein entries:     CO4A1_HUMAN (see all proteins):
    COL4A5    COL4A3    COL4A2    MSR1    COL4A6    C1QTNF9
    C1QTNF9B    COL4A4

    Find genes that share paralogs with COL4A1           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 COL4A1 (see all 4204)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0644984
    Brain small vessel disease with hemorrhage (BSVDH)4--see VAR_0644982 G R mis40--------
    VAR_0300314
    Porencephaly 1 (POREN1)4--see VAR_0300312 G R mis40--------
    VAR_0644964
    Brain small vessel disease with hemorrhage (BSVDH)4--see VAR_0644962 G D mis40--------
    VAR_0441594
    Hereditary angiopathy with nephropathy aneurysms and muscle cramps (HANAC)4--see VAR_0441592 G V mis40--------
    VAR_0644944
    Hereditary angiopathy with nephropathy aneurysms and muscle cramps (HANAC)4--see VAR_0644942 G R mis40--------
    VAR_0644934
    Hereditary angiopathy with nephropathy aneurysms and muscle cramps (HANAC)4--see VAR_0644932 G R mis40--------
    VAR_0644994
    Porencephaly 1 (POREN1)4--see VAR_0644992 G R mis40--------
    VAR_0441614
    Hereditary angiopathy with nephropathy aneurysms and muscle cramps (HANAC)4--see VAR_0441612 G E mis40--------
    VAR_0300324
    Porencephaly 1 (POREN1)4--see VAR_0300322 G R mis40--------
    VAR_0644974
    Brain small vessel disease with hemorrhage (BSVDH)4--see VAR_0644972 G R mis40--------

    HapMap Linkage Disequilibrium report for COL4A1 (110801310 - 110959496 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for COL4A1 (see all 17):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2748002CNV Deletion23290073
    esv2748003CNV Deletion23290073
    esv2748001CNV Deletion23290073
    esv1710742CNV Deletion17803354
    esv3081CNV Deletion18987735
    esv2748000CNV Deletion23290073
    esv2741067CNV Deletion23290073
    nsv1182CNV Loss18451855
    nsv64357CNV Loss16902084
    nsv456115CNV Loss19166990

    Human Gene Mutation Database (HGMD): COL4A1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL4A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL4A1

    (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: 120130   
    OMIM disorders: 175780  607595  611773  614519  
    UniProtKB/Swiss-Prot: CO4A1_HUMAN, P02462
  • Brain small vessel disease with hemorrhage (BSVDH) [MIM:607595]: An autosomal dominant disease
    characterized by weakening of the blood vessels in the brain and retinal arteriolar tortuosity. In affected
    individuals, stroke is often the first symptom and is usually caused by bleeding in the brain (hemorrhagic
    stroke) rather than a lack of blood flow in the brain (ischemic stroke). Patients also have leukoencephalopathy
    and may experience seizures and migraine headaches accompanied by visual sensations known as auras. Note=The
    disease is caused by mutations affecting the gene represented in this entry
  • Hereditary angiopathy with nephropathy aneurysms and muscle cramps (HANAC) [MIM:611773]: The clinical
    renal manifestations include hematuria and bilateral large cysts. Histologic analysis revealed complex basement
    membrane defects in kidney and skin. The systemic angiopathy appears to affect both small vessels and large
    arteries. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Porencephaly 1 (POREN1) [MIM:175780]: A neurologic disorder characterized by a fluid-filled cysts or
    cavities within the cerebral hemispheres, neurologic manifestations, facial paresis, and visual defects. Affected
    individuals typically have hemiplegia, seizures, and intellectual disability. Porencephaly type 1 is usually
    unilateral and results from focal destructive lesions such as fetal vascular occlusion or birth trauma. Note=The
    disease is caused by mutations affecting the gene represented in this entry

  • 20 diseases for COL4A1:    
    About MalaCards
    hemorrhage, intracerebral    col4a1-related brain small-vessel disease    angiopathy, hereditary, with nephropathy, aneurysms, and muscle    hereditary angiopathy with nephropathy, aneurysms, and muscle cramps syndrome
    autosomal dominant type 1 porencephaly    col4a1-related disorders    porencephaly    brain small vessel disease with hemorrhage
    familial porencephaly    brain small vessel disease with axenfeld-rieger anomaly    chronic purulent otitis media    malignant cylindroma
    arachnoid cysts    muscular dystrophy-dystroglycanopathy , type a, 7    schizencephaly    torch syndrome
    pseudo-torch syndrome    hydranencephaly    thin basement membrane nephropathy    walker-warburg syndrome

    2 diseases from the University of Copenhagen DISEASES database for COL4A1:
    Alport syndrome     pseudo-TORCH syndrome

    Find genes that share disorders with COL4A1           About GenesLikeMe

    5 Novoseek inferred disease relationships for COL4A1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    porencephaly 82.4 4 19238787 (1), 17379824 (1), 19194877 (1)
    intracerebral hemorrhage 47.9 4 19238787 (1), 19194877 (1)
    neovascularization 35.1 1 10811134 (1)
    renal disease 31.9 4 19238787 (1), 18160688 (1), 9047092 (1)
    diabetic nephropathies 23.7 2 9047092 (2)

    GeneTests: COL4A1
    GeneReviews: COL4A1
    Genetic Association Database (GAD): COL4A1
    Human Genome Epidemiology (HuGE) Navigator: COL4A1 (16 documents)

    Export disorders for COL4A1 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 COL4A1 gene, integrated from 10 sources (see all 176):
    (articles sorted by number of sources associating them with COL4A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete primary structure of the alpha 1-chain of human basement membrane (type IV) collagen. (PubMed id 3691802)1, 2, 3 Soininen R.... Tryggvason K. (FEBS Lett. 1987)
    2. COL4A1 mutation in two preterm siblings with antenatal onset of parenchymal hemorrhage. (PubMed id 19194877)1, 2, 9 de Vries L.S....Mancini G. (Ann. Neurol. 2009)
    3. COL4A1 mutations and hereditary angiopathy, nephropathy, aneurysms, and muscle cramps. (PubMed id 18160688)1, 2, 9 Plaisier E....Ronco P. (N. Engl. J. Med. 2007)
    4. Genetic risk for myocardial infarction determined by polymorphisms of candidate genes in a Japanese population. (PubMed id 18077766)1, 4, 9 Yamada Y....Nozawa Y. (J. Med. Genet. 2008)
    5. Anti-angiogenic cues from vascular basement membrane collagen. (PubMed id 10811134)1, 2, 9 Colorado P.C.... Kalluri R. (Cancer Res. 2000)
    6. Characterization of the anti-angiogenic properties of arresten, an alpha1beta1 integrin-dependent collagen-derived tumor suppressor. (PubMed id 18775695)1, 2, 9 Nyberg P.... Kalluri R. (Exp. Cell Res. 2008)
    7. Human alpha1 type IV collagen NC1 domain exhibits distinct antiangiogenic activity mediated by alpha1beta1 integrin. (PubMed id 16151532)1, 2, 9 Sudhakar A.... Kalluri R. (J. Clin. Invest. 2005)
    8. Sequence variants in COL4A1 and COL4A2 genes in Ecuadorian families with keratoconus. (PubMed id 21527998)1, 2 Karolak J.A.... Gajecka M. (Mol. Vis. 2011)
    9. Large-scale association analysis identifies 13 new susceptibility loci for coronary artery disease. (PubMed id 21378990)1, 4 Schunkert H....Samani N.J. (Nat. Genet. 2011)
    10. Genome-wide association study for coronary artery calcification with follow-up in myocardial infarction. (PubMed id 22144573)1, 4 O'Donnell C.J....Witteman J.C. (Circulation 2011)

    (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: 1282 HGNC: 2202 AceView: COL4A1 Ensembl:ENSG00000187498 euGenes: HUgn1282
    ECgene: COL4A1 Kegg: 1282 H-InvDB: COL4A1

    (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 COL4A1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for COL4A1 gene:
    Search GeneIP for patents involving COL4A1

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



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