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COL3A1 Gene

protein-coding   GIFtS: 70
GCID: GC02P189803

Collagen, Type III, Alpha 1

(Previous names: Ehlers-Danlos syndrome type IV, autosomal dominant)
(Previous symbol: EDS4A)
  See COL3A1-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 III, Alpha 11 2
EDS4A1 2
Ehlers-Danlos Syndrome Type IV, Autosomal Dominant1 2
Alpha1 (III) Collagen2
Collagen Alpha-1(III) Chain2
Collagen, Fetal2

External Ids:    HGNC: 22011   Entrez Gene: 12812   Ensembl: ENSG000001685427   OMIM: 1201805   UniProtKB: P024613   

Export aliases for COL3A1 gene to outside databases

Previous GC identifers: GC02P187975 GC02P188522 GC02P190041 GC02P189664 GC02P189547 GC02P181698


(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 COL3A1 Gene:
This gene encodes the pro-alpha1 chains of type III collagen, a fibrillar collagen that is found in extensible
connective tissues such as skin, lung, uterus, intestine and the vascular system, frequently in association with
type I collagen. Mutations in this gene are associated with Ehlers-Danlos syndrome types IV, and with aortic and
arterial aneurysms. Two transcripts, resulting from the use of alternate polyadenylation signals, have been
identified for this gene. (provided by R. Dalgleish, Feb 2008)

GeneCards Summary for COL3A1 Gene:
COL3A1 (collagen, type III, alpha 1) is a protein-coding gene. Diseases associated with COL3A1 include ehlers-danlos syndrome type iv, and familial cervical artery dissections. GO annotations related to this gene include integrin binding and SMAD binding. An important paralog of this gene is COL4A6.

UniProtKB/Swiss-Prot: CO3A1_HUMAN, P02461
Function: Collagen type III occurs in most soft connective tissues along with type I collagen. Involved in
regulation of cortical development. Is the major ligand of GPR56 in the developing brain and binding to GPR56
inhibits neuronal migration and activates the RhoA pathway by coupling GPR56 to GNA13 and possibly GNA12

Gene Wiki entry for COL3A1 (Collagen, type III, 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_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the COL3A1 gene promoter:
         Pbx1a   Bach2   FOXD1   Nkx2-5   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   NF-kappaB   NF-kappaB1   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOL3A1 promoter sequence
   Search Chromatin IP Primers for COL3A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COL3A1


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

Entrez Gene cytogenetic band: 2q31   Ensembl cytogenetic band:  2q32.2   HGNC cytogenetic band: 2q32.2

COL3A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COL3A1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P189803:  view genomic region     (about GC identifiers)

Start:
189,839,046 bp from pter      End:
189,877,472 bp from pter
Size:
38,427 bases      Orientation:
plus 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: CO3A1_HUMAN, P02461 (See protein sequence)
Recommended Name: Collagen alpha-1(III) chain precursor  
Size: 1466 amino acids; 138564 Da
Subunit: Trimers of identical alpha 1(III) chains. The chains are linked to each other by interchain disulfide
bonds. Trimers are also cross-linked via hydroxylysines
6 PDB 3D structures from and Proteopedia for COL3A1:
2V53 (3D)        3DMW (3D)        4AE2 (3D)        4AEJ (3D)        4AK3 (3D)        4GYX (3D)    
Secondary accessions: D3DPH4 P78429 Q15112 Q16403 Q53S91 Q541P8 Q6LDB3 Q6LDJ2 Q6LDJ3 Q7KZ56
Q8N6U4 Q9UC88 Q9UC89 Q9UC90 Q9UC91
Alternative splicing: 2 isoforms:  P02461-1   P02461-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for COL3A1: NX_P02461

Explore proteomics data for COL3A1 at MOPED

Post-translational modifications: 

  • Proline residues at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of
    the chains1
  • O-linked glycan consists of a Glc-Gal disaccharide bound to the oxygen atom of a post-translationally added
    hydroxyl group1
  • Glycosylation2 at Lys263, Ser1145
  • Modification sites at PhosphoSitePlus

  • See COL3A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000081.1  
    ENSEMBL proteins: 
     ENSP00000304408   ENSP00000415346   ENSP00000315243  
    Reactome Protein details: P02461

    COL3A1 Human Recombinant Protein Products:

    EMD Millipore Purified and/or Recombinant COL3A1 Protein
    R&D Systems Recombinant & Natural Proteins for COL3A1 (Collagen III alpha 1/COL3A1)
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Protein for COL3A1
    OriGene Protein Over-expression Lysate for COL3A1
    OriGene MassSpec for COL3A1
    OriGene Custom Protein Services for COL3A1
    GenScript Custom Purified and Recombinant Proteins Services for COL3A1
    Novus Biologicals COL3A1 Proteins
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for COL3A1
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for COL3A1 

    COL3A1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of COL3A1
    Browse R&D Systems for Antibodies
    OriGene Antibodies for COL3A1
    OriGene Custom Antibody Services for COL3A1
    Novus Biologicals COL3A1 Antibodies
    Abcam antibodies for COL3A1 (P08123, P20908, P02461)
    Browse Antibodies at Cloud-Clone Corp.
    ThermoFisher Antibodies for COL3A1
    LSBio Antibodies in human, mouse, rat for COL3A1

    COL3A1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for COL3A1
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for COL3A1 


    (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:
     IPR000885 Fib_collagen_C
     IPR001007 VWF_C
     IPR008160 Collagen

    Graphical View of Domain Structure for InterPro Entry P02461

    ProtoNet protein and cluster: P02461

    4 Blocks protein domains:
    IPB000885 Fibrillar collagen
    IPB001007 von Willebrand factor
    IPB008160 Collagen triple helix repeat
    IPB008161 Collagen helix repeat


    UniProtKB/Swiss-Prot: CO3A1_HUMAN, P02461
    Domain: The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by
    controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen
    fibrils. It binds a calcium ion which is essential for its function
    Similarity: Belongs to the fibrillar collagen family
    Similarity: Contains 1 fibrillar collagen NC1 domain
    Similarity: Contains 1 VWFC domain


    Find genes that share domains with COL3A1           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: CO3A1_HUMAN, P02461
    Function: Collagen type III occurs in most soft connective tissues along with type I collagen. Involved in
    regulation of cortical development. Is the major ligand of GPR56 in the developing brain and binding to GPR56
    inhibits neuronal migration and activates the RhoA pathway by coupling GPR56 to GNA13 and possibly GNA12

         Genatlas biochemistry entry for COL3A1:
    collagen type III,alpha 1,fibril forming,putative down-regulated c-Myc target gene,

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005178integrin binding NAS14970208
    GO:0005201extracellular matrix structural constituent IMP7487954
    GO:0005515protein binding IPI16754721
    GO:0046332SMAD binding IEA--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with COL3A1           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for COL3A1:
     Increased gamma-H2AX phosphory  Synthetic lethal with imatinib 

         9 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Col3a1):
     cardiovascular system  digestive/alimentary  growth/size/body  homeostasis/metabolism  integument 
     liver/biliary system  mortality/aging  muscle  respiratory system 

    Find genes that share phenotypes with COL3A1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Col3a1tm1Jae for COL3A1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COL3A1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for COL3A1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for COL3A1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COL3A1

    miRNA
    Products:
        
    miRTarBase miRNAs that target COL3A1:
    hsa-mir-29b-3p (MIRT005567), hsa-mir-29c-3p (MIRT000927), hsa-mir-455-3p (MIRT037808), hsa-mir-335-5p (MIRT018299)

    Block miRNA regulation of human, mouse, rat COL3A1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate COL3A1 (see all 21):
    hsa-miR-520d-5p hsa-let-7d hsa-miR-202 hsa-miR-29a hsa-miR-29c hsa-miR-767-5p hsa-let-7c hsa-miR-380*
    SwitchGear 3'UTR luciferase reporter plasmidCOL3A1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for COL3A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL3A1

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for COL3A1

    Clone
    Products:
         
    OriGene clones in human, mouse for COL3A1 (see all 6)
    OriGene ORF clones in mouse, rat for COL3A1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: COL3A1 (NM_000090)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL3A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL3A1

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for COL3A1
    Browse ESI BIO Cell Lines and PureStem Progenitors for COL3A1 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL3A1


    (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
    CO3A1_HUMAN, P02461: Secreted, extracellular space, extracellular matrix (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    endoplasmic reticulum4
    lysosome1

    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:0005586collagen type III NAS1672129
    GO:0005615extracellular space NAS9036918
    GO:0005788endoplasmic reticulum lumen TAS--

    Find genes that share ontologies with COL3A1           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 COL3A1 About   (see all 15)  
    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 COL3A1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for COL3A1 (see all 15)
        MAPK Signaling
    Molecular Mechanisms of Cancer
    PTEN Pathway
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway

    1 GeneGo (Thomson Reuters) Pathway for COL3A1
        Cell adhesion ECM remodeling

    4 BioSystems Pathways for COL3A1
        Focal Adhesion
    Senescence and Autophagy
    Endothelins
    Inflammatory Response Pathway

    Selected Reactome Pathways for COL3A1 (see all 11)
        Integrin cell surface interactions
    NCAM1 interactions
    Assembly of collagen fibrils and other multimeric structures
    Collagen degradation
    ECM proteoglycans

    1 PharmGKB Pathway for COL3A1
        Platelet Aggregation Inhibitor Pathway, Pharmacodynamics

    5 Kegg Pathways  (Kegg details for COL3A1):
        PI3K-Akt signaling pathway
    Focal adhesion
    ECM-receptor interaction
    Protein digestion and absorption
    Amoebiasis

        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL3A1 (see all 8): 
              Osteogenesis in human mouse rat
              Fibrosis in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Atherosclerosis in human mouse rat
              Wound Healing in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for COL3A1

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

    Selected Interacting proteins for COL3A1 (P024611, 2, 3 ENSP000003044084) via UniProtKB, MINT, STRING, and/or I2D (see all 98)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000228321P013753, ENSP000003928584I2D: score=1 STRING: ENSP00000392858
    TNFP013753, ENSP000003986984I2D: score=1 STRING: ENSP00000398698
    ENSG00000204490P013753I2D: score=1 
    ENSG00000206439P013753I2D: score=1 
    ENSG00000223952P013753I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 27):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development IEA--
    GO:0001568blood vessel development IEA--
    GO:0007160cell-matrix adhesion IDA16912226
    GO:0007179transforming growth factor beta receptor signaling pathway IDA16360482
    GO:0007229integrin-mediated signaling pathway IMP14970208

    Find genes that share ontologies with COL3A1           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 COL3A1 (CO3A1)

    1 DrugBank Compound for COL3A1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Collagenase-- 9001-12-1target--17016423 2145268 17139284

    8 Novoseek inferred chemical compound relationships for COL3A1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    nppa 68.3 2 14993121 (1), 15582321 (1)
    procollagen 51.4 2 9076960 (1), 17487505 (1)
    nppb 38.7 2 14993121 (1), 15582321 (1)
    ribonucleic acid 12.1 2 16360482 (1), 15582321 (1)
    thymidine 0 2 19741209 (1), 8918626 (1)
    aspartate 0 1 11168790 (1)
    glutamate 0 2 1352273 (1), 8098182 (1)
    cyclosporin a 0 8 10831628 (5), 9636386 (1)



    Find genes that share compounds with COL3A1           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 COL3A1 gene: 
    NM_000090.3  

    Unigene Cluster for COL3A1:

    Collagen, type III, alpha 1
    Hs.443625  [show with all ESTs]
    Unigene Representative Sequence: NM_000090
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000304636(uc002uqj.1) ENST00000470167 ENST00000450867 ENST00000467886
    ENST00000487010 ENST00000317840(uc010frw.1)
    miRNA
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    Block miRNA regulation of human, mouse, rat COL3A1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate COL3A1 (see all 21):
    hsa-miR-520d-5p hsa-let-7d hsa-miR-202 hsa-miR-29a hsa-miR-29c hsa-miR-767-5p hsa-let-7c hsa-miR-380*
    SwitchGear 3'UTR luciferase reporter plasmidCOL3A1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for COL3A1
    Predesigned siRNA for gene silencing in human, mouse, rat COL3A1
    Clone
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    OriGene ORF clones in mouse, rat for COL3A1
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: COL3A1 (NM_000090)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for COL3A1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL3A1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for COL3A1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat COL3A1
      QuantiTect SYBR Green Assays in human, mouse, rat COL3A1
      QuantiFast Probe-based Assays in human, mouse, rat COL3A1

    Additional mRNA sequence: 

    AK021531.1 AK091853.1 AK308010.1 BC028178.1 BX649097.1 M13146.1 M59227.1 S79877.1 
    X01655.1 X06700.1 X07240.1 X14420.1 

    Selected DOTS entries (see all 53):

    DT.100893398  DT.87024767  DT.95126490  DT.100893393  DT.99969260  DT.100046024  DT.95126542  DT.97761863 
    DT.100893402  DT.99975383  DT.100893410  DT.95196532  DT.92471487  DT.100893395  DT.40239493  DT.101974976 
    DT.40124083  DT.97814164  DT.95126654  DT.120985447  DT.100741033  DT.100762161  DT.100893411  DT.120985475 

    Selected AceView cDNA sequences (see all 1770):

    NM_000090 BU628046 CA413816 AU119414 BM702152 BQ181913 AA347957 H89012 
    AI754852 H89890 CB215260 AI827248 BM667293 CA422262 CA412948 AW002774 
    AA319923 CF995759 BQ573699 AA338118 BQ024609 CA415296 AI571615 CA415007 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for COL3A1 (see all 8)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                            -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -   
    SP4:                                                                                                                                                            
    SP5:                                -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -   

    ExUns: 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31a · 31b ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37a · 37b ^ 38a · 38b ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^
    SP1:                                                                                                                    -                                       
    SP2:                    -     -     -     -     -     -     -                                                           -                                       
    SP3:  -     -     -     -     -     -     -     -     -     -                                                                                                   
    SP4:                                                                                                                                                            
    SP5:  -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -   

    ExUns: 45 ^ 46 ^ 47 ^ 48a · 48b · 48c ^ 49 ^ 50a · 50b ^ 51a · 51b ^ 52a · 52b · 52c · 52d
    SP1:                    -                                                                     
    SP2:                    -                                                                     
    SP3:                                                                                          
    SP4:                                                                                          
    SP5:  -     -     -     -     -                                                               


    ECgene alternative splicing isoforms for COL3A1

    (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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    COL3A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GATCAGGCCA
    COL3A1 Expression
    About this image


    COL3A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 33) fully expand
     
     Cartilage (Muscoskeletal System)    fully expand to see all 6 entries
             Central Intermediate Lamina Cells Zeugopod Synovial Joint
     
     Limb (Muscoskeletal System)    fully expand to see all 6 entries
             Central Intermediate Lamina Cells Zeugopod Synovial Joint
     
     Bone (Muscoskeletal System)    fully expand to see all 4 entries
             Presumptive Suture Cells Rostral Sutures
     
     Fibroblasts
             Dermal Fibroblasts Dorsal Dermis
             Detroit 551
     
     Dermis (Integumentary System)    fully expand to see all 5 entries
             Dermal Fibroblasts Dorsal Dermis
    COL3A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COL3A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.443625
        Pathway & Disease-focused RT2 Profiler PCR Arrays including COL3A1 (see all 8): 
              Osteogenesis in human mouse rat
              Fibrosis in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Atherosclerosis in human mouse rat
              Wound Healing in human mouse rat

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL3A1

    (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 COL3A1 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Col3a11 , 5 collagen, type III, alpha 11, 5 87.63(n)1
    90.64(a)1
      1 (23.67 cM)5
    128251  NM_009930.21  NP_034060.21 
     453115385 
    chicken
    (Gallus gallus)
    Aves COL3A11 collagen, type III, alpha 1 71.24(n)
    72.68(a)
      396340  NM_205380.2  NP_990711.2 
    lizard
    (Anolis carolinensis)
    Reptilia COL3A16
    collagen, type III, alpha 1
    73(a)
    1 ↔ 1
    GL343290.1(1466689-1531165)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC060753.12   -- 77.76(n)    BC060753.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Cg25C6
    Collagen type IV
    27(a)
    1 → many
    2L(5029609-5037279)


    ENSEMBL Gene Tree for COL3A1 (if available)
    TreeFam Gene Tree for COL3A1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COL3A1 gene
    COL4A62  COL11A22  COL4A52  COL24A12  COL4A42  COL5A32  COL1A12  COL4A22  
    COL5A22  COL5A12  COL4A32  COL1A22  COL7A12  COL2A12  COL27A12  COL4A12  
    COL11A12  
    17 SIMAP similar genes for COL3A1 using alignment to 10 protein entries:     CO3A1_HUMAN (see all proteins):
    COL2A1    COL1A1    COL5A2    ECM2    COL1A2    MARCO
    SFTPD    C1QTNF9    COL7A1    C1QTNF9B    COL6A6    MSR1
    COL24A1    COL5A1    COL11A1    COL28A1    GLDN

    Find genes that share paralogs with COL3A1           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 COL3A1 (see all 1138)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0111554
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0111552 G E mis40--------
    VAR_0111154
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0111152 G R mis40--------
    VAR_0018064
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0018062 G E mis40--------
    VAR_0111034
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0111032 G R mis40--------
    VAR_0017904
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0017902 G V mis40--------
    VAR_0018054
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0018052 G V mis40--------
    VAR_0111044
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0111042 G V mis40--------
    VAR_0111074
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0111072 G D mis40--------
    VAR_0110954
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0110952 G D mis40--------
    VAR_0111134
    Ehlers-Danlos syndrome 4 (EDS4)4--see VAR_0111132 G V mis40--------

    HapMap Linkage Disequilibrium report for COL3A1 (189839046 - 189877472 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for COL3A1 (see all 14):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1030122CNV Deletion17803354
    esv2721257CNV Deletion23290073
    esv993048CNV Deletion20482838
    esv2721255CNV Deletion23290073
    esv990670CNV Deletion20482838
    esv2721256CNV Deletion23290073
    esv2203663CNV Deletion18987734
    esv268920CNV Insertion20981092
    esv272418CNV Insertion20981092
    nsv459992CNV Loss19166990

    Human Gene Mutation Database (HGMD): COL3A1
    Locus Specific Mutation Databases (LSDB): COL3A1

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COL3A1
    DNA2.0 Custom Variant and Variant Library Synthesis for COL3A1

    (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

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    OMIM gene information: 120180   
    OMIM disorders: 130050  130020  
    UniProtKB/Swiss-Prot: CO3A1_HUMAN, P02461
  • Ehlers-Danlos syndrome 3 (EDS3) [MIM:130020]: A connective tissue disorder characterized by
    hyperextensible skin, atrophic cutaneous scars due to tissue fragility and joint hyperlaxity. It is a form of
    Ehlers-Danlos syndrome characterized by marked joint hyperextensibility without skeletal deformity. Note=The
    disease is caused by mutations affecting the gene represented in this entry
  • Ehlers-Danlos syndrome 4 (EDS4) [MIM:130050]: The most severe form of Ehlers-Danlos syndrome, a
    connective tissue disorder characterized by hyperextensible skin, atrophic cutaneous scars due to tissue
    fragility and joint hyperlaxity. Characterized by the joint and dermal manifestations as in other forms of the
    syndrome, characteristic facial features (acrogeria) in most patients, and by proneness to spontaneous rupture of
    bowel and large arteries. The vascular complications may affect all anatomical areas. Note=The disease is caused
    by mutations affecting the gene represented in this entry
  • Aortic aneurysm, familial abdominal (AAA) [MIM:100070]: A common multifactorial disorder characterized by
    permanent dilation of the abdominal aorta, usually due to degenerative changes in the aortic wall.
    Histologically, AAA is characterized by signs of chronic inflammation, destructive remodeling of the
    extracellular matrix, and depletion of vascular smooth muscle cells. Note=Disease susceptibility is associated
    with variations affecting the gene represented in this entry

  • 16 diseases for COL3A1:    
    About MalaCards
    ehlers-danlos syndrome type iv    familial cervical artery dissections    acrogeria, gottron type    hiatus hernia
    ehlers-danlos syndrome, hypermobility type    ehlers-danlos syndrome    thoracic aortic aneurysm    hypermobility syndrome
    familial cerebral saccular aneurysm    larsen-like syndrome    ehlers-danlos syndrome, autosomal dominant, hypermobility type    cornelia de lange syndrome 4
    abdominal aortic aneurysm    intracranial aneurysm    usual interstitial pneumonia    aortic aneurysm

    3 diseases from the University of Copenhagen DISEASES database for COL3A1:
    Ehlers-Danlos syndrome     Loeys-Dietz syndrome     Pneumothorax

    Find genes that share disorders with COL3A1           About GenesLikeMe

    Selected Novoseek inferred disease relationships for COL3A1 gene (see all 19)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    eds iv 96.8 10 1757960 (1), 7833919 (1), 9036918 (1), 8411057 (1) (see all 10)
    ehlers-danlos syndrome 95.9 54 1757960 (2), 8317500 (2), 7487954 (2), 11577371 (2) (see all 46)
    ehlers-danlos syndrome, type ii 78.5 1 2049575 (1)
    ehlers-danlos syndrome, type i 78.5 1 1684560 (1)
    vascular rupture 76.6 1 8881656 (1)
    connective tissue diseases 69.4 3 9546243 (1), 17053184 (1), 19751346 (1)
    marfan syndrome 56.6 1 19639654 (1)
    osteogenesis imperfecta 53.8 3 8950675 (1), 18272325 (1), 1905723 (1)
    intracranial aneurysm 53.3 12 18642782 (3), 10436112 (2), 8255472 (1)
    collagen fibril 52.6 1 9036918 (1)

    GeneTests: COL3A1
    GeneReviews: COL3A1
    Genetic Association Database (GAD): COL3A1
    Human Genome Epidemiology (HuGE) Navigator: COL3A1 (25 documents)

    Export disorders for COL3A1 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)
    About This Section

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    PubMed articles for COL3A1 gene, integrated from 10 sources (see all 269):
    (articles sorted by number of sources associating them with COL3A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A base substitution at a splice site in the COL3A1 gene causes exon skipping and generates abnormal type III procollagen in a patient with Ehlers-Danlos syndrome type IV. (PubMed id 2145268)1, 2, 7, 9 Cole W.G.... Bateman J.F. (J. Biol. Chem. 1990)
    2. Nucleotide and amino acid sequences of the entire human alpha 1 (III) collagen. (PubMed id 2780304)1, 2, 3 Janeczko R.A. and Ramirez F. (Nucleic Acids Res. 1989)
    3. Analysis of the COL3A1 gene in patients with spontaneous cervical artery dissections. (PubMed id 12140670)1, 4, 9 von Pein F....Grond-Ginsbach C. (J. Neurol. 2002)
    4. Genetic association between functional haplotype of collagen type III alpha 1 and chronic hepatitis B and cirrhosis in Koreans. (PubMed id 19000145)1, 4, 9 Lee S.K....Kwack K. (Tissue Antigens 2008)
    5. Association between COL3A1 collagen gene exon 31 polymorphism and risk of floppy mitral valve/mitral valve prolapse. (PubMed id 15193836)1, 4, 9 Chou H.T....Tsai F.J. (Int. J. Cardiol. 2004)
    6. Parental somatic and germ-line mosaicism for a multiexon deletion with unusual endpoints in a type III collagen (COL3A1) allele produces Ehlers-Danlos syndrome type IV in the heterozygous offspring. (PubMed id 8317500)1, 2, 9 Milewicz D.M....Byers P.H. (Am. J. Hum. Genet. 1993)
    7. The relationship between COL3A1 exon 31 polymorphism and pelvic organ prolapse. (PubMed id 19152942)1, 4, 9 Jeon M.J....Bai S.W. (J. Urol. 2009)
    8. Collagen type III alpha I is a gastro-oesophageal reflux disease susceptibility gene and a male risk factor for hiatus hernia. (PubMed id 19398442)1, 4, 9 Asling B....LagerstrAPm-Fermer M. (Gut 2009)
    9. [Correlation of COL3A1 gene with type III collagen stability in intracranial aneurysm]. (PubMed id 18642782)1, 4, 9 Hua T....Zhao J.Z. (Zhonghua Yi Xue Za Zhi 2008)
    10. Genomic organization of the human COL3A1 and COL5A2 genes: COL5A2 has evolved differently than the other minor fibrillar collagen genes. (PubMed id 11566270)1, 2, 9 Valkkila M....Ala-Kokko L. (Matrix Biol. 2001)

    (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: 1281 HGNC: 2201 AceView: COL3A1 Ensembl:ENSG00000168542 euGenes: HUgn1281
    ECgene: COL3A1 Kegg: 1281 H-InvDB: COL3A1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for COL3A1 Pharmacogenomics, SNPs, Pathways
    COL3A1http://www.le.ac.uk/genetics/collagen/col3a1.html
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=COL3A1[genesymbol]
    Wikipedia http://en.wikipedia.org/wiki/Type-III_collagen

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for COL3A1 gene:
    Search GeneIP for patents involving COL3A1

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



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