Mmp13 (matrix metallopeptidase 13) - Rat Genome Database

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Gene: Mmp13 (matrix metallopeptidase 13) Rattus norvegicus
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Symbol: Mmp13
Name: matrix metallopeptidase 13
RGD ID: 620196
Description: 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); INTERACTS WITH (+)-schisandrin B; (-)-epigallocatechin 3-gallate; (R)-lipoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagenase 3; collagenase-3; interstitial collagenase; matrix metalloproteinase 13; matrix metalloproteinase-13; MMP-13; UMRCASE
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8812,782,829 - 12,793,108 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl812,782,813 - 12,793,105 (+)EnsemblGRCr8
mRatBN7.284,497,960 - 4,508,239 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl84,497,960 - 4,508,239 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx88,457,570 - 8,467,849 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.086,755,355 - 6,765,634 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.084,757,612 - 4,767,891 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.085,522,739 - 5,533,018 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,522,739 - 5,533,018 (+)Ensemblrn6Rnor6.0
Rnor_5.085,527,980 - 5,538,259 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.484,158,887 - 4,169,166 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera86,061,454 - 6,071,733 (+)NCBICelera
RGSC_v3.184,158,913 - 4,169,165 (+)NCBI
Cytogenetic Map8q11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-acanthoic acid  (ISO)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(1->4)-beta-D-glucan  (ISO)
(R)-lipoic acid  (EXP,ISO)
(S)-nicotine  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP)
2-acetyl-1-alkyl-sn-glycero-3-phosphocholine  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP,ISO)
2-deoxy-D-glucose  (ISO)
2-palmitoylglycerol  (ISO)
3,4-dichloroaniline  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (EXP)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-nitroquinoline N-oxide  (ISO)
5'-S-methyl-5'-thioadenosine  (ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (EXP)
acrolein  (ISO)
acrylamide  (ISO)
afimoxifene  (ISO)
AICA ribonucleotide  (ISO)
aldehydo-D-glucosamine  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
aminoguanidine  (EXP)
ammonium chloride  (EXP)
Ammothamnine  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
apocynin  (ISO)
arachidonic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
astaxanthin  (EXP)
Azoxymethane  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
Benzo[k]fluoranthene  (ISO)
berberine  (ISO)
beta-D-glucosamine  (EXP,ISO)
beta-hexachlorocyclohexane  (ISO)
bicalutamide  (ISO)
bilirubin IXalpha  (ISO)
bisphenol A  (EXP)
bisphenol AF  (ISO)
BQ 123  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP)
calcitriol  (ISO)
candesartan  (EXP)
capsaicin  (EXP)
carbon nanotube  (ISO)
casticin  (EXP)
CGP 52608  (ISO)
chloramphenicol  (ISO)
chloroquine  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
ciprofloxacin  (ISO)
cisplatin  (ISO)
clindamycin  (ISO)
cobalt atom  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cordycepin  (ISO)
corosolic acid  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cycloheximide  (ISO)
dapagliflozin  (EXP)
deguelin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
dibenziodolium  (ISO)
dieckol  (ISO)
dihydroxyacetone  (ISO)
diltiazem  (EXP)
dimethyl sulfoxide  (ISO)
dimethylarsinic acid  (EXP,ISO)
dioxygen  (EXP,ISO)
diquat  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
doxycycline  (ISO)
ebselen  (EXP)
elemental selenium  (ISO)
epoxiconazole  (ISO)
esculetin  (EXP)
ethanol  (EXP,ISO)
ferrostatin-1  (EXP)
fisetin  (EXP)
fluoranthene  (ISO)
folic acid  (ISO)
furan  (EXP)
gadolinium trichloride  (EXP)
Genipin  (ISO)
guanethidine  (EXP)
hyaluronic acid  (ISO)
ibuprofen  (EXP)
irigenin  (ISO)
iron(2+) sulfate (anhydrous)  (EXP,ISO)
isoflavones  (ISO)
isotretinoin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
L-proline betaine  (ISO)
lipoic acid  (EXP,ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
Malonoben  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
manumycin A  (ISO)
masoprocol  (ISO)
methylmercury chloride  (ISO)
microcystin-LR  (ISO)
minocycline  (ISO)
Morroniside  (ISO)
N(5)-ethyl-L-glutamine  (EXP)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (EXP)
nalidixic acid  (ISO)
naproxen  (EXP)
nickel atom  (ISO)
nicotine  (EXP,ISO)
nimodipine  (EXP)
norfloxacin  (ISO)
ofloxacin  (ISO)
okadaic acid  (ISO)
ouabain  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (ISO)
phenobarbital  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pioglitazone  (EXP)
platycodin D  (ISO)
potassium dichromate  (ISO)
prinomastat  (ISO)
progesterone  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (ISO)
raloxifene  (EXP)
rebaudioside A  (EXP)
resveratrol  (EXP,ISO)
rimonabant  (EXP)
rotenone  (ISO)
rottlerin  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
salubrinal  (ISO)
sarpogrelate  (EXP)
SB 203580  (EXP,ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
sevoflurane  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium chloride  (EXP)
sodium silicate  (EXP)
sotorasib  (ISO)
streptozocin  (EXP)
sumatriptan  (EXP)
T-2 toxin  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thapsigargin  (EXP)
Theaflavin 3,3'-digallate  (EXP)
thioacetamide  (EXP,ISO)
thiram  (ISO)
thymoquinone  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trametinib  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
trovafloxacin  (ISO)
tyrphostin AG 1478  (ISO)
valproic acid  (ISO)
verapamil  (EXP)
vorinostat  (ISO)
zinc atom  (ISO)
zinc oxide  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Different bone growth rates are associated with changes in the expression pattern of types II and X collagens and collagenase 3 in proximal growth plates of the rat tibia. Alvarez J, etal., J Bone Miner Res. 2000 Jan;15(1):82-94.
2. Expression patterns of matrix metalloproteinases and vascular endothelial growth factor during epiphyseal ossification. Alvarez J, etal., J Bone Miner Res. 2005 Jun;20(6):1011-21. Epub 2005 Feb 7.
3. Genetic variations in MMP9 and MMP13 contribute to tooth agenesis in a Brazilian population. Antunes LS, etal., J Oral Sci. 2013;55(4):281-6.
4. Global analyses of gene expression in early experimental osteoarthritis. Appleton CT, etal., Arthritis Rheum. 2007 Jun;56(6):1854-68.
5. Expression of collagenase-3 in the rat ovary during the ovulatory process. Balbin M, etal., J Endocrinol. 1996 Jun;149(3):405-15.
6. Collagenase-3 binds to a specific receptor and requires the low density lipoprotein receptor-related protein for internalization. Barmina OY, etal., J Biol Chem. 1999 Oct 15;274(42):30087-93.
7. Early cartilage degeneration in a rat experimental model of developmental dysplasia of the hip. Bo N, etal., Connect Tissue Res. 2012;53(6):513-20. doi: 10.3109/03008207.2012.700346. Epub 2012 Jul 20.
8. Expression of collagenase-3 (matrix metalloproteinase-13) in transitional-cell carcinoma of the urinary bladder. Bostrom PJ, etal., Int J Cancer. 2000 Nov 1;88(3):417-23.
9. Novel phosphoinositide 3-kinase delta,gamma inhibitor: potent anti-inflammatory effects and joint protection in models of rheumatoid arthritis. Boyle DL, etal., J Pharmacol Exp Ther. 2014 Feb;348(2):271-80. doi: 10.1124/jpet.113.205955. Epub 2013 Nov 15.
10. Spatial and temporal pattern of expression of interstitial collagenase, stromelysin/transin, gelatinase A, and TIMP-1 during experimental gastric ulcer healing. Calabro A, etal., Digestion. 2004;70(2):127-38. Epub 2004 Sep 16.
11. Ultrasound stimulates MMP-13 expression through p38 and JNK pathway in osteoblasts. Chiu YC, etal., J Cell Physiol. 2008 May;215(2):356-65.
12. Differential regulation of MMP-13 expression in two models of experimentally induced periodontal disease in rats. de Aquino SG, etal., Arch Oral Biol. 2009 Jul;54(7):609-17. doi: 10.1016/j.archoralbio.2009.03.007. Epub 2009 Apr 24.
13. Matrix metalloproteinase-13/collagenase-3 deletion promotes collagen accumulation and organization in mouse atherosclerotic plaques. Deguchi JO, etal., Circulation. 2005 Oct 25;112(17):2708-15. Epub 2005 Oct 17.
14. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
15. The Bifunctional Rat Pancreatic Secretory Trypsin Inhibitor/Monitor Peptide Provides Protection against Premature Activation of Pancreatic Juice. Graf R, etal., Pancreatology 2003;3(3):195-206.
16. c-Jun N-terminal kinase is required for metalloproteinase expression and joint destruction in inflammatory arthritis. Han Z, etal., J Clin Invest. 2001 Jul;108(1):73-81.
17. Clinical relevance of matrix metalloproteinase-13 determined with a new highly specific and sensitive ELISA in ascitic fluid of advanced ovarian carcinoma patients. Hantke B, etal., Biol Chem. 2003 Aug;384(8):1247-51.
18. Enhanced interstitial collagenase (matrix metalloproteinase-13) production of Kupffer cell by gadolinium chloride prevents pig serum-induced rat liver fibrosis. Hironaka K, etal., Biochem Biophys Res Commun. 2000 Jan 7;267(1):290-5.
19. Matrix metalloproteinase-2, -9 and -13 are involved in fibronectin degradation of rat lung granulomatous fibrosis caused by Angiostrongylus cantonensis. Hsu CC and Lai SC, Int J Exp Pathol. 2007 Dec;88(6):437-43.
20. Morphological and functional characterization of non-alcoholic fatty liver disease induced by a methionine-choline-deficient diet in C57BL/6 mice. Itagaki H, etal., Int J Clin Exp Pathol. 2013 Nov 15;6(12):2683-96. eCollection 2013.
21. Mechanism of Yiqi Huayu Bushen Recipe in treating cervical syndrome with kidney deficiency in rats Jiang JC, etal., Zhong Xi Yi Jie He Xue Bao. 2008 Dec;6(12):1280-5. doi: 10.3736/jcim200812114.
22. Collagenase-3 (MMP-13) is expressed by tumor cells in invasive vulvar squamous cell carcinomas. Johansson N, etal., Am J Pathol. 1999 Feb;154(2):469-80.
23. Combination of tumor necrosis factor-alpha ablation and matrix metalloproteinase inhibition prevents heart failure after pressure overload in tissue inhibitor of metalloproteinase-3 knock-out mice. Kassiri Z, etal., Circ Res. 2005 Aug 19;97(4):380-90. Epub 2005 Jul 21.
24. Differential expression of matrix metalloproteinases in bacterial meningitis. Kieseier BC, etal., Brain. 1999 Aug;122 ( Pt 8):1579-87.
25. MMP-13 is over-expressed in renal cell carcinoma bone metastasis and is induced by TGF-beta1. Kominsky SL, etal., Clin Exp Metastasis. 2008;25(8):865-70. Epub 2008 Aug 16.
26. Different collagenase gene products have different roles in degradation of type I collagen. Krane SM, etal., J Biol Chem. 1996 Nov 8;271(45):28509-15.
27. Oral methylthioadenosine administration attenuates fibrosis and chronic liver disease progression in Mdr2-/- mice. Latasa MU, etal., PLoS One. 2010 Dec 29;5(12):e15690. doi: 10.1371/journal.pone.0015690.
28. Mutations in MMP9 and MMP13 determine the mode of inheritance and the clinical spectrum of metaphyseal anadysplasia. Lausch E, etal., Am J Hum Genet. 2009 Aug;85(2):168-78. doi: 10.1016/j.ajhg.2009.06.014. Epub 2009 Jul 16.
29. Bone marrow-derived mesenchymal cells and MMP13 contribute to experimental choroidal neovascularization. Lecomte J, etal., Cell Mol Life Sci. 2011 Feb;68(4):677-86. doi: 10.1007/s00018-010-0476-6. Epub 2010 Aug 11.
30. MMP/TIMP expression in spontaneously hypertensive heart failure rats: the effect of ACE- and MMP-inhibition. Li H, etal., Cardiovasc Res. 2000 May;46(2):298-306.
31. Allogeneic adipose-derived stem cell transplantation on knee osteoarthritis rats and its effect on MMP-13 and DDR2. Li J, etal., Exp Ther Med. 2019 Jul;18(1):99-104. doi: 10.3892/etm.2019.7554. Epub 2019 May 8.
32. Effects of 17 beta-estradiol on the expression of interstitial collagenases-8 and -13 (MMP-8 and MMP-13) and tissue inhibitor of metalloproteinase-1 (TIMP-1) in ovariectomized rat osteoblastic cells. Li J, etal., J Mol Histol 2004 Nov;35(8-9):723-31.
33. The functional polymorphisms on promoter region of matrix metalloproteinase-12, -13 genes may alter the risk of epithelial ovarian carcinoma in chinese. Li Y, etal., Int J Gynecol Cancer. 2009 Jan-Feb;19(1):129-33.
34. Herb formula "Fufangqishe-Pill" prevents upright posture-induced intervertebral disc degeneration at the lumbar in rats. Liang QQ, etal., J Pharmacol Sci. 2010;113(1):23-31.
35. Prolonged upright posture induces degenerative changes in intervertebral discs of rat cervical spine. Liang QQ, etal., Spine (Phila Pa 1976). 2011 Jan 1;36(1):E14-9. doi: 10.1097/BRS.0b013e3181d2dec2.
36. Distinct expression of gelatinase A [matrix metalloproteinase (MMP)-2], collagenase-3 (MMP-13), membrane type MMP 1 (MMP-14), and tissue inhibitor of MMPs type 1 mediated by physiological signals during formation and regression of the rat corpus luteum. Liu K, etal., Endocrinology. 1999 Nov;140(11):5330-8.
37. Alendronate reduced peri-tunnel bone loss and enhanced tendon graft to bone tunnel healing in anterior cruciate ligament reconstruction. Lui PP, etal., Eur Cell Mater. 2013 Jan 16;25:78-96.
38. Anabolic and catabolic mRNA levels of the intervertebral disc vary with the magnitude and frequency of in vivo dynamic compression. Maclean JJ, etal., J Orthop Res. 2004 Nov;22(6):1193-200.
39. Comparative effect of nimesulide and ibuprofen on the urinary levels of collagen type II C-telopeptide degradation products and on the serum levels of hyaluronan and matrix metalloproteinases-3 and -13 in patients with flare-up of osteoarthritis. Manicourt DH, etal., Drugs R D. 2005;6(5):261-71.
40. Collagenase-3 induction in rat lung fibroblasts requires the combined effects of tumor necrosis factor-alpha and 12-lipoxygenase metabolites: a model of macrophage-induced, fibroblast-driven extracellular matrix remodeling during inflammatory lung injury. Mariani TJ, etal., Mol Biol Cell. 1998 Jun;9(6):1411-24.
41. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
42. Rebamipide attenuates pain severity and cartilage degeneration in a rat model of osteoarthritis by downregulating oxidative damage and catabolic activity in chondrocytes. Moon SJ, etal., Osteoarthritis Cartilage. 2012 Nov;20(11):1426-38. doi: 10.1016/j.joca.2012.08.002. Epub 2012 Aug 10.
43. Matrix metalloproteinases as diagnostic (MMP-13) and prognostic (MMP-2, MMP-9) markers of prostate cancer. Morgia G, etal., Urol Res. 2005 Feb;33(1):44-50. Epub 2004 Oct 22.
44. Focal cerebral ischemia induces changes in both MMP-13 and aggrecan around individual neurons. Nagel S, etal., Brain Res. 2005 Sep 14;1056(1):43-50.
45. Immunolocalization of matrix metalloproteinase-13 on bone surface under osteoclasts in rat tibia. Nakamura H, etal., Bone. 2004 Jan;34(1):48-56.
46. Gene dosage alterations revealed by cDNA microarray analysis in cervical cancer: identification of candidate amplified and overexpressed genes. Narayan G, etal., Genes Chromosomes Cancer. 2007 Apr;46(4):373-84.
47. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
48. Postnatal expression in hyaline cartilage of constitutively active human collagenase-3 (MMP-13) induces osteoarthritis in mice. Neuhold LA, etal., J Clin Invest. 2001 Jan;107(1):35-44.
49. Collagenase-3 expression in breast myofibroblasts as a molecular marker of transition of ductal carcinoma in situ lesions to invasive ductal carcinomas. Nielsen BS, etal., Cancer Res. 2001 Oct 1;61(19):7091-100.
50. Matrix metalloproteinase 13 is induced in fibroblasts in polyomavirus middle T antigen-driven mammary carcinoma without influencing tumor progression. Nielsen BS, etal., PLoS ONE. 2008 Aug 13;3(8):e2959.
51. Genetic analysis of polymorphisms in biologically relevant candidate genes in patients with abdominal aortic aneurysms. Ogata T, etal., J Vasc Surg. 2005 Jun;41(6):1036-42.
52. Transforming growth factor-alpha attenuates hepatic fibrosis: possible involvement of matrix metalloproteinase-1. Ohyama T, etal., Liver Int. 2011 Apr;31(4):572-84. doi: 10.1111/j.1478-3231.2011.02475.x. Epub 2011 Feb 15.
53. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
54. Macrophage migration inhibitory factor up-regulates matrix metalloproteinase-9 and -13 in rat osteoblasts. Relevance to intracellular signaling pathways. Onodera S, etal., J Biol Chem 2002 Mar 8;277(10):7865-74.
55. Evolution of matrix metalloprotease and tissue inhibitor expression during heart failure progression in the infarcted rat. Peterson JT, etal., Cardiovasc Res. 2000 May;46(2):307-15.
56. Macrophage-mediated phagocytosis of apoptotic cholangiocytes contributes to reversal of experimental biliary fibrosis. Popov Y, etal., Am J Physiol Gastrointest Liver Physiol. 2010 Mar;298(3):G323-34. doi: 10.1152/ajpgi.00394.2009. Epub 2010 Jan 7.
57. Rat collagenase. Cloning, amino acid sequence comparison, and parathyroid hormone regulation in osteoblastic cells. Quinn CO, etal., J Biol Chem 1990 Dec 25;265(36):22342-7.
58. Embryogenesis of the rat heart: the expression of collagenases. Ratajska A and Cleutjens JP, Basic Res Cardiol. 2002 May;97(3):189-97.
59. GOA pipeline RGD automated data pipeline
60. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
61. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
62. Gene expression of MMP8 and MMP13 during embryonic development of bone and cartilage in the rat mandible and hind limb. Sasano Y, etal., J Histochem Cytochem. 2002 Mar;50(3):325-32.
63. Parathyroid hormone regulates the rat collagenase-3 promoter in osteoblastic cells through the cooperative interaction of the activator protein-1 site and the runt domain binding sequence. Selvamurugan N, etal., J Biol Chem. 1998 Apr 24;273(17):10647-57.
64. Deletion of the transforming growth factor beta receptor type II gene in articular chondrocytes leads to a progressive osteoarthritis-like phenotype in mice. Shen J, etal., Arthritis Rheum. 2013 Dec;65(12):3107-19. doi: 10.1002/art.38122.
65. Heparan sulfate proteoglycans mediate interstitial flow mechanotransduction regulating MMP-13 expression and cell motility via FAK-ERK in 3D collagen. Shi ZD, etal., PLoS One. 2011 Jan 5;6(1):e15956. doi: 10.1371/journal.pone.0015956.
66. Maternal hypoxia alters matrix metalloproteinase expression patterns and causes cardiac remodeling in fetal and neonatal rats. Tong W, etal., Am J Physiol Heart Circ Physiol. 2011 Nov;301(5):H2113-21. doi: 10.1152/ajpheart.00356.2011. Epub 2011 Aug 19.
67. Elevated expression of matrix metalloproteinase-13 in abdominal aortic aneurysms. Tromp G, etal., Ann Vasc Surg. 2004 Jul;18(4):414-20.
68. Acute and chronic hypoxia as well as 7-day recovery from chronic hypoxia affects the distribution of pulmonary mast cells and their MMP-13 expression in rats. Vajner L, etal., Int J Exp Pathol. 2006 Oct;87(5):383-91.
69. Gene expression and molecular changes in cerebral arteries following subarachnoid hemorrhage in the rat. Vikman P, etal., J Neurosurg. 2006 Sep;105(3):438-44.
70. Increased expression of matrix metalloproteinases in the murine zymosan-induced multiple organ dysfunction syndrome. Volman TJ, etal., J Pathol. 2004 Aug;203(4):968-75.
71. Regulation of expression of collagenase-3 in normal, differentiating rat osteoblasts. Winchester SK, etal., J Cell Physiol. 1999 Dec;181(3):479-88.
72. Expression pattern of matrix metalloproteinases-13 in a rat model of alcoholic liver fibrosis. Yan S, etal., Hepatobiliary Pancreat Dis Int. 2005 Nov;4(4):569-72.
73. MMP13 promoter polymorphism is associated with atherosclerosis in the abdominal aorta of young black males. Yoon S, etal., Matrix Biol. 2002 Oct;21(6):487-98.
74. [Regulatory mechanism of malignant behavior of endometriosis mediated by puerarin.] Yu CQ, etal., Zhong Xi Yi Jie He Xue Bao. 2009 Jan;7(1):41-7.
75. Tumor-derived matrix metalloproteinase-13 (MMP-13) correlates with poor prognoses of invasive breast cancer. Zhang B, etal., BMC Cancer. 2008 Mar 28;8:83.
76. [Comparison of doxycycline, losartan, and their combination on the expression of matrix metalloproteinase, tissue inhibitor of matrix metalloproteinase, and collagen remodeling in the noninfarcted myocardium after acute myocardial infarction in rats] Zhang P, etal., Zhongguo Yi Xue Ke Xue Yuan Xue Bao. 2005 Feb;27(1):53-61.
Additional References at PubMed
PMID:8576151   PMID:9065415   PMID:11953314   PMID:12213812   PMID:12663239   PMID:14645243   PMID:14702107   PMID:14982932   PMID:15026307   PMID:15563592   PMID:15581614   PMID:15601621  
PMID:16167086   PMID:16256123   PMID:16639721   PMID:17116693   PMID:17485851   PMID:17568546   PMID:17607299   PMID:17623656   PMID:17987127   PMID:18052689   PMID:18164633   PMID:18404723  
PMID:18464888   PMID:18470577   PMID:18615687   PMID:18807189   PMID:18814267   PMID:18985055   PMID:19050895   PMID:19121369   PMID:19241444   PMID:19300451   PMID:19346731   PMID:19847888  
PMID:20097749   PMID:20870727   PMID:21055467   PMID:21180139   PMID:21342246   PMID:21444811   PMID:21447140   PMID:21450970   PMID:22357747   PMID:22517354   PMID:22961837   PMID:22992737  
PMID:23192728   PMID:23277113   PMID:23886643   PMID:23913860   PMID:23974514   PMID:23981230   PMID:24126863   PMID:25128628   PMID:25190659   PMID:25595313   PMID:26558633   PMID:26721462  
PMID:28157489   PMID:28265573   PMID:28419442   PMID:29860993   PMID:29928874   PMID:31061278   PMID:31666602   PMID:31960421   PMID:33356628   PMID:34463227   PMID:34643076   PMID:34656826  
PMID:34830409   PMID:36409042   PMID:38061116  


Genomics

Comparative Map Data
Mmp13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8812,782,829 - 12,793,108 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl812,782,813 - 12,793,105 (+)EnsemblGRCr8
mRatBN7.284,497,960 - 4,508,239 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl84,497,960 - 4,508,239 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx88,457,570 - 8,467,849 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.086,755,355 - 6,765,634 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.084,757,612 - 4,767,891 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.085,522,739 - 5,533,018 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,522,739 - 5,533,018 (+)Ensemblrn6Rnor6.0
Rnor_5.085,527,980 - 5,538,259 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.484,158,887 - 4,169,166 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera86,061,454 - 6,071,733 (+)NCBICelera
RGSC_v3.184,158,913 - 4,169,165 (+)NCBI
Cytogenetic Map8q11NCBI
MMP13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811102,942,995 - 102,955,732 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11102,942,995 - 102,955,732 (-)Ensemblhg38GRCh38
GRCh3711102,813,724 - 102,826,461 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611102,318,934 - 102,331,672 (-)NCBIBuild 36Build 36hg18NCBI36
Build 3411102,318,933 - 102,331,672NCBI
Celera1199,975,301 - 99,988,043 (-)NCBICelera
Cytogenetic Map11q22.2NCBI
HuRef1198,741,671 - 98,754,423 (-)NCBIHuRef
CHM1_111102,696,655 - 102,709,340 (-)NCBICHM1_1
T2T-CHM13v2.011102,946,765 - 102,959,501 (-)NCBIT2T-CHM13v2.0
Mmp13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3997,272,514 - 7,283,333 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl97,272,514 - 7,283,331 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm3897,272,514 - 7,283,333 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl97,272,514 - 7,283,331 (+)Ensemblmm10GRCm38
MGSCv3797,272,514 - 7,283,333 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3697,272,545 - 7,283,331 (+)NCBIMGSCv36mm8
Celera94,675,357 - 4,686,177 (+)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Mmp13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554126,106,994 - 6,118,760 (-)Ensembl
ChiLan1.0NW_0049554126,106,994 - 6,118,760 (-)NCBIChiLan1.0ChiLan1.0
MMP13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v29103,742,962 - 103,755,946 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan111104,831,140 - 104,844,113 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01197,890,811 - 97,902,778 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111101,374,960 - 101,387,702 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11101,377,001 - 101,387,679 (-)EnsemblpanPan2panpan1.1
MMP13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1528,793,568 - 28,864,832 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl528,850,522 - 28,864,121 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha528,800,013 - 28,811,179 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0528,904,844 - 28,915,995 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl528,903,544 - 28,915,284 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1528,939,682 - 28,951,055 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0528,819,585 - 28,830,954 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0528,994,055 - 29,005,429 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Mmp13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494786,490,310 - 86,496,608 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365515,040,084 - 5,050,384 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365515,040,084 - 5,050,384 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MMP13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl933,549,008 - 33,561,162 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1933,549,003 - 33,616,700 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2937,492,665 - 37,504,574 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MMP13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1194,322,473 - 94,370,665 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl194,322,979 - 94,334,747 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604331,533,765 - 31,547,392 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Mmp13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249182,228,688 - 2,239,852 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Mmp13
52 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:504
Count of miRNA genes:262
Interacting mature miRNAs:315
Transcripts:ENSRNOT00000011507
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 3 12 72 23 36 8 56 8 6 139 80 11 58 33 60 28 6 6

Sequence


Ensembl Acc Id: ENSRNOT00000011507   ⟹   ENSRNOP00000011507
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl812,782,813 - 12,793,105 (+)Ensembl
mRatBN7.2 Ensembl84,497,960 - 4,508,239 (+)Ensembl
Rnor_6.0 Ensembl85,522,739 - 5,533,018 (+)Ensembl
RefSeq Acc Id: NM_133530   ⟹   NP_598214
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8812,782,829 - 12,793,108 (+)NCBI
mRatBN7.284,497,960 - 4,508,239 (+)NCBI
Rnor_6.085,522,739 - 5,533,018 (+)NCBI
Rnor_5.085,527,980 - 5,538,259 (+)NCBI
RGSC_v3.484,158,887 - 4,169,166 (+)RGD
Celera86,061,454 - 6,071,733 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_598214 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA72124 (Get FASTA)   NCBI Sequence Viewer  
  AAB47407 (Get FASTA)   NCBI Sequence Viewer  
  AAM51172 (Get FASTA)   NCBI Sequence Viewer  
  EDL78538 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000011507
GenBank Protein P23097 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_598214   ⟸   NM_133530
- Peptide Label: precursor
- UniProtKB: P23097 (UniProtKB/Swiss-Prot),   G3V742 (UniProtKB/TrEMBL),   A6JN28 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000011507   ⟸   ENSRNOT00000011507
Protein Domains
Peptidase metallopeptidase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P23097-F1-model_v2 AlphaFold P23097 1-466 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13695731
Promoter ID:EPDNEW_R6255
Type:single initiation site
Name:Mmp13_1
Description:matrix metallopeptidase 13
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.085,522,723 - 5,522,783EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620196 AgrOrtholog
BioCyc Gene G2FUF-31793 BioCyc
Ensembl Genes ENSRNOG00000008478 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000011507 ENTREZGENE
Gene3D-CATH 2.110.10.10 UniProtKB/Swiss-Prot
  3.40.390.10 UniProtKB/Swiss-Prot
InterPro Hemopexin-like_dom UniProtKB/Swiss-Prot
  Hemopexin-like_dom_sf UniProtKB/Swiss-Prot
  Hemopexin-like_repeat UniProtKB/Swiss-Prot
  Hemopexin_CS UniProtKB/Swiss-Prot
  M10A_MMP UniProtKB/Swiss-Prot
  MetalloPept_cat_dom_sf UniProtKB/Swiss-Prot
  Pept_M10_metallopeptidase UniProtKB/Swiss-Prot
  Pept_M10A UniProtKB/Swiss-Prot
  Pept_M10A_Zn_BS UniProtKB/Swiss-Prot
  Peptidase_Metallo UniProtKB/Swiss-Prot
  Peptidoglycan-bd-like UniProtKB/Swiss-Prot
  PGBD-like_sf UniProtKB/Swiss-Prot
NCBI Gene 171052 ENTREZGENE
PANTHER MATRIX METALLOPROTEINASE UniProtKB/Swiss-Prot
  PTHR10201:SF165 UniProtKB/Swiss-Prot
Pfam Hemopexin UniProtKB/Swiss-Prot
  Peptidase_M10 UniProtKB/Swiss-Prot
  PG_binding_1 UniProtKB/Swiss-Prot
PhenoGen Mmp13 PhenoGen
PIRSF Peptidase_M10A_matrix UniProtKB/Swiss-Prot
PRINTS MATRIXIN UniProtKB/Swiss-Prot
PROSITE CYSTEINE_SWITCH UniProtKB/Swiss-Prot
  HEMOPEXIN UniProtKB/Swiss-Prot
  HEMOPEXIN_2 UniProtKB/Swiss-Prot
  ZINC_PROTEASE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000008478 RatGTEx
SMART SM00120 UniProtKB/Swiss-Prot
  ZnMc UniProtKB/Swiss-Prot
Superfamily-SCOP Metalloproteases ('zincins'), catalytic domain UniProtKB/Swiss-Prot
  SSF47090 UniProtKB/Swiss-Prot
  SSF50923 UniProtKB/Swiss-Prot
UniProt A6JN28 ENTREZGENE, UniProtKB/TrEMBL
  G3V742 ENTREZGENE, UniProtKB/TrEMBL
  MMP13_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Mmp13  matrix metallopeptidase 13    matrix metalloproteinase 13  Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Mmp13  matrix metalloproteinase 13      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation expression induced by parathyroid hormone in osteoblastic cells 728937