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

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 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)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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, and ehlers-danlos syndrome type iv, and among its related super-pathways are Collagen biosynthesis and modifying enzymes and ECM-receptor interaction. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.2  NT_005403.17  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for COL3A1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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
Subcellular location: Secreted, extracellular space, extracellular matrix (By similarity)
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:

  • UniProtKB: Proline residues at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of
    the chains
  • UniProtKB: O-linked glycan consists of a Glc-Gal disaccharide bound to the oxygen atom of a post-translationally added
    hydroxyl group
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P02461

  • COL3A1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    COL3A1 Protein Expression
    REFSEQ proteins: NP_000081.1  
    ENSEMBL proteins: 
     ENSP00000304408   ENSP00000415346   ENSP00000315243  
    Reactome Protein details: P02461
    Human Recombinant Protein Products for COL3A1: 
    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. 

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (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--

    COL3A1 for ontologies           About GeneDecksing



    COL3A1 Antibody Products: 
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    Abcam antibodies for COL3A1
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    LSBio Antibodies in human, mouse, rat for COL3A1 

    Assay Products for COL3A1: 
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    Browse ELISAs at Cloud-Clone Corp. 
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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


    COL3A1 for domains           About GeneDecksing


    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, 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, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    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): 5/6 molecular function terms (GO ID links to tree view) (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--
         
    COL3A1 for ontologies           About GeneDecksing


    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  homeostasis/metabolism  integument 
     liver/biliary system  mortality/aging  muscle  respiratory system 

    COL3A1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Col3a1tm1Jae for COL3A1

       inGenious Targeting Laboratory - Custom generated mouse model solutions for COL3A1 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions 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
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    miRTarBase miRNAs that target COL3A1:
    hsa-mir-29b (MIRT005567), hsa-mir-29c (MIRT000927)

    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat COL3A1
    8/21 QIAGEN miScript miRNA 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:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for COL3A1
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    Gene Editing
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    Sirion Biotech Customized adenovirus for overexpression of COL3A1

    Clone
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    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
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    GenScript: all cDNA clones in your preferred vector: COL3A1 (NM_000090)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat COL3A1
    Sirion Biotech Customized lentivirus for stable overexpression of COL3A1 
                         Customized lentivirus expression plasmids for stable overexpression of COL3A1 

    Cell Line
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    Search LifeMap BioReagents cell lines for COL3A1
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for COL3A1


    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for COL3A1 About   (see all 21)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.74
    Intrinsic Prothrombin Activation Pathway0.40
    Collagen formation0.74
    Extracellular matrix organization0.39
    Assembly of collagen fibrils and other multimeric structures0.65
    Blood Coagulation Cascade0.39
    2Non-integrin membrane-ECM interactions
    Non-integrin membrane-ECM interactions0.44
    ECM-receptor interaction0.42
    Syndecan interactions0.44
    ECM proteoglycans0.38
    3Focal Adhesion
    Focal Adhesion0.64
    Focal adhesion0.64
    4Cell adhesion ECM remodeling
    Cell adhesion ECM remodeling0.31
    Metalloproteases in connective tissue degradation0.31
    5Integrin Pathway
    Integrin Pathway0.67
    UPA-UPAR Pathway0.56
    FAK1 Signaling0.67
    Inhibition of Angiogenesis by TSP10.50
    GnRH Signaling0.56
    Transendothelial Migration of Leukocytes0.38

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 EMD Millipore Pathways for COL3A1
        Cell adhesion ECM remodeling
    Metalloproteases in connective tissue degradation

    5/15 Downloadable PowerPoint Slides of QIAGEN 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

    5/17        Reactome Pathways for COL3A1 (see all 17)
        Developmental Biology
    Assembly of collagen fibrils and other multimeric structures
    ECM proteoglycans
    Extracellular matrix organization
    Collagen biosynthesis and modifying enzymes

    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


    COL3A1 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for COL3A1

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

    5/96 Interacting proteins for COL3A1 (P024612, 3 ENSP000003044084) via UniProtKB, MINT, STRING, and/or I2D (see all 96)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000204490P013753I2D: score=1 
    ENSG00000206439P013753I2D: score=1 
    ENSG00000223952P013753I2D: score=1 
    ENSG00000228321P013753I2D: score=1 
    ENSG00000228849P013753I2D: score=1 
    About this table

    Gene Ontology (GO): 5/25 biological process terms (GO ID links to tree view) (see all 25):    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

    COL3A1 for ontologies           About GeneDecksing



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

    COL3A1 for compounds           About GeneDecksing

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

    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)

    Search CenterWatch for drugs/clinical trials and news about COL3A1 / CO3A1

    (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,
    Conferences by KenesGroup, 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, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat COL3A1
      QIAGEN 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 

    24/53 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 

    24/1770 AceView cDNA sequences (see all 1770):

    CN481352 AI658625 BM971545 BQ268873 BQ575166 AU154270 CN481866 H88499 
    CN483531 AW471381 AU116959 BQ015115 AL046064 AI919076 CA415296 H89155 
    W21531 BG434336 AA314204 CA412917 BM675688 AI827248 BP374465 CA419295 

    GeneLoc Exon Structure

    5/8 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™, 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

    COL3A1 expression in normal human tissues (normalized intensities)      COL3A1 embryonic expression: see
    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 
     5/29 selected tissues (see all 29) 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
     
     Kidney (Urinary System)    fully expand to see all 5 entries
             Metanephric Mesenchyme Cells Metanephric Mesenchyme
             Metanephros
             visceral organ/metanephros/pelvis   
     
     Heart (Cardiovascular System)    fully expand to see all 5 entries
             Cardiac Fibroblasts Myocardium
             Coronary Artery Smooth Muscle Cells (CASMC)   
             Cardiac Myocytes   
     
     Lower Urinary Tract (Urinary System)    fully expand to see all 5 entries
             Ureter
             visceral organ   

    See COL3A1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for COL3A1

    SOURCE GeneReport for Unigene cluster: Hs.443625
        SABiosciences Expression via Pathway-Focused 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

    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat COL3A1
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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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for COL3A1 gene from 5/11 species (see all 11)    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 87.81(n)1
    90.98(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 72.82(n)
    74.71(a)
      396340  NM_205380.2  NP_990711.2 
    lizard
    (Anolis carolinensis)
    Reptilia COL3A16
    Uncharacterized protein
    72(a)
    1 ↔ 1
    GL343290.1(1466689-1531165)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC060753.12   -- 77.76(n)    BC060753.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G158301 hypothetical protein 45.83(n)
    37.75(a)
      838153  NM_101451.1  NP_173035.1 


    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)
    About This Section
    Paralogs for COL3A1 gene
    COL4A62  COL11A22  COL4A52  COL24A12  COL4A42  COL5A32  COL1A12  COL4A22  
    COL5A22  COL5A12  COL4A32  COL1A22  COL7A12  COL2A12  COL27A12  COL4A12  
    COL11A12  
    10 SIMAP similar genes for COL3A1 using alignment to 5 protein entries:     CO3A1_HUMAN (see all proteins):
    COL2A1    COL1A1    ECM2    COL5A2    COL1A2    COL7A1
    SFTPD    C1QTNF9    C1QTNF9B    COL28A1

    COL3A1 for paralogs           About GeneDecksing



    (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) 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

    10/1138 SNPs in COL3A1 are shown (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) 10/14 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
    SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    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 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

  • 20/50 diseases for COL3A1 (see all 50):    About MalaCards
    ehlers-danlos syndrome    ehlers-danlos syndrome type iv    abdominal aortic aneurysm    larsen-like syndrome
    acrogeria, gottron type    hypermobility syndrome    hiatus hernia    familial thoracic aortic aneurysm and dissection
    intracranial aneurysm    usual interstitial pneumonia    thoracic aortic aneurysm    pfeiffer syndrome
    mitral valve prolapse    aortic aneurysm    marfan syndrome    coronary stenosis
    varicose veins    osteogenesis imperfecta    loeys-dietz syndrome    pneumothorax

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

    COL3A1 for disorders           About GeneDecksing

    10/19 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

    PubMed articles for COL3A1 gene, integrated from 9 sources (see all 267):
    (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. (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. (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. (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. (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. (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. (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. (2009)
    8. Collagen type III alpha I (COL3A1) is a Gastro-oesophageal reflux disease (GORD) susceptibility gene and a male risk factor for hiatus hernia (HH). (PubMed id 19398442)1, 4, 9 Asling B....LagerstrAPm-Fermer M. (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. (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. (2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 1281 HGNC: 2201 AceView: COL3A1 Ensembl:ENSG00000168542 euGenes: HUgn1281
    ECgene: COL3A1 Kegg: 1281 H-InvDB: COL3A1

    (According to HUGE)
    About This Section
      --

    (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 COL3A1 Pharmacogenomics, SNPs, Pathways
    COL3A1http://www.le.ac.uk/genetics/collagen/col3a1.html
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL3A1
    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.)
    About This Section
    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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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