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    mmp13a matrix metallopeptidase 13a [ Danio rerio (zebrafish) ]

    Gene ID: 387293, updated on 28-Oct-2024

    Summary

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    Official Symbol
    mmp13aprovided by ZNC
    Official Full Name
    matrix metallopeptidase 13aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-031202-2
    See related
    Ensembl:ENSDARG00000012395 AllianceGenome:ZFIN:ZDB-GENE-031202-2
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    mmp13; cb1034
    Summary
    Predicted to enable metalloendopeptidase activity. Acts upstream of or within macrophage chemotaxis. Predicted to be located in extracellular matrix. Predicted to be active in extracellular space. Is expressed in several structures, including extension; heart; intermediate cell mass of mesoderm; leukocyte; and post-vent region. Human ortholog(s) of this gene implicated in anodontia; artery disease (multiple); bone disease (multiple); and ovarian carcinoma. Orthologous to human MMP13 (matrix metallopeptidase 13). [provided by Alliance of Genome Resources, Oct 2024]
    Orthologs
    all
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    Genomic context

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    See mmp13a in Genome Data Viewer
    Location:
    chromosome: 10
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 10 NC_007121.7 (38593657..38619868)
    105 previous assembly GRCz10 (GCF_000002035.5) 10 NC_007121.6 (38649900..38676124)

    Chromosome 10 - NC_007121.7Genomic Context describing neighboring genes Neighboring gene alkaline ceramidase 3 Neighboring gene matrix metalloproteinase-18 Neighboring gene uncharacterized LOC103911776 Neighboring gene uncharacterized LOC137496605

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Matrix metalloproteinase-13 is required for zebra fish (Danio rerio) development and is a target for glucocorticoids. Hillegass JM, et al. Toxicol Sci, 2007 Nov. PMID 17728286
    2. Matrix Metalloproteinase 13 Activity is Required for Normal and Hypoxia-Induced Precocious Hatching in Zebrafish Embryos. Small CD, et al. J Dev Biol, 2020 Jan 31. PMID 32023839, Free PMC Article
    3. Nitrite Improves Heart Regeneration in Zebrafish. Rochon ER, et al. Antioxid Redox Signal, 2020 Feb 20. PMID 31724431, Free PMC Article
    4. EGF-mediated suppression of cell extrusion during mucosal damage attenuates opportunistic fungal invasion. Wurster S, et al. Cell Rep, 2021 Mar 23. PMID 33761358, Free PMC Article
    5. Characterization of the zebrafish matrix metalloproteinase 9 gene and its developmental expression pattern. Yoong S, et al. Gene Expr Patterns, 2007 Jan. PMID 16815100

    See all (137) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The data suggest that MMP9 and MMP13 might play a key role in the inflammatory phase of heart regeneration in zebrafish, by mediating leukocyte recruitment via the activation of chemokines, in particular, CXCL8.
      Title: Matrix metalloproteinases (MMPs) mediate leukocyte recruitment during the inflammatory phase of zebrafish heart regeneration.
    2. MeHg impairs tail development at least partially by activation of the tissue remodeling proteases Mmp9 and Mmp13.
      Title: Methyl mercury suppresses the formation of the tail primordium in developing zebrafish embryos.
    3. JNK-Mmp13 signaling pathway plays an essential role in regulating the innate immune cell migration in response to severe injury in vivo
      Title: In vivo interstitial migration of primitive macrophages mediated by JNK-matrix metalloproteinase 13 signaling in response to acute injury.
    4. Zebra fish embryogenesis requires MMP-13 and dexamethasone and hydrocortisone modulate the expression of this gene, leading to increased activity and potentially contributing to subsequent dysmorphogenesis.
      Title: Matrix metalloproteinase-13 is required for zebra fish (Danio rerio) development and is a target for glucocorticoids.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metalloendopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metalloendopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metallopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in collagen catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within macrophage chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    collagenase 3a
    Names
    MMPLg
    MMPLh
    matrix metallopeptidase 13a (collagenase 3)
    matrix metalloproteinase 13
    matrix metalloproteinase 13a
    NP_001277408.1
    XP_009303831.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001290479.1 → NP_001277408.1  collagenase 3a precursor

      Status: VALIDATED

      Source sequence(s)
      LO018336
      UniProtKB/TrEMBL
      A0A8M1P6J4
      Conserved Domains (3) summary
      cd00094
      Location:286 → 475
      HX; Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of ...
      pfam00413
      Location:112 → 268
      Peptidase_M10; Matrixin
      pfam01471
      Location:28 → 91
      PG_binding_1; Putative peptidoglycan binding domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007121.7 Reference GRCz11 Primary Assembly

      Range
      38593657..38619868
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009305556.3 → XP_009303831.1  collagenase 3a isoform X1

      UniProtKB/TrEMBL
      A0A8M3AX13, F1QCX8
      Related
      ENSDARP00000012407.7, ENSDART00000011573.9
      Conserved Domains (4) summary
      cd00094
      Location:286 → 475
      HX; Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of ...
      cd04278
      Location:112 → 268
      ZnMc_MMP; Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate ...
      pfam00413
      Location:112 → 268
      Peptidase_M10; Matrixin
      pfam01471
      Location:28 → 91
      PG_binding_1; Putative peptidoglycan binding domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_201503.1: Suppressed sequence

      Description
      NM_201503.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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