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MMP13 Gene

protein-coding   GIFtS: 74
GCID: GC11M102847

Matrix Metallopeptidase 13 (Collagenase 3)

(Previous name: matrix metalloproteinase 13 (collagenase 3))
  See MMP13-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
Matrix Metallopeptidase 13 (Collagenase 3)1 2     Matrix Metalloproteinase-133
Matrix Metalloproteinase 13 (Collagenase 3)1 2     EC 3.4.248
Collagenase 31 2     EC 3.4.24.228
MMP-132 3     EC 3.4.24.248
CLG32 5     EC 3.4.24.358
MANDP12 5     EC 3.4.24.658
EC 3.4.24.-3     EC 3.4.24.78

External Ids:    HGNC: 71591   Entrez Gene: 43222   Ensembl: ENSG000001377457   OMIM: 6001085   UniProtKB: P454523   

Export aliases for MMP13 gene to outside databases

Previous GC identifers: GC11M105007 GC11M104170 GC11M102351 GC11M102318 GC11M098741


(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 MMP13 Gene:
Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in
normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in
disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are
activated when cleaved by extracellular proteinases. The protein encoded by this gene cleaves type II collagen
more efficiently than types I and III. It may be involved in articular cartilage turnover and cartilage
pathophysiology associated with osteoarthritis. The gene is part of a cluster of MMP genes which localize to
chromosome 11q22.3. (provided by RefSeq, Jul 2008)

GeneCards Summary for MMP13 Gene:
MMP13 (matrix metallopeptidase 13 (collagenase 3)) is a protein-coding gene. Diseases associated with MMP13 include spondyloepimetaphyseal dysplasia, missouri type, and diverticulitis. GO annotations related to this gene include metalloendopeptidase activity and calcium ion binding. An important paralog of this gene is MMP20.

UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452
Function: Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process

summary for MMP13 Gene:
Matrix metalloproteases (matrix metalloproteinase, MMPs), also called matrixins, are zinc-dependent
endopeptidases that are the major proteases involved in ECM degradation. MMPs are capable of degrading a
wide range of extracellular molecules and a number of bioactive molecules. 24 matrixin genes have been
identified in humans, which can be organized into six groups based on domain organization and substrate
preference: Collagenases (MMP-1, -8 and -13), Gelatinases (MMP-2 and MMP-9), Stromelysins (MMP-3, -10 and
-11), Matrilysin (MMP-7 and MMP-26), Membrane-type (MT)-MMPs (MMP-14, -15, -16, -17, -24 and -25) and others
(MMP-12, -19, -20, -21, -23, -27 and -28). MMP activity is regulated by two major endogenous inhibitors:
alpha2-macroglobulin and tissue inhibitors of metalloproteases (TIMPs). MMPs play a central role in cell
proliferation, migration, differentiation, angiogenesis, apoptosis and host defences. Dysregulatoin of MMPs
has been implicated in many diseases including arthritis, chronic ulcers, encephalomyelitis and cancer.
Tumour metastasis is a multistep process involving the dessemination of tumor cells from the primary tumor
to secondarys at a distant organ or tissue. One of the first steps in metastasis is the degradation of the
basement membrane, a process in which MMPs have been implicated. MMPs are secreted by tumor cells themselves
or by surrounding stromal cells stimulated by the nearby tumor. Numerous studies have linked altered MMP
expression in different human cancers with poor disease prognosis. MMP-1, -2, -3, -7, -9, -13 and -14 all
have elevated expression in primary tumors and/or metastases. Synthetic or natural inhibitors of MMPs result
in inhibition of metastasis, while up-regulation of MMPs led to enhanced cancer cell invasion.

Gene Wiki entry for MMP13 (Matrix metallopeptidase 13) 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:
NC_000011.10  NC_018922.2  NT_033899.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the MMP13 gene promoter:
         CREB   STAT1   deltaCREB   FOXO3a   FOXO3   FOXO3b   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidMMP13 promoter sequence
   Search Chromatin IP Primers for MMP13

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat MMP13


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

Entrez Gene cytogenetic band: 11q22.3   Ensembl cytogenetic band:  11q22.2   HGNC cytogenetic band: 11q22.3

MMP13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MMP13 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M102847:  view genomic region     (about GC identifiers)

Start:
102,813,721 bp from pter      End:
102,826,463 bp from pter
Size:
12,743 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452 (See protein sequence)
Recommended Name: Collagenase 3 precursor  
Size: 471 amino acids; 53820 Da
Cofactor: Binds 4 calcium ions per subunit
Cofactor: Binds 2 zinc ions per subunit
Selected PDB 3D structures from and Proteopedia for MMP13 (see all 33):
1EUB (3D)        1FLS (3D)        1FM1 (3D)        1PEX (3D)        1UC1 (3D)        1XUC (3D)    
Secondary accessions: A8K846 B2RCZ3 Q6NWN6

Explore the universe of human proteins at neXtProt for MMP13: NX_P45452

Explore proteomics data for MMP13 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn117, Asn152
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for MMP13 (P45452) (see all 22)
     GIQSLYG  PRCGVPD  GLLAHAF  NGYIYFF 


    See MMP13 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_002418.1  
    ENSEMBL proteins: 
     ENSP00000260302   ENSP00000339672  
    Reactome Protein details: P45452

    MMP13 Human Recombinant Protein Products:

    EMD Millipore Purified and/or Recombinant MMP13 Protein
    R&D Systems Recombinant & Natural Proteins for MMP13 (MMP-13)
    Enzo Life Sciences proteins for MMP13
    Browse OriGene full length recombinant human proteins expressed in human HEK293 cells
    OriGene Protein Over-expression Lysate for MMP13
    OriGene Custom MassSpec
    OriGene Custom Protein Services for MMP13
    GenScript Custom Purified and Recombinant Proteins Services for MMP13
    Novus Biologicals MMP13 Proteins
    Novus Biologicals MMP13 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    ProSpec Recombinant Protein for MMP13
    Cloud-Clone Corp. Proteins for MMP13

     
    Search eBioscience for Proteins for MMP13 

    MMP13 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of MMP13
    R&D Systems Antibodies for MMP13 (MMP-13)
    OriGene Antibodies for MMP13
    OriGene Custom Antibody Services for MMP13
    Novus Biologicals MMP13 Antibodies
    Abcam antibodies for MMP13
    Cloud-Clone Corp. Antibodies for MMP13
    ThermoFisher Antibody for MMP13
    LSBio Antibodies in human, mouse, rat for MMP13

    MMP13 Assay Products:

    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for MMP13
    R&D Systems ELISAs for MMP13 (MMP-13)         (see all)
    GenScript MMP13-Activity-based Protease?src=genec Assay for Compound Screening
    Enzo Life Sciences assays for MMP13
    Cloud-Clone Corp. ELISAs for MMP13
    Cloud-Clone Corp. CLIAs for MMP13
    eBioscience ELISAs for MMP13:  
                        Human MMP-13 Platinum ELISA 96 tests


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ENDOLIG: Endogenous ligands

    IUPHAR Guide to PHARMACOLOGY protein family classification: MMP13
    Cell-surface protein and extracellular matrix metalloproteinases

    Selected InterPro protein domains (see all 11):
     IPR024079 MetalloPept_cat_dom
     IPR021158 Pept_M10A_Zn_BS
     IPR021190 Pept_M10A
     IPR000585 Hemopexin-like_dom
     IPR018486 Hemopexin_CS

    Graphical View of Domain Structure for InterPro Entry P45452

    ProtoNet protein and cluster: P45452

    3 Blocks protein domains:
    IPB000585 Hemopexin repeat
    IPB001818 Matrixin
    IPB002477 Putative peptidoglycan binding domain 1


    UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452
    Domain: The conserved cysteine present in the cysteine-switch motif binds the catalytic zinc ion, thus inhibiting
    the enzyme. The dissociation of the cysteine from the zinc ion upon the activation-peptide release activates the
    enzyme
    Similarity: Belongs to the peptidase M10A family
    Similarity: Contains 4 hemopexin repeats


    Find genes that share domains with MMP13           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: MMP13_HUMAN, P45452
    Function: Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process

         Genatlas biochemistry entry for MMP13:
    matrix metalloproteinase 13,regulator of matrix remodeling component of the MMP cluster,expressed in the synovial
    membrane and synovial fibroblasts of patients with rheumatoid arthritis,overexpressed by smooth muscle cells in
    abdominal aortic aneurysm

         Enzyme Numbers (IUBMB): EC 3.4.24.242 EC 3.4.24.-1 EC 3.4.24.72 EC 3.4.24.352 EC 3.4.24.652 EC 3.4.242 EC 3.4.24.222

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004222metalloendopeptidase activity IEA--
    GO:0005509calcium ion binding IEA--
    GO:0008233peptidase activity ----
    GO:0008237metallopeptidase activity ----
    GO:0008270zinc ion binding IEA--
         
    Find genes that share ontologies with MMP13           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for MMP13:
     Increased gamma-H2AX phosphory 

         7 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Mmp13):
     cardiovascular system  cellular  growth/size/body  homeostasis/metabolism  integument 
     limbs/digits/tail  skeleton 

    Find genes that share phenotypes with MMP13           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for MMP13: Mmp13tm1.1Werb Mmp13tm1Smk

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for MMP13
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for MMP13

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for MMP13
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for MMP13

    miRNA
    Products:
        
    miRTarBase miRNAs that target MMP13:
    hsa-mir-9-5p (MIRT000025), hsa-mir-100-5p (MIRT003420), hsa-mir-132-3p (MIRT021796), hsa-mir-143-3p (MIRT021540), hsa-mir-140-5p (MIRT003961), hsa-mir-125b-5p (MIRT006990), hsa-mir-27a-3p (MIRT006557), hsa-mir-27b-3p (MIRT003427)

    Block miRNA regulation of human, mouse, rat MMP13 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate MMP13 (see all 11):
    hsa-miR-100* hsa-miR-148b hsa-miR-513a-5p hsa-miR-27a hsa-miR-218-1* hsa-miR-1267 hsa-miR-3647-3p hsa-miR-152
    SwitchGear 3'UTR luciferase reporter plasmidMMP13 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for MMP13
    Predesigned siRNA for gene silencing in human, mouse, rat MMP13

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for MMP13

    Clone
    Products:
         
    OriGene clones in human, mouse for MMP13 (see all 6)
    OriGene ORF clones in mouse, rat for MMP13
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: MMP13 (NM_002427)
    Sino Biological Human cDNA Clone for MMP13
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for MMP13
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat MMP13

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for MMP13
    Browse ESI BIO Cell Lines and PureStem Progenitors for MMP13 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MMP13


    (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
    MMP13_HUMAN, P45452: Secreted, extracellular space, extracellular matrix (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular4
    nucleus2
    cytoskeleton1
    cytosol1
    endoplasmic reticulum1
    lysosome1
    mitochondrion1
    peroxisome1
    plasma membrane1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005578proteinaceous extracellular matrix IEA--
    GO:0005615extracellular space TAS8207000
    GO:0031012extracellular matrix ----

    Find genes that share ontologies with MMP13           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 MMP13 About   (see all 12)  
    See pathways by source

    SuperPathContained pathways About
    1Matrix Metalloproteinases
    Matrix Metalloproteinases0.68
    Activation of Matrix Metalloproteinases0.37
    Inhibition of Matrix Metalloproteinases0.68
    2G protein signaling Ras family GTPases in kinase cascades scheme
    Immune response Oncostatin M signaling via MAPK in human cells0.39
    Oncostatin M Signaling Pathway0.37
    3Cell adhesion ECM remodeling
    Metalloproteases in connective tissue degradation0.31
    Cell adhesion ECM remodeling0.31
    4Degradation of the extracellular matrix
    Degradation of the extracellular matrix0.43
    Extracellular matrix organization0.34
    Collagen degradation0.43
    5Collagen biosynthesis and modifying enzymes
    Collagen formation0.75
    Assembly of collagen fibrils and other multimeric structures0.62


    Find genes that share SuperPaths with MMP13           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    4 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for MMP13
        Inhibition of Matrix Metalloproteinases
    Transendothelial Migration of Leukocytes
    UPA-UPAR Pathway
    Pancreatic Adenocarcinoma

    5 GeneGo (Thomson Reuters) Pathways for MMP13
        Development Hedgehog and PTH signaling pathways in bone and cartilage development
    Cell adhesion ECM remodeling
    Cell adhesion Plasmin signaling
    Development Glucocorticoid receptor signaling
    Immune response Oncostatin M signaling via MAPK in human cells

    4 BioSystems Pathways for MMP13
        Matrix Metalloproteinases
    AGE/RAGE pathway
    Oncostatin M Signaling Pathway
    Endochondral Ossification


    4 Reactome Pathways for MMP13
        Assembly of collagen fibrils and other multimeric structures
    Degradation of the extracellular matrix
    Collagen degradation
    Activation of Matrix Metalloproteinases


        Pathway & Disease-focused RT2 Profiler PCR Arrays including MMP13: 
              Fibrosis in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Tumor Metastasis in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for MMP13

    STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

    Selected Interacting proteins for MMP13 (P454523 ENSP000002603024) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCL7P800983, ENSP000002003074I2D: score=1 STRING: ENSP00000200307
    LRP1Q079543, ENSP000002430774I2D: score=1 STRING: ENSP00000243077
    MMP14P502813, ENSP000003082084I2D: score=1 STRING: ENSP00000308208
    ADAMTS5Q9UNA03, ENSP000002849874I2D: score=1 STRING: ENSP00000284987
    COL2A1P024583, ENSP000003698894I2D: score=1 STRING: ENSP00000369889
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006508proteolysis TAS8207000
    GO:0022617extracellular matrix disassembly TAS--
    GO:0030198extracellular matrix organization TAS--
    GO:0030282bone mineralization IEA--
    GO:0030574collagen catabolic process TAS--

    Find genes that share ontologies with MMP13           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
       Enzo Life Sciences drugs & compounds for MMP13
    Selected ApexBio Compounds for MMP13 (see all 15)     About this table
    CompoundAction CAS #
    ARP 100Selective inhibitor of MMP-2[704888-90-4]
    ARP 101Selective inhibitor of MMP-2[849773-63-3]
    Batimastat (BB-94)potent and synthetic inhibitor of a broad spectrum of MMPs[130370-60-4]
    CL 82198 hydrochlorideSelective inhibitor of MMP-13[307002-71-7]
    CP 471474Broad spectrum MMP inhibitor[210755-45-6]
    CTS-1027potent small molecule inhibitor of MMPs[193022-04-7]
    GM 6001Broad-spectrum MMP inhibitor[142880-36-2]
    MarimastatBroad spectrum inhibitor of MMPs[154039-60-8]
    NSC 405020novel small molecule inhibitor of MT1-MMP[7497-7-6]
    ONO 4817Broad spectrum MMP inhibitor[223472-31-9]

    Compounds for MMP13 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    GI 254023XSelective ADAM10 metalloprotease inhibitor[260264-93-5]
    MarimastatBroad spectrum MMP inhibitor[154039-60-8]
    GM 6001Broad-spectrum MMP inhibitor[142880-36-2]
    UK 383367Potent and selective BMP-1 (PCP) inhibitor[348622-88-8]
    Batimastat Potent, broad spectrum MMP inhibitor [130370-60-4]

    1 HMDB Compound for MMP13    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Selected DrugBank Compounds for MMP13 (see all 14)    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    WAY-151693n-hydroxy-2-[(4-methoxy-benzenesulfonyl)-pyridin-3-ylmethyl-amino]-3-methyl-benzamide (see all 2)--target--17139284 17016423 10592235
    1-Methyloxy-4-Sulfone-Benzene-- --target--17139284 17016423
    3-Methylpyridine-- 108-99-6target--17139284 17016423
    Hydroxyaminovaline-- --target--17139284 17016423
    Marimastat-- 154039-60-8targetinhibitor10852638 10669951
    2-{4-[4-(4-Chloro-Phenoxy)-Benzenesulfonyl]-Tetrahydro-Pyran-4-Yl}-N-Hydroxy-Acetamide-- --target--10592235
    4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYLMETHYL]-TETRAHYDRO-PYRAN-4-CARBOXYLIC ACID HYDROXYAMIDE-- --target--10592235
    4-{[1-METHYL-2,4-DIOXO-6-(3-PHENYLPROP-1-YN-1-YL)-1,4-DIHYDROQUINAZOLIN-3(2H)-YL]METHYL}BENZOIC ACID-- --target--10592235
    5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE-- --target--10592235
    BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE-- --target--10592235

    2 IUPHAR Ligands for MMP13 (MMP13)    About this table
    LigandTypeActionAffinityPubmed IDs
    CL82198
    InhibitorInhibition--
    WAY170523
    InhibitorInhibition--

    Selected Novoseek inferred chemical compound relationships for MMP13 gene (see all 76)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hydroxamate 66.3 15 10986126 (2), 16603129 (2), 16612565 (1), 19239231 (1) (see all 7)
    2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid 66.1 2 11352241 (1), 12932292 (1)
    (4-aminophenyl)mercuric acetate 59.5 9 7608162 (2), 17076612 (1)
    thps 58.4 1 12437092 (1)
    batimastat 55.5 4 10415727 (1), 11774278 (1), 15268899 (1)
    sb 203580 51.1 16 19100962 (1), 12009331 (1), 14631115 (1), 19656660 (1) (see all 11)
    matrigel 50 6 11774278 (1), 16407850 (1), 20463600 (1), 17322299 (1)
    pge2 49 45 15612948 (5), 19998410 (4), 19447216 (3), 18562219 (2) (see all 16)
    glycosaminoglycan 47.9 8 9437511 (1), 11817583 (1), 17208315 (1), 17397292 (1) (see all 7)
    vegf 45.3 29 19883500 (2), 12810425 (2), 14555274 (2), 18839188 (2) (see all 23)



    Find genes that share compounds with MMP13           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 MMP13 gene: 
    NM_002427.3  

    Unigene Cluster for MMP13:

    Matrix metallopeptidase 13 (collagenase 3)
    Hs.2936  [show with all ESTs]
    Unigene Representative Sequence: NM_002427
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000260302(uc001phl.3) ENST00000340273
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat MMP13 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate MMP13 (see all 11):
    hsa-miR-100* hsa-miR-148b hsa-miR-513a-5p hsa-miR-27a hsa-miR-218-1* hsa-miR-1267 hsa-miR-3647-3p hsa-miR-152
    SwitchGear 3'UTR luciferase reporter plasmidMMP13 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AK222748.1 AK292211.1 AK315341.1 AY256443.1 AY256444.1 BC067522.1 BC067523.1 BC074807.2 
    BC074808.2 X75308.1 X81334.1 

    2 DOTS entries:

    DT.413417  DT.95158006 

    Selected AceView cDNA sequences (see all 74):

    CA415123 CA412841 AA448726 BC074807 BG771388 AY256443 AA329883 X75308 
    BC067522 C02454 BP352104 BX110082 AY256444 AA926873 CA414772 AA329956 
    BC074808 N69322 NM_002427 CA413743 AA298256 X81334 AX930362 CA413504 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    MMP13 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAATAAAATA
    MMP13 Expression
    About this image


    MMP13 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 25 entries
             Hypertrophic Chondrocytes Rib
             Zeugopod Growth Plate
             HyStem+TGFbeta3+GDF5-induced 7SMOO32 cells
             bone marrow   
     
     Cartilage (Muscoskeletal System)    fully expand to see all 22 entries
             Terminal Chondrocytes Temporomandibular Joint
             HyStem+TGFbeta3+GDF5-induced 7SMOO32 cells
             fetal cartilage   
     
     Epidermis (Integumentary System)
             MSC-containing human skin substitute (Grafix)
     
     Blood (Cardiovascular System)
             bone marrow   
    MMP13 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    MMP13 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.2936

    UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452
    Tissue specificity: Seems to be specific to breast carcinomas

        Pathway & Disease-focused RT2 Profiler PCR Arrays including MMP13: 
              Fibrosis in human mouse rat
              Extracellular Matrix & Adhesion Molecules in human mouse rat
              Tumor Metastasis in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for MMP13 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Mmp131 , 5 matrix metallopeptidase 131, 5 85.35(n)1
    86.84(a)1
      9 (2.46 cM)5
    173861  NM_008607.21  NP_032633.11 
     72725145 
    chicken
    (Gallus gallus)
    Aves MMP131 matrix metallopeptidase 13 (collagenase 3) 73.63(n)
    70.79(a)
      395683  XM_003640587.2  XP_003640635.1 
    lizard
    (Anolis carolinensis)
    Reptilia MMP136
    matrix metallopeptidase 13 (collagenase 3)
    70(a)
    1 ↔ 1
    3(192012497-192024513)
    African clawed frog
    (Xenopus laevis)
    Amphibia gene2 collagenase-3 76.09(n)    U41824.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC049472.12   -- 74.6(n)    BC049472.1 
    worm
    (Caenorhabditis elegans)
    Secernentea C31B8.83
    CELE_C31B8.81
    CELE_C31B8.81 37(a)3
    46.17(n)1
    35.29(a)1
      V(2905685-2909407)3
    1787481  NM_071389.41  NP_503790.11 


    ENSEMBL Gene Tree for MMP13 (if available)
    TreeFam Gene Tree for MMP13 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for MMP13 gene
    MMP202  MMP82  MMP142  MMP252  MMP162  MMP72  MMP242  MMP152  
    MMP32  MMP112  MMP272  MMP172  MMP102  MMP12  
    Selected SIMAP similar genes for MMP13 using alignment to 4 protein entries:     MMP13_HUMAN (see all proteins) (see all similar genes):
    AURA2    FAM175A    NF2    LINC00596    MMP8    MMP1
    GLT8D2    MMP3    DNAPTP3    MMP10    MMP27    MMP7
    MMP20    MMP12    MMP26    MMP2    mmp20    MMP14

    Find genes that share paralogs with MMP13           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 MMP13 (see all 374)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0634344
    Metaphyseal anadysplasia 1 (MANDP1)4--see VAR_0634342 H N mis40--------
    VAR_0327534
    Spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO)4--see VAR_0327532 F S mis40--------
    VAR_0634324
    Metaphyseal anadysplasia 1 (MANDP1)4--see VAR_0634322 F S mis40--------
    VAR_0634334
    Metaphyseal anadysplasia 1 (MANDP1)4--see VAR_0634332 M T mis40--------
    rs354616721,2
    C--98749834(+) GGGGGG/-AAGTG 1 -- int11Minor allele frequency- -:0.50NA 2
    rs178605211,2
    C,F--98754836(-) ACCAG-/GCAGTA 1 -- us2k1 tfbs32Minor allele frequency- G:0.39NS NA 182
    rs2000980691,2
    C--102682808(+) AAAAA-/AGAAGG 1 -- ds50010--------
    rs1167448291,2
    F--102682833(+) GTGCAG/ATGGCC 1 -- ds50011Minor allele frequency- A:0.03WA 118
    rs1889889231,2
    --102683023(+) GCCTGA/CACTCG 1 -- ds50010--------
    rs1453369931,2
    --102683075(+) TCAAGC/TCTGGG 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for MMP13 (102813721 - 102826463 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for MMP13:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv464CNV Insertion18451855
    nsv898335CNV Loss21882294
    nsv465CNV Loss18451855

    Human Gene Mutation Database (HGMD): MMP13
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing MMP13
    DNA2.0 Custom Variant and Variant Library Synthesis for MMP13

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600108   
    OMIM disorders: 602111  
    UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452
  • Spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:602111]: A bone disease characterized by
    moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic shortening of the lower limbs
    with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae in childhood.
    Epimetaphyseal changes improve with age. Note=The disease is caused by mutations affecting the gene represented
    in this entry
  • Metaphyseal anadysplasia 1 (MANDP1) [MIM:602111]: A bone development disorder characterized by skeletal
    anomalies that resolve spontaneously with age. Clinical characteristics are evident from the first months of life
    and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature
    in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic
    micromelia. Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for MMP13 (see all 22):    
    About MalaCards
    spondyloepimetaphyseal dysplasia, missouri type    diverticulitis    metaphyseal anadysplasia 1    metaphyseal chondrodysplasia spahr type
    metaphyseal anadysplasia    periapical granuloma    malignant ovarian cyst    enchondroma
    ovarian cyst    localized scleroderma    neurofibroma    osteoarthritis
    coronary artery aneurysm    gastric cardia adenocarcinoma    keratoacanthoma    spondyloepimetaphyseal dysplasia
    salivary gland cancer    lumbar disc herniation    gingivitis    arthritis

    2 diseases from the University of Copenhagen DISEASES database for MMP13:
    Osteoarthritis     Rheumatoid arthritis

    Find genes that share disorders with MMP13           About GenesLikeMe

    Selected Novoseek inferred disease relationships for MMP13 gene (see all 96)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    osteoarthritis 82.4 81 15067375 (3), 15498796 (3), 8730110 (2), 19606871 (2) (see all 48)
    chondrosarcoma 71.3 50 9665469 (7), 18554405 (5), 19126648 (3), 19301259 (3) (see all 22)
    arthritis 64.1 46 12010565 (3), 15140772 (3), 19248099 (3), 12878172 (2) (see all 21)
    rheumatoid arthritis 61.6 46 19379726 (2), 19497915 (2), 9166290 (2), 9259418 (2) (see all 28)
    collagen fibril 51.7 7 12192005 (1), 17055235 (1), 17295208 (1), 12747275 (1) (see all 7)
    necrosis 51.1 35 9040946 (2), 12687541 (1), 12746902 (1), 12010565 (1) (see all 32)
    periapical granuloma 50.6 3 15876293 (2)
    tumors 47.9 180 18698413 (7), 19035119 (7), 18373849 (6), 10027405 (5) (see all 76)
    metastasis 45.3 41 11802203 (2), 12673424 (2), 9933692 (1), 14667142 (1) (see all 25)
    hnscc 45.3 6 16302191 (3), 17334397 (1)

    Genetic Association Database (GAD): MMP13
    Human Genome Epidemiology (HuGE) Navigator: MMP13 (35 documents)

    Export disorders for MMP13 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for MMP13 gene, integrated from 10 sources (see all 927):
    (articles sorted by number of sources associating them with MMP13)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and expression of collagenase-3, a novel human matrix metalloproteinase produced by breast carcinomas. (PubMed id 8207000)1, 2, 3, 9 Freije J.M.P.... Lopez-Otin C. (J. Biol. Chem. 1994)
    2. MMP13 promoter polymorphism is associated with atherosclerosis in the abdominal aorta of young black males. (PubMed id 12392760)1, 4, 9 Yoon S....Tromp G. (Matrix Biol. 2002)
    3. Mutations in MMP9 and MMP13 determine the mode of inheritance and the clinical spectrum of metaphyseal anadysplasia. (PubMed id 19615667)1, 2, 9 Lausch E.... Zabel B. (Am. J. Hum. Genet. 2009)
    4. Polymorphism +17 C/G in matrix metalloprotease MMP8 decreases lung cancer risk. (PubMed id 19094243)1, 4, 9 GonzA!lez-Arriaga P....TardA^n A. (BMC Cancer 2008)
    5. MMP-13 promoter polymorphisms in patients with chronic periodontitis: effects on GCF MMP-13 levels and outcome of periodontal therapy. (PubMed id 19453573)1, 4, 9 Pirhan D....Berdeli A. (J. Clin. Periodontol. 2009)
    6. [Association of functional polymorphisms on MMP-12 and MMP-13 gene promoter region with epithelial ovarian carcinoma]. (PubMed id 20376807)1, 4, 9 Jia J....Li Y. (Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2010)
    7. The functional polymorphisms on promoter region of matrix metalloproteinase-12, -13 genes may alter the risk of epithelial ovarian carcinoma in Chinese. (PubMed id 19258954)1, 4, 9 Li Y....Wang D.J. (Int. J. Gynecol. Cancer 2009)
    8. Functional polymorphisms and haplotypes in the promoter of the MMP2 gene are associated with risk of nasopharyngeal carcinoma. (PubMed id 17607721)1, 4, 9 Zhou G....He F. (Hum. Mutat. 2007)
    9. Promoter polymorphisms in matrix metalloproteinases and their inhibitors: few associations with breast cancer susceptibility and progression. (PubMed id 17033924)1, 4, 9 Lei H....FAPrsti A. (Breast Cancer Res. Treat. 2007)
    10. Variation in the matrix metalloproteinase-3, -7, -12 and -13 genes is associated with functional status in rheumatoid arthritis. (PubMed id 17373931)1, 4, 9 Ye S....Dennison E. (Int. J. Immunogenet. 2007)

    (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: 4322 HGNC: 7159 AceView: MMP13 Ensembl:ENSG00000137745 euGenes: HUgn4322
    ECgene: MMP13 H-InvDB: MMP13

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for MMP13 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for MMP13 Genetics and Cytogenetics in Oncology and Haematology
    NIEHS-SNPshttp://egp.gs.washington.edu/data/mmp13/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for MMP13 gene:
    Search GeneIP for patents involving MMP13

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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