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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

COL4A1 Gene

protein-coding   GIFtS: 70
GCID: GC13M110801

collagen, type IV, alpha 1
 Explore 47 diseases affiliated with
COL4A1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for COL4A1    

Aliases
for COL4A1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Collagen, Type IV, Alpha 11 2     Collagen Alpha-1(IV) Chain2
HANAC2     Collagen IV, Alpha-1 Polypeptide2
ICH2     Collagen Of Basement Membrane, Alpha-1 Chain2
POREN12     EC 3.4.238
Arresten1     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


Summaries
for COL4A1 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for COL4A1:
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)

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)


Genomic Views
for COL4A1 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000013.10  NC_018924.1  NT_009952.14  
Regulatory elements:
   SABiosciences 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 plasmid: COL4A1 promoter sequence
   Search SABiosciences Chromatin IP Primers for COL4A1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for COL4A1 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
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
Subcellular location: Secreted, extracellular space, extracellular matrix, basement membrane
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

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
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P02462

    • 2 DME Specific Peptides for COL4A1 (P02462)
     VTGLVGI  GFPGPQG 

    COL4A1 Protein expression data from MOPED and PaxDb:    About this image 
    COL4A1 Protein Expression
    REFSEQ proteins: NP_001836.2  
    ENSEMBL proteins: 
     ENSP00000364979   ENSP00000380382   ENSP00000443348  
    Reactome Protein details: P02462
    Human Recombinant Protein Products for COL4A1: 
    EMD Millipore Purified and/or Recombinant COL4A1 Protein
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    Novus Biologicals COL4A1 Proteins
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Uscn

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005587collagen type IV IEA--
    GO:0005604basement membrane ----
    GO:0005788endoplasmic reticulum lumen TAS--
    GO:0031012colocalizes with extracellular matrix ISS--

    COL4A1 for ontologies           About GeneDecksing



    COL4A1 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of COL4A1
    R&D Systems Antibodies for COL4A1 (Collagen IV alpha 1)
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    Abcam antibodies for COL4A1 
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    ThermoFisher Antibodies for COL4A1

    Assay Products for COL4A1: 
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    OriGene Custom Immunoassay Development
    Browse OriGene Fluorogenic Cell Assay Kits
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    GenScript Custom Assay Services for COL4A1
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs and CLIAs at Uscn

    Protein Domains /
    Families
    for COL4A1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    COL4A1 for domains           About GeneDecksing

    3 InterPro domains/families:
     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 families:
    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


    Function
    for COL4A1 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    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): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005201extracellular matrix structural constituent IEA--
    GO:0005515protein binding IPI12011424
    GO:0048407platelet-derived growth factor binding IDA8900172
         
    COL4A1 for ontologies           About GeneDecksing


    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 
     hematopoietic system  homeostasis/metabolism  mortality/aging  muscle  nervous system 
     other  renal/urinary system  reproductive system  vision/eye 

    COL4A1 for phenotypes           About GeneDecksing

    Animal Models:
         Mouse knock-out Col4a1/Col4a2Col4a1/tm1Epo for COL4A1
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for COL4A1 

    miRNA
    Products:            		miRTarBase miRNAs that target COL4A1:
    hsa-mir-29a (MIRT003221), hsa-mir-29b (MIRT005568), hsa-mir-29c (MIRT001927)

    OriGene 3'-UTR Clone: COL4A1
    Browse MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat COL4A1
    8/68 QIAGEN miScript miRNA 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 plasmid: COL4A1 3' UTR sequence
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for COL4A1 (see all 7)
    OriGene shRNA RFP: COL4A1
    OriGene siRNA: COL4A1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat COL4A1
    Sirion Biotech Custom design and validation of potent shRNA sequences against COL4A1 

    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for COL4A1
    Sirion Biotech Customized adenovirus for overexpression of COL4A1 
    Sirion Biotech Customized adenovirus for potent knockdown of COL4A1

    Clone
    Products:             		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for COL4A1 (see all 4)
    OriGene untagged cDNA clones in CMV expression vector in human, 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
    Products:             		GenScript Custom overexpressing Cell Line Services for COL4A1
    LifeMap BioReagents: cell line associated with COL4A1: PureStem ES-210, Ecto-ntu Progenitor
    Sirion Biotech Customized stable knockdown cell line services for COL4A1 
    Sirion Biotech Customized inducible knockdown cell line services for COL4A1

    In Situ Assay
    Products:       
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL4A1


    Pathways & Interactions
    for COL4A1 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/22 super-pathways (see all 22) About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Cell adhesion_Integrin-mediated cell adhesion and migration
    		Cell adhesion_Integrin-mediated cell adhesion and migration1.00
    		Cytoskeleton remodeling Integrin outside-in signaling0.37
    		Cell adhesion Integrin-mediated cell adhesion and migration1.00
    		Cell adhesion_Endothelial cell contacts by non-junctional mechanisms0.21
    		Cytoskeleton remodeling_Integrin outside-in signaling0.37
    		Cell adhesion Endothelial cell contacts by non-junctional mechanisms0.21
    2Integrin Pathway
    		Integrin Pathway1.00
    		UPA-UPAR Pathway0.51
    		FAK1 Signaling0.67
    		Transendothelial Migration of Leukocytes0.38
    		GnRH Signaling0.56
    		Inhibition of Angiogenesis by TSP10.37
    3Collagen formation
    		Collagen formation1.00
    		Extracellular matrix organization0.54
    		Collagen biosynthesis and modifying enzymes0.74
    		Secretion of collagens0.49
    		Assembly of collagen fibrils and other multimeric structures0.65
    4Rho Family GTPases
    		Rho Family GTPases1.00
    		MAPK Signaling0.51
    		ERK Signaling0.61
    		ILK Signaling0.45
    		Molecular Mechanisms of Cancer0.51
    5Gelatin degradation by MMP19
    		Gelatin degradation by MMP191.00
    		Anchoring fibril formation0.39
    		Gelatin degradation by MMP1, 2, 3, 7, 8, 9, 12, 130.64

    Pathway sources
    See GeneCards unified pathways
    Show all pathways

    5/6 EMD Millipore Pathways for COL4A1 (see all 6)
        Cell adhesion Integrin-mediated cell adhesion and migration
    Cytoskeleton remodeling Integrin outside-in signaling
    Cell adhesion ECM remodeling
    Metalloproteases in connective tissue degradation
    Cell adhesion Plasmin signaling

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

    5/15 Downloadable PowerPoint Slides of QIAGEN 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

    1 BioSystems Pathway for COL4A1 
        Focal Adhesion

    5/17        Reactome Pathways for COL4A1 (see all 17)
        Developmental Biology
    Assembly of collagen fibrils and other multimeric structures
    Gelatin degradation by MMP19
    Anchoring fibril formation
    Extracellular matrix organization

    1 PharmGKB Pathway for COL4A1
        Platelet Aggregation Inhibitor Pathway, Pharmacodynamics

    5/6         Kegg Pathways  (Kegg details for COL4A1) (see all 6):
        Focal adhesion
    ECM-receptor interaction
    Protein digestion and absorption
    Amoebiasis
    Pathways in cancer


    COL4A1 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for COL4A1

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

    5/98 Interacting proteins for COL4A1 (P024621, 2, 3 ENSP000003649794) via UniProtKB, MINT, STRING, and/or I2D (see all 98)
    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): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001525angiogenesis IEA--
    GO:0007411axon guidance TAS--
    GO:0007528neuromuscular junction development IEA--
    GO:0030198extracellular matrix organization TAS--
    GO:0030855epithelial cell differentiation ----

    COL4A1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for COL4A1 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    COL4A1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for COL4A1
    2 Novoseek 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)

    Search CenterWatch for drugs/clinical trials and news about COL4A1 / CO4A1 

    Transcripts
    for COL4A1 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    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
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000375820(uc001vqw.4) ENST00000397198 ENST00000467182 ENST00000474391
    ENST00000543140

    miRNA
    Products:             		 OriGene 3'-UTR Clone: COL4A1
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat COL4A1
    8/68 QIAGEN miScript miRNA 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 plasmid: COL4A1 3' UTR sequence
    Inhib. RNA
    Products:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for COL4A1 (see all 7)
    OriGene shRNA RFP: COL4A1
    OriGene siRNA: COL4A1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat COL4A1
    Sirion Biotech Custom design and validation of potent shRNA sequences against COL4A1 
    Clone
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    GenScript: all cDNA clones in your preferred vector: COL4A1 (NM_001845)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL4A1 
    Primer
    Products:            		 OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for COL4A1
    Browse OriGene validated miRNA SYBR primer pairs
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat COL4A1
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat COL4A1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COL4A1

    Additional cDNA 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 

    24/685 AceView cDNA sequences (see all 685):

    AF400431 BQ880964 AI125979 W46231 AA167181 BU677787 CD559094 BI092437 
    BM712591 AA887116 AW014980 AA576937 CA335271 BP336308 BX480408 CA420547 
    AA593204 AI587219 BQ716250 BU627180 AW273358 BM987230 AI753366 AI926547 

    GeneLoc Exon Structure


    Expression
    for COL4A1 gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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

    COL4A1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    10/17 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 17) 
    Tissue Anatomical Compartment CellCategory (developmental path)
    HeartEpicardiumSubepicardial CellsEpicardium
    LimbForelimb Dorsal MusclesMultinuclear MyocytesSkeletal Muscle
    LimbForelimb Ventral MusclesMultinuclear MyocytesSkeletal Muscle
    LimbHindlimb Dorsal MuscleMultinuclear MyocytesSkeletal Muscle
    LimbHindlimb Ventral MuscleMultinuclear MyocytesSkeletal Muscle
    Skeletal MuscleAnterior Neck MusclesMultinuclear MyocytesSkeletal Muscle
    Skeletal MuscleCervical Back MusclesMultinuclear MyocytesSkeletal Muscle
    Skeletal MuscleLumbar Back MusclesMultinuclear MyocytesSkeletal Muscle
    Skeletal MuscleLumbar Vertebrae Column MusclesMultinuclear MyocytesSkeletal Muscle
    Skeletal MusclePelvic MusclesMultinuclear MyocytesSkeletal Muscle
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 5 LifeMap Cells 
    NameCategory
    mK4 (Cell line)Kidney
    mK3 (Cell line)Kidney
    PureStem™ progenitor T42 (Embryonic Progenitor Cell)
    Extraembryonic endoderm-like cells (Generation of extrae...)
    Definitive endoderm-like cells (A scalable, suspensi...)

    See COL4A1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for COL4A1

    SOURCE GeneReport for Unigene cluster: Hs.17441

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

        SABiosciences Expression via Pathway-Focused 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
    for COL4A1 gene

    (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)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for COL4A1 gene from 5/18 species (see all 18)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves COL4A11 collagen, type IV, alpha 1 69.84(n)
    74.62(a)    		   395530  NM_001162399.1  NP_001155871.1 
    lizard
    (Anolis carolinensis)    		 Reptilia COL4A16
    		 --
    		 71(a)
    		 1 ↔ 1
    		 1(137145643-137242050)
    zebrafish
    (Danio rerio)    		 Actinopterygii col4a11 collagen, type IV, alpha 1 61.41(n)
    63.77(a)    		   554269  XM_688948.5  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
    for COL4A1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for COL4A1 gene
    COL4A62  COL19A12  COL11A22  COL4A52  COL24A12  COL4A42  COL5A32  COL1A12  
    COL16A12  COL4A22  COL5A22  COL5A12  COL4A32  COL22A12  COL1A22  COL7A12  
    COL27A12  COL2A12  COL3A12  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

    COL4A1 for paralogs           About GeneDecksing



    Genomic Variants
    for COL4A1 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/3535 NCBI SNPs in COL4A1 are shown (see all 3535)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 13 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1139941031,2
    		Cpathogenic94356697(-) CCACCA/TTGGGG 2 M L mis10--------
    rs1139941041,2
    		Cpathogenic94471765(-) CAAGGG/TCGACA 2 G V mis10--------
    rs1139941051,2
    		Cpathogenic94476711(-) CACCAA/GGGCTG 2 R G mis10--------
    rs1139941061,2
    		Cpathogenic94476739(-) CAAGGA/GGGAGC 2 E G mis10--------
    rs1139941081,2
    		Cpathogenic94482696(-) TAATGA/GCTTAC 2 D G mis10--------
    rs1139941091,2
    		Cpathogenic94484652(-) TTCCCA/GGCATT 2 S G mis10--------
    rs1139941111,2
    		Cpathogenic94489559(-) CCCTGA/GTGTCA 2 D G mis10--------
    rs1139941121,2
    		Cpathogenic94493439(-) CCAAAA/GGAGAC 2 R G mis10--------
    rs1139941131,2
    		Cpathogenic94501581(-) TTCCAC/GGTCCA 2 R G mis10--------
    rs1139941141,2
    		Cpathogenic94508705(-) GGATCC/GGCTAC 2 R G mis10--------

    HapMap Linkage Disequilibrium report for COL4A1 (110801310 - 110959496 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 23 variations for COL4A1
         15/20 CNVs (see all 20): 76486 87030 76492 76485 87035 87026 76488 76489 87033 87028 87029 76491 66552 87034 53407
         3 Indels: 40016 41893 11697
    Human Gene Mutation Database (HGMD): COL4A1

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    Disorders / Diseases
    for COL4A1 gene

    (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.)
    About This Section
    COL4A1 for disorders           About GeneDecksing

    OMIM gene information: 120130   
    OMIM disorders: 175780  607595  611773  
    UniProtKB/Swiss-Prot: CO4A1_HUMAN, P02462
  • Defects in COL4A1 are a cause of brain small vessel disease with hemorrhage (BSVDH) [MIM:607595]. Brain small
    • vessel diseases underlie 20 to 30 percent of ischemic strokes and a larger proportion of intracerebral hemorrhages.
    Inheritance is autosomal dominant
  • Defects in COL4A1 are the cause of 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
  • Defects in COL4A1 are a cause of familial porencephaly (POREN1) [MIM:175780]. Porencephaly is a term used for
    • any cavitation or cerebrospinal fluid-filled cyst in the brain. Porencephaly type 1 is usually unilateral and results
    from focal destructive lesions such as fetal vascular occlusion or birth trauma. Type 2, or schizencephalic
    porencephaly, is usually symmetric and represents a primary defect or arrest in the development of the cerebral
    ventricles

    20/47 diseases for COL4A1 (see all 47):    About MalaCards
    walker-warburg syndrome    porencephaly    brain small vessel disease with hemorrhage    autosomal recessive alport syndrome
    malignant cylindroma    familial porencephaly    alport syndrome    squamous cell carcinoma
    goodpasture syndrome    intracranial aneurysm    hydranencephaly    oral squamous cell carcinoma
    cramps    esophageal squamous cell carcinoma    polycystic kidney disease    aggressive periodontitis
    hematuria    hemiplegia    cerebral hemorrhage    nephropathy

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

    5 Novoseek 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
    COL4A1-Related Disorders

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

    Export disorders for COL4A1 gene to outside databases

    Publications
    for COL4A1 gene

    (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)
    About This Section

    PubMed articles for COL4A1 gene, integrated from 9 sources (see all 165):
    (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. (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. (2009)
    3. COL4A1 mutations and hereditary angiopathy, nephropathy, aneurysms, and muscle cramps. (PubMed id 18160688)1, 2, 9 Plaisier E....Ronco P. (2007)
    4. Anti-angiogenic cues from vascular basement membrane collagen. (PubMed id 10811134)1, 2, 9 Colorado P.C.... Kalluri R. (2000)
    5. 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. (2008)
    6. 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. (2005)
    7. Sequence variants in COL4A1 and COL4A2 genes in Ecuad orian families with keratoconus. (PubMed id 21527998)1, 2 Karolak J.A....Gajecka M. (2011)
    8. Ophthalmological features associated with COL4A1 muta tions. (PubMed id 20385946)1, 2 Coupry I....Goizet C. (2010)
    9. A dominantly inherited mutation in collagen IV A1 (CO L4A1) causing childhood onset stroke without porencephaly. (PubMed id 19477666)1, 2 Shah S....Jardine P. (2010)
    10. Novel COL4A1 mutations associated with HANAC syndrome : a role for the triple helical CB3[IV] domain. (PubMed id 20818663)1, 2 Plaisier E....Ronco P. (2010)

    External Searches for COL4A1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing COL4A1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 1282 HGNC: 2202 AceView: COL4A1 Ensembl:ENSG00000187498 euGenes: HUgn1282
    ECgene: COL4A1 Kegg: 1282 H-InvDB: COL4A1

    Other Databases showing COL4A1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing COL4A1 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for COL4A1 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for COL4A1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		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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    About This Section

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