Mmp3 (matrix metallopeptidase 3) - Rat Genome Database
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Gene: Mmp3 (matrix metallopeptidase 3) Rattus norvegicus
Analyze
Symbol: Mmp3
Name: matrix metallopeptidase 3
RGD ID: 621317
Description: Predicted to have metalloendopeptidase activity. Involved in several processes, including cellular response to cell-matrix adhesion; cellular response to interleukin-1; and response to estradiol. Localizes to several cellular components, including cell body; dendrite; and extracellular space. Biomarker of several diseases, including abdominal aortic aneurysm; degenerative disc disease; gastric ulcer; glomerulonephritis (multiple); and primary biliary cholangitis. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); carcinoma (multiple); end stage renal disease; osteoarthritis; and von Hippel-Lindau disease. Orthologous to human MMP3 (matrix metallopeptidase 3); PARTICIPATES IN rheumatoid arthritis pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2-amino-2-deoxy-D-glucopyranose.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: matrix metalloproteinase 3; matrix metalloproteinase-3; MMP-3; PTR1 protein; SL-1; stromelysin-1; transin-1
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.085,676,608 - 5,698,579 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,676,665 - 5,698,579 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.085,680,382 - 5,701,427 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,315,601 - 4,329,146 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.184,315,600 - 4,329,146 (+)NCBI
Celera86,200,234 - 6,213,783 (+)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
abdominal aortic aneurysm  (IEP)
allergic contact dermatitis  (IEP,ISO)
Alport syndrome  (ISO)
arteriosclerosis  (ISO)
astrocytoma  (ISO)
atrial fibrillation  (ISO)
breast cancer  (ISO)
Breast Neoplasms  (ISO)
Carotid Artery Injuries  (IEP)
carotid stenosis  (ISO)
cartilage disease  (IEP)
cataract  (ISO)
celiac disease  (ISO)
Cerebral Hemorrhage  (ISO)
Chronic Allograft Nephropathy  (ISO)
cognitive disorder  (IEP)
colon cancer  (IEP)
Colorectal Neoplasms  (ISO)
congestive heart failure  (ISO)
conjunctivochalasis  (ISO)
coronary artery disease  (ISO)
Coronary Disease  (ISO)
coronary restenosis  (ISO)
crescentic glomerulonephritis  (IEP)
degenerative disc disease  (IEP)
diabetes mellitus  (ISO)
Diabetic Nephropathies  (ISO)
dry eye syndrome  (ISO)
end stage renal disease  (ISO)
Endotoxemia  (IEP)
esophagus adenocarcinoma  (ISO)
Experimental Arthritis  (IEP,ISO)
Experimental Liver Cirrhosis  (IEP)
gastric ulcer  (IEP)
glomerulonephritis  (IEP,ISO)
Gouty Arthritis  (ISO)
Hyperalgesia  (IMP,ISO)
Hypoxia-Ischemia, Brain  (IEP)
idiopathic pulmonary fibrosis  (ISO)
Immunoglobulin Light-chain Amyloidosis  (ISO)
Knee Osteoarthritis  (IMP)
lung cancer  (ISO)
lymphangioleiomyomatosis  (ISO)
Lymphatic Metastasis  (ISO)
Mammary Neoplasms, Experimental  (IMP)
myocardial infarction  (ISO)
Neoplasm Invasiveness  (ISO)
Neoplasm Metastasis  (IEP)
osteoarthritis  (ISO)
Parkinsonian Disorders  (IEP)
periodontitis  (IEP)
Peripheral Nerve Injuries  (IEP)
peripheral nervous system disease  (ISO)
polymyalgia rheumatica  (ISO)
primary biliary cholangitis  (IEP)
psoriatic arthritis  (ISO)
pulmonary fibrosis  (ISO)
pulmonary tuberculosis  (ISO)
renal cell carcinoma  (ISO)
Reperfusion Injury  (IEP)
rheumatoid arthritis  (ISO)
Sjogren's syndrome  (ISO)
Stroke  (IEP)
systemic scleroderma  (ISO)
Takayasu's arteritis  (ISO)
Tendon Injuries  (IEP)
thrombosis  (ISO)
Transplant Rejection  (ISO)
type 2 diabetes mellitus  (IEP)
Ulcer  (ISO)
Venous Thrombosis  (IEP)
von Hippel-Lindau disease  (ISO)
Wounds, Penetrating  (IEP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-citrinin  (ISO)
(R)-lipoic acid  (ISO)
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
3,4-dichloroaniline  (EXP)
3-hydroxypicolinic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
3-phenylprop-2-enal  (ISO)
4-nitroquinoline N-oxide  (ISO)
5-aminolevulinic acid  (ISO)
5-chloro-7-iodoquinolin-8-ol  (ISO)
5-fluorouracil  (ISO)
5-iodotubercidin  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
acetylsalicylic acid  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha-naphthoflavone  (EXP)
aluminium oxide  (ISO)
ammonium chloride  (EXP)
anandamide  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
avobenzone  (ISO)
azathioprine  (ISO)
azithromycin  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (EXP,ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
BQ 123  (ISO)
Butylparaben  (EXP)
C60 fullerene  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloramphenicol  (ISO)
choline  (ISO)
chondroitin sulfate  (ISO)
ciprofloxacin  (ISO)
cisplatin  (ISO)
cobalt atom  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
curcumin  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
DDT  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibenzo[a,l]pyrene  (ISO)
dieckol  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
disulfiram  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
doxycycline  (ISO)
EC 3.1.1.4 (phospholipase A2) inhibitor  (ISO)
enalapril  (ISO)
endosulfan  (EXP,ISO)
enzacamene  (EXP)
ethanol  (EXP,ISO)
farnesol  (ISO)
fluoranthene  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fucoidan  (ISO)
gemcitabine  (ISO)
genistein  (EXP)
geraniol  (ISO)
glycitein  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hyaluronic acid  (ISO)
hydroquinone  (ISO)
ibuprofen  (ISO)
Indeno[1,2,3-cd]pyrene  (ISO)
isoprenaline  (EXP,ISO)
L-methionine  (ISO)
L-proline betaine  (ISO)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
lovastatin  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
manganese(II) chloride  (EXP)
megestrol acetate  (EXP)
melittin  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
mibolerone  (ISO)
mifepristone  (ISO)
minocycline  (ISO)
moxifloxacin  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
nickel atom  (ISO)
nickel sulfate  (ISO)
nicotine  (ISO)
NSC 23766  (ISO)
ofloxacin  (EXP)
ozone  (EXP)
paclitaxel  (EXP,ISO)
paracetamol  (ISO)
paraquat  (ISO)
PD 168393  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
phenytoin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
pravastatin  (ISO)
prinomastat  (ISO)
progesterone  (ISO)
prostaglandin E2  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resorcinol  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
rofecoxib  (ISO)
SB 203580  (ISO)
serpentine asbestos  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP,ISO)
sodium arsenite  (ISO)
sodium azide  (ISO)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
streptozocin  (EXP,ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
thioacetamide  (EXP,ISO)
titanium dioxide  (ISO)
tofacitinib  (ISO)
triclosan  (ISO)
zerumbone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:1963430   PMID:2431284   PMID:2841336   PMID:9573338   PMID:11869290   PMID:12867428   PMID:15044600   PMID:15504731   PMID:15698619   PMID:15863497   PMID:16150423   PMID:17456343  
PMID:17539323   PMID:18072934   PMID:18172013   PMID:18404723   PMID:18754875   PMID:18765931   PMID:18832569   PMID:19022250   PMID:19389428   PMID:19397203   PMID:19463894   PMID:20162718  
PMID:20548288   PMID:20969476   PMID:21055467   PMID:21330369   PMID:22615070   PMID:22961837   PMID:23086831   PMID:23277113   PMID:23845380   PMID:24006456   PMID:25062286   PMID:25536219  
PMID:26047379   PMID:26075533   PMID:26087281   PMID:27339256   PMID:27425890   PMID:28265573   PMID:28753453   PMID:29197741   PMID:29462373   PMID:29523370   PMID:29928874   PMID:31493243  


Genomics

Comparative Map Data
Mmp3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.085,676,608 - 5,698,579 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,676,665 - 5,698,579 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.085,680,382 - 5,701,427 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,315,601 - 4,329,146 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.184,315,600 - 4,329,146 (+)NCBI
Celera86,200,234 - 6,213,783 (+)NCBICelera
Cytogenetic Map8q11NCBI
MMP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11102,835,801 - 102,843,609 (-)EnsemblGRCh38hg38GRCh38
GRCh3811102,835,801 - 102,843,609 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711102,706,528 - 102,714,342 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611102,211,738 - 102,219,552 (-)NCBINCBI36hg18NCBI36
Build 3411102,211,742 - 102,219,550NCBI
Celera1199,868,135 - 99,875,949 (-)NCBI
Cytogenetic Map11q22.2NCBI
HuRef1198,634,450 - 98,642,264 (-)NCBIHuRef
CHM1_111102,589,497 - 102,597,395 (-)NCBICHM1_1
Mmp3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3997,445,822 - 7,455,975 (+)NCBIGRCm39mm39
GRCm3897,445,822 - 7,455,975 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl97,445,822 - 7,455,975 (+)EnsemblGRCm38mm10GRCm38
MGSCv3797,445,822 - 7,455,975 (+)NCBIGRCm37mm9NCBIm37
MGSCv3697,445,822 - 7,455,975 (+)NCBImm8
Celera94,846,374 - 4,856,527 (+)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
MMP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111101,267,561 - 101,275,432 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11101,267,566 - 101,275,354 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01197,776,729 - 97,784,549 (-)NCBIMhudiblu_PPA_v0panPan3
MMP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl528,949,631 - 28,958,222 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1528,949,631 - 28,957,915 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
MMP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl933,411,065 - 33,454,000 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1933,446,969 - 33,453,995 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2937,394,116 - 37,401,146 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MMP3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1194,216,156 - 94,224,437 (-)NCBI
ChlSab1.1 Ensembl194,216,173 - 94,224,264 (-)Ensembl
Mmp3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462487839,282 - 47,386 (+)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:26
Count of miRNA genes:26
Interacting mature miRNAs:26
Transcripts:ENSRNOT00000012310
Prediction methods:Miranda, Rnahybrid
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 circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 6 3 4 10
Below cutoff 3 4 14 7 11 7 6 8 26 13 20 8 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012310   ⟹   ENSRNOP00000012310
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl85,676,665 - 5,698,237 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091704   ⟹   ENSRNOP00000075241
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl85,686,298 - 5,698,579 (+)Ensembl
RefSeq Acc Id: NM_133523   ⟹   NP_598207
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.085,676,608 - 5,698,579 (+)NCBI
Rnor_5.085,680,382 - 5,701,427 (+)NCBI
RGSC_v3.484,315,601 - 4,329,146 (+)RGD
Celera86,200,234 - 6,213,783 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_598207 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA26448 (Get FASTA)   NCBI Sequence Viewer  
  EDL78534 (Get FASTA)   NCBI Sequence Viewer  
  EDL78535 (Get FASTA)   NCBI Sequence Viewer  
  P03957 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_598207   ⟸   NM_133523
- Peptide Label: preproprotein
- Sequence:
RefSeq Acc Id: ENSRNOP00000012310   ⟸   ENSRNOT00000012310
RefSeq Acc Id: ENSRNOP00000075241   ⟸   ENSRNOT00000091704
Protein Domains
ZnMc

Transcriptome

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

Promoters
RGD ID:13695737
Promoter ID:EPDNEW_R6257
Type:single initiation site
Name:Mmp3_1
Description:matrix metallopeptidase 3
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_6.085,676,607 - 5,676,667EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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:621317 AgrOrtholog
Ensembl Genes ENSRNOG00000032626 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012310 UniProtKB/TrEMBL
  ENSRNOP00000075241 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012310 UniProtKB/TrEMBL
  ENSRNOT00000091704 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.110.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.40.390.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro 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
  Peptidase_Metallo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidoglycan-bd-like UniProtKB/Swiss-Prot
  PGBD-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 171045 ENTREZGENE
Pfam Hemopexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_M10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PG_binding_1 UniProtKB/Swiss-Prot
PharmGKB MMP3 RGD
PhenoGen Mmp3 PhenoGen
PIRSF Peptidase_M10A_matrix UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS MATRIXIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CYSTEINE_SWITCH UniProtKB/Swiss-Prot
  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
UniGene Rn.32086 ENTREZGENE
UniProt A0A0G2KA34_RAT UniProtKB/TrEMBL
  F1LPL9_RAT UniProtKB/TrEMBL
  MMP3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Mmp3  matrix metallopeptidase 3    matrix metalloproteinase 3  Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Mmp3  matrix metalloproteinase 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_process may have an important role during early tooth development 729121