Mmp13 (matrix metallopeptidase 13) - Rat Genome Database
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Gene: Mmp13 (matrix metallopeptidase 13) Rattus norvegicus
Analyze
Symbol: Mmp13
Name: matrix metallopeptidase 13
RGD ID: 620196
Description: Exhibits several functions, including fibronectin binding activity; low-density lipoprotein particle receptor binding activity; and metal ion binding activity. Involved in several processes, including animal organ development; embryonic hindlimb morphogenesis; and estrous cycle. Localizes to several cellular components, including Golgi apparatus; intercellular canaliculus; and lysosome. 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; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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 Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.284,497,960 - 4,508,239 (+)NCBI
Rnor_6.0 Ensembl85,522,739 - 5,533,018 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.085,522,739 - 5,533,018 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.085,527,980 - 5,538,259 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,158,887 - 4,169,166 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.184,158,913 - 4,169,165 (+)NCBI
Celera86,061,454 - 6,071,733 (+)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (EXP,ISO)
(R)-lipoic acid  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (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)
3,4-dichloroaniline  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4-nitroquinoline N-oxide  (ISO)
5-aza-2'-deoxycytidine  (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)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
apocynin  (ISO)
arachidonic acid  (ISO)
arsenous acid  (EXP,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)
BQ 123  (ISO)
cadmium atom  (ISO)
caffeine  (EXP)
calcitriol  (ISO)
candesartan  (EXP)
capsaicin  (EXP)
carbon nanotube  (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)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (ISO)
Deguelin  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
dibenziodolium  (ISO)
dieckol  (ISO)
dihydroxyacetone  (ISO)
diltiazem  (EXP)
dimethylarsinic acid  (ISO)
dioxygen  (EXP,ISO)
diuron  (EXP)
doxorubicin  (ISO)
doxycycline  (ISO)
ebselen  (EXP)
elemental selenium  (ISO)
esculetin  (EXP)
ethanol  (EXP,ISO)
fluoranthene  (ISO)
folic acid  (ISO)
furan  (EXP)
gadolinium trichloride  (EXP)
Genipin  (ISO)
guanethidine  (EXP)
hyaluronic acid  (ISO)
ibuprofen  (EXP)
iron(2+) sulfate (anhydrous)  (EXP,ISO)
isoflavones  (ISO)
isotretinoin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
L-proline betaine  (ISO)
lipoic acid  (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)
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  (ISO)
nimodipine  (EXP)
norfloxacin  (ISO)
ofloxacin  (ISO)
ouabain  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (EXP,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)
resveratrol  (EXP,ISO)
rimonabant  (EXP)
rotenone  (ISO)
rottlerin  (ISO)
sarpogrelate  (EXP)
SB 203580  (EXP,ISO)
selenium atom  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
streptozocin  (EXP)
sumatriptan  (EXP)
T-2 toxin  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thioacetamide  (EXP,ISO)
thymoquinone  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
trovafloxacin  (ISO)
tyrphostin AG 1478  (ISO)
valproic acid  (ISO)
verapamil  (EXP)
zinc atom  (ISO)
zinc oxide  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
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19. Hsu CC and Lai SC, Int J Exp Pathol. 2007 Dec;88(6):437-43.
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29. Li J, etal., J Mol Histol 2004 Nov;35(8-9):723-31.
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35. Maclean JJ, etal., J Orthop Res. 2004 Nov;22(6):1193-200.
36. Manicourt DH, etal., Drugs R D. 2005;6(5):261-71.
37. Mariani TJ, etal., Mol Biol Cell. 1998 Jun;9(6):1411-24.
38. MGD data from the GO Consortium
39. Moon SJ, etal., Osteoarthritis Cartilage. 2012 Nov;20(11):1426-38. doi: 10.1016/j.joca.2012.08.002. Epub 2012 Aug 10.
40. Morgia G, etal., Urol Res. 2005 Feb;33(1):44-50. Epub 2004 Oct 22.
41. Nagel S, etal., Brain Res. 2005 Sep 14;1056(1):43-50.
42. Nakamura H, etal., Bone. 2004 Jan;34(1):48-56.
43. Narayan G, etal., Genes Chromosomes Cancer. 2007 Apr;46(4):373-84.
44. NCBI rat LocusLink and RefSeq merged data July 26, 2002
45. Neuhold LA, etal., J Clin Invest. 2001 Jan;107(1):35-44.
46. Nielsen BS, etal., Cancer Res. 2001 Oct 1;61(19):7091-100.
47. Nielsen BS, etal., PLoS ONE. 2008 Aug 13;3(8):e2959.
48. Ogata T, etal., J Vasc Surg. 2005 Jun;41(6):1036-42.
49. Ohyama T, etal., Liver Int. 2011 Apr;31(4):572-84. doi: 10.1111/j.1478-3231.2011.02475.x. Epub 2011 Feb 15.
50. OMIM Disease Annotation Pipeline
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52. Peterson JT, etal., Cardiovasc Res. 2000 May;46(2):307-15.
53. 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.
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56. RGD automated data pipeline
57. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
58. RGD automated import pipeline for gene-chemical interactions
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61. Shen J, etal., Arthritis Rheum. 2013 Dec;65(12):3107-19. doi: 10.1002/art.38122.
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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  


Genomics

Comparative Map Data
Mmp13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.284,497,960 - 4,508,239 (+)NCBI
Rnor_6.0 Ensembl85,522,739 - 5,533,018 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.085,522,739 - 5,533,018 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.085,527,980 - 5,538,259 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,158,887 - 4,169,166 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.184,158,913 - 4,169,165 (+)NCBI
Celera86,061,454 - 6,071,733 (+)NCBICelera
Cytogenetic Map8q11NCBI
MMP13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11102,942,995 - 102,955,732 (-)EnsemblGRCh38hg38GRCh38
GRCh3811102,942,995 - 102,955,732 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711102,813,724 - 102,826,461 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611102,318,934 - 102,331,672 (-)NCBINCBI36hg18NCBI36
Build 3411102,318,933 - 102,331,672NCBI
Celera1199,975,301 - 99,988,043 (-)NCBI
Cytogenetic Map11q22.2NCBI
HuRef1198,741,671 - 98,754,423 (-)NCBIHuRef
CHM1_111102,696,655 - 102,709,340 (-)NCBICHM1_1
Mmp13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3997,272,514 - 7,283,333 (+)NCBIGRCm39mm39
GRCm39 Ensembl97,272,514 - 7,283,331 (+)Ensembl
GRCm3897,272,514 - 7,283,333 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl97,272,514 - 7,283,331 (+)EnsemblGRCm38mm10GRCm38
MGSCv3797,272,514 - 7,283,333 (+)NCBIGRCm37mm9NCBIm37
MGSCv3697,272,545 - 7,283,331 (+)NCBImm8
Celera94,675,357 - 4,686,177 (+)NCBICelera
Cytogenetic Map9A1NCBI
Mmp13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554126,106,994 - 6,118,760 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554126,106,994 - 6,118,760 (-)NCBIChiLan1.0ChiLan1.0
MMP13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111101,374,960 - 101,387,702 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11101,377,001 - 101,387,679 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01197,890,811 - 97,902,778 (-)NCBIMhudiblu_PPA_v0panPan3
MMP13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl528,850,522 - 28,864,121 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1528,793,568 - 28,864,832 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Mmp13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365515,040,084 - 5,050,384 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MMP13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl933,549,003 - 33,568,076 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1933,549,003 - 33,616,700 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2937,492,665 - 37,504,574 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MMP13
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1194,322,473 - 94,370,665 (-)NCBI
ChlSab1.1 Ensembl194,322,979 - 94,334,747 (-)Ensembl
Mmp13
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249182,228,688 - 2,239,852 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124608226Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125942267Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8210812847108128Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8210812847108128Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8210812847108128Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8210812847108128Rat

miRNA Target Status

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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2
Low 1 4 4 10 1 1
Below cutoff 2 6 2 13 2 2 2 29 11 11 8 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011507   ⟹   ENSRNOP00000011507
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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  
  P23097 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_598214   ⟸   NM_133530
- Peptide Label: precursor
- UniProtKB: G3V742 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011507   ⟸   ENSRNOT00000011507
Protein Domains
ZnMc

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620196 AgrOrtholog
Ensembl Genes ENSRNOG00000008478 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011507 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011507 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.101.10 UniProtKB/TrEMBL
  2.110.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.390.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Collagenase_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hemopexin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hemopexin-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hemopexin-like_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Hemopexin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  M10A_MMP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MetalloPept_cat_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_M10_metallopeptidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_M10A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_M10A_Zn_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_Metallo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidoglycan-bd-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PGBD-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PGBDSf UniProtKB/TrEMBL
KEGG Report rno:171052 UniProtKB/TrEMBL
NCBI Gene 171052 ENTREZGENE
PANTHER PTHR10201:SF165 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Hemopexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_M10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PG_binding_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Mmp13 PhenoGen
PIRSF Peptidase_M10A_matrix UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS MATRIXIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CYSTEINE_SWITCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HEMOPEXIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HEMOPEXIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_PROTEASE UniProtKB/Swiss-Prot
SMART SM00120 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnMc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47090 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF50923 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt 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