Mmp13 matrix metallopeptidase 13 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Mmp13provided by RGD
Official Full Name: matrix metallopeptidase 13provided by RGD
Primary source: RGD:620196
See related: EnsemblRapid:ENSRNOG00000008478 AllianceGenome:RGD:620196
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables several functions, including fibronectin binding activity; low-density lipoprotein particle receptor binding activity; and metal ion binding activity. Involved in several processes, including embryonic hindlimb morphogenesis; endochondral ossification; and estrous cycle. Located in extracellular space and intercellular canaliculus. Used to study brain ischemia; degenerative disc disease; and myocardial infarction. Biomarker of several diseases, including bone disease (multiple); gastric ulcer; liver cirrhosis (multiple); meningococcal meningitis; and silicosis. 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, Dec 2024]
Expression: Biased expression in Thymus (RPKM 2.9), Muscle (RPKM 1.6) and 5 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q11

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (12782829..12793108)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (4497960..4508239)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (5522739..5533018)

Chromosome 8 - NC_086026.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

miR-99b-3p/Mmp13 axis regulates NLRP3 inflammasome-dependent microglial pyroptosis and alleviates neuropathic pain via the promotion of autophagy.
Title: miR-99b-3p/Mmp13 axis regulates NLRP3 inflammasome-dependent microglial pyroptosis and alleviates neuropathic pain via the promotion of autophagy.
Increased expression of angiopoietin-like protein 4 regulates matrix metalloproteinase-13 expression in Porphyromonas gingivalis lipopolysaccharides-stimulated gingival fibroblasts and ligature-induced experimental periodontitis.
Title: Increased expression of angiopoietin-like protein 4 regulates matrix metalloproteinase-13 expression in Porphyromonas gingivalis lipopolysaccharides-stimulated gingival fibroblasts and ligature-induced experimental periodontitis.
Parathyroid Hormone-regulation of Runx2 by MiR-290 for Matrix Metalloproteinase-13 Expression in Rat Osteoblastic Cells.
Title: Parathyroid Hormone-regulation of Runx2 by MiR-290 for Matrix Metalloproteinase-13 Expression in Rat Osteoblastic Cells.
Regulation of transforming growth factor-beta1-stimulation of Runx2 acetylation for matrix metalloproteinase 13 expression in osteoblastic cells.
Title: Regulation of transforming growth factor-β1-stimulation of Runx2 acetylation for matrix metalloproteinase 13 expression in osteoblastic cells.
Differential MMP 1 and MMP 13 expression in proliferation and ligamentization phases of graft remodeling in anterior cruciate ligament reconstruction.
Title: Differential MMP 1 and MMP 13 expression in proliferation and ligamentization phases of graft remodeling in anterior cruciate ligament reconstruction.
Bone marrow mesenchymal stem cell-derived exosomes inhibit chondrocyte apoptosis and the expression of MMPs by regulating Drp1-mediated mitophagy.
Title: Bone marrow mesenchymal stem cell-derived exosomes inhibit chondrocyte apoptosis and the expression of MMPs by regulating Drp1-mediated mitophagy.
Trabecular Bone Parameters, TIMP-2, MMP-8, MMP-13, VEGF Expression and Immunolocalization in Bone and Cartilage in Newborn Offspring Prenatally Exposed to Fumonisins.
Title: Trabecular Bone Parameters, TIMP-2, MMP-8, MMP-13, VEGF Expression and Immunolocalization in Bone and Cartilage in Newborn Offspring Prenatally Exposed to Fumonisins.
miR-873-3p targets HDAC4 to stimulate matrix metalloproteinase-13 expression upon parathyroid hormone exposure in rat osteoblasts.
Title: miR-873-3p targets HDAC4 to stimulate matrix metalloproteinase-13 expression upon parathyroid hormone exposure in rat osteoblasts.
Notch Signaling Regulates MMP-13 Expression via Runx2 in Chondrocytes.
Title: Notch Signaling Regulates MMP-13 Expression via Runx2 in Chondrocytes.
Studied protective action of vitamin D in articular cartilage degradation models through inhibition of matrix metallopeptidase 9 (MMP-9) and matrix metallopeptidase 13 (MMP-13). Results showed a possibility that vitamin D deficiency may be a stimulus for MMP production in normal articular cartilage.
Title: Vitamin D Inhibits Activities of Metalloproteinase-9/-13 in Articular Cartilage In Vivo and In Vitro.

Submit: New GeneRIF Correction See all GeneRIFs (73)

General gene information

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Markers

Mmp13 (e-PCR), detects polymorphism
- UniSTS:259370

Mmp13 (e-PCR), detects polymorphism
- UniSTS:498392

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
enables collagen binding	IEA Inferred from Electronic Annotation more info
enables collagen binding	ISO Inferred from Sequence Orthology more info
enables collagen binding	ISS Inferred from Sequence or Structural Similarity more info
enables endopeptidase activity	ISO Inferred from Sequence Orthology more info
enables fibronectin binding	IPI Inferred from Physical Interaction more info	PubMed
enables low-density lipoprotein particle receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables metalloendopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables metalloendopeptidase activity	IDA Inferred from Direct Assay more info	PubMed
enables metalloendopeptidase activity	IEA Inferred from Electronic Annotation more info
enables metalloendopeptidase activity	ISO Inferred from Sequence Orthology more info
enables peptidase activity	ISO Inferred from Sequence Orthology more info
enables serine-type endopeptidase activity	TAS Traceable Author Statement more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in bone mineralization	IEA Inferred from Electronic Annotation more info
involved_in bone mineralization	ISO Inferred from Sequence Orthology more info
involved_in bone morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in bone morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to fluid shear stress	IEP Inferred from Expression Pattern more info	PubMed
involved_in collagen catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in collagen catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within collagen catabolic process	ISO Inferred from Sequence Orthology more info
involved_in collagen catabolic process	ISO Inferred from Sequence Orthology more info
involved_in collagen catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic hindlimb morphogenesis	IEP Inferred from Expression Pattern more info	PubMed
involved_in endochondral ossification	IEA Inferred from Electronic Annotation more info
involved_in endochondral ossification	IEP Inferred from Expression Pattern more info	PubMed
involved_in endochondral ossification	ISO Inferred from Sequence Orthology more info
involved_in estrous cycle	IEP Inferred from Expression Pattern more info	PubMed
involved_in extracellular matrix disassembly	IEA Inferred from Electronic Annotation more info
involved_in extracellular matrix disassembly	ISO Inferred from Sequence Orthology more info
involved_in extracellular matrix disassembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in growth plate cartilage development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within growth plate cartilage development	ISO Inferred from Sequence Orthology more info
involved_in heart development	IDA Inferred from Direct Assay more info	PubMed
involved_in luteolysis	IEP Inferred from Expression Pattern more info	PubMed
involved_in ossification	IEP Inferred from Expression Pattern more info	PubMed
involved_in osteoblast differentiation	IEP Inferred from Expression Pattern more info	PubMed
involved_in parturition	IEP Inferred from Expression Pattern more info	PubMed
involved_in positive regulation of pancreatic trypsinogen secretion	IDA Inferred from Direct Assay more info	PubMed
involved_in protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
involved_in proteolysis	ISO Inferred from Sequence Orthology more info
involved_in response to estrogen	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to hormone	IDA Inferred from Direct Assay more info	PubMed
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to mechanical stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular matrix	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in intercellular canaliculus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: collagenase 3

Names: MMP-13; UMRCASE; interstitial collagenase; matrix metalloproteinase-13

NP_598214.1

EC 3.4.24.-

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)

NM_133530.1 → NP_598214.1 collagenase 3 precursor

See identical proteins and their annotated locations for NP_598214.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/Swiss-Prot

P23097

UniProtKB/TrEMBL

A6JN28, G3V742

Related

ENSRNOP00000011507.4, ENSRNOT00000011507.7

Conserved Domains (3) summary

cd00094
Location:282 → 472

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:113 → 268

Peptidase_M10; Matrixin

pfam01471
Location:40 → 92

PG_binding_1; Putative peptidoglycan binding domain