Mmp16 (matrix metallopeptidase 16) - Rat Genome Database

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Gene: Mmp16 (matrix metallopeptidase 16) Rattus norvegicus
Analyze
Symbol: Mmp16
Name: matrix metallopeptidase 16
RGD ID: 620199
Description: Predicted to enable metalloaminopeptidase activity; metalloendopeptidase activity; and zinc ion binding activity. Involved in response to odorant. Predicted to be located in extracellular matrix and extracellular region. Predicted to be integral component of plasma membrane. Orthologous to human MMP16 (matrix metallopeptidase 16); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol 3-benzoate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: matrix metalloproteinase 16; matrix metalloproteinase-16; membrane-type matrix metalloproteinase 3; membrane-type-3 matrix metalloproteinase; MMP-16; MT-MMP 3; Mt3-mmp; MT3MMP; MTMMP3
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
mRatBN7.2531,312,280 - 31,556,276 (+)NCBI
Rnor_6.0 Ensembl531,568,419 - 31,810,484 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0531,568,344 - 31,818,368 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0536,239,463 - 36,484,341 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4532,352,311 - 32,586,469 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1532,352,489 - 32,586,648 (+)NCBI
Celera530,477,009 - 30,710,815 (+)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
amitriptyline  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
Butylbenzyl phthalate  (ISO)
calcitriol  (ISO)
cefaloridine  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (ISO)
coumestrol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
diethyl phthalate  (ISO)
diisobutyl phthalate  (ISO)
diisononyl phthalate  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
elemental selenium  (ISO)
entinostat  (ISO)
geldanamycin  (ISO)
genistein  (ISO)
mercury dibromide  (ISO)
methotrexate  (ISO)
methylmercury chloride  (ISO)
mifepristone  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel sulfate  (ISO)
paclitaxel  (ISO)
paracetamol  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP)
potassium chromate  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium fluoride  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
thimerosal  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:7559440   PMID:18022611   PMID:18784838   PMID:24970228   PMID:27229514  


Genomics

Candidate Gene Status
Mmp16 is a candidate Gene for QTL Vetf3
Comparative Map Data
Mmp16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2531,312,280 - 31,556,276 (+)NCBI
Rnor_6.0 Ensembl531,568,419 - 31,810,484 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0531,568,344 - 31,818,368 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0536,239,463 - 36,484,341 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4532,352,311 - 32,586,469 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1532,352,489 - 32,586,648 (+)NCBI
Celera530,477,009 - 30,710,815 (+)NCBICelera
Cytogenetic Map5q13NCBI
MMP16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl888,032,011 - 88,328,025 (-)EnsemblGRCh38hg38GRCh38
GRCh38888,032,009 - 88,327,483 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37889,044,239 - 89,339,712 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36889,118,576 - 89,408,833 (-)NCBINCBI36hg18NCBI36
Build 34889,150,576 - 89,408,664NCBI
Celera885,244,102 - 85,534,339 (-)NCBI
Cytogenetic Map8q21.3NCBI
HuRef884,259,378 - 84,549,728 (-)NCBIHuRef
CHM1_1889,091,126 - 89,381,311 (-)NCBICHM1_1
Mmp16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39417,853,072 - 18,117,479 (+)NCBIGRCm39mm39
GRCm39 Ensembl417,852,893 - 18,119,145 (+)Ensembl
GRCm38417,853,072 - 18,117,479 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl417,852,893 - 18,119,145 (+)EnsemblGRCm38mm10GRCm38
MGSCv37417,780,629 - 18,045,881 (+)NCBIGRCm37mm9NCBIm37
MGSCv36417,780,629 - 18,043,779 (+)NCBImm8
Celera417,643,862 - 17,905,148 (+)NCBICelera
Cytogenetic Map4A3NCBI
cM Map47.08NCBI
Mmp16
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554175,303,290 - 5,545,589 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554175,298,334 - 5,545,121 (-)NCBIChiLan1.0ChiLan1.0
MMP16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1886,693,022 - 86,983,028 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl886,701,882 - 86,982,518 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0884,736,752 - 85,026,711 (-)NCBIMhudiblu_PPA_v0panPan3
MMP16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12933,896,133 - 34,207,560 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2933,917,907 - 34,207,466 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2934,056,176 - 34,360,687 (-)NCBI
ROS_Cfam_1.02934,093,268 - 34,403,773 (-)NCBI
UMICH_Zoey_3.12934,106,198 - 34,398,221 (-)NCBI
UNSW_CanFamBas_1.02934,114,566 - 34,418,869 (-)NCBI
UU_Cfam_GSD_1.02934,536,488 - 34,840,936 (-)NCBI
Mmp16
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530345,246,022 - 45,504,496 (+)NCBI
SpeTri2.0NW_0049365442,297,698 - 2,546,683 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MMP16
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl448,556,967 - 48,862,986 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1448,556,826 - 48,867,959 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2453,295,213 - 53,606,489 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MMP16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1883,122,904 - 83,407,910 (-)NCBI
ChlSab1.1 Ensembl883,132,315 - 83,407,933 (-)Ensembl
Vero_WHO_p1.0NW_02366603957,498,698 - 57,789,347 (+)NCBI
Mmp16
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247443,544,258 - 3,806,097 (+)NCBI

Position Markers
D5Wox36  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2531,547,367 - 31,547,578 (+)MAPPER
Rnor_6.0531,809,466 - 31,809,674NCBIRnor6.0
Rnor_5.0536,478,685 - 36,478,893UniSTSRnor5.0
RGSC_v3.4532,585,451 - 32,585,659UniSTSRGSC3.4
Celera530,709,797 - 30,710,005UniSTS
Cytogenetic Map5q13UniSTS
AW532313  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2531,360,600 - 31,360,759 (+)MAPPER
Rnor_6.0531,616,409 - 31,616,567NCBIRnor6.0
Rnor_5.0536,287,477 - 36,287,635UniSTSRnor5.0
RGSC_v3.4532,400,967 - 32,401,125UniSTSRGSC3.4
Celera530,525,242 - 30,525,400UniSTS
RH 3.4 Map5162.72UniSTS
Cytogenetic Map5q13UniSTS
AB021228  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2531,547,101 - 31,547,244 (+)MAPPER
Rnor_6.0531,809,200 - 31,809,342NCBIRnor6.0
Rnor_5.0536,478,419 - 36,478,561UniSTSRnor5.0
RGSC_v3.4532,585,185 - 32,585,327UniSTSRGSC3.4
Celera530,709,531 - 30,709,673UniSTS
Cytogenetic Map5q13UniSTS
BE115606  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2531,548,182 - 31,548,350 (+)MAPPER
Rnor_6.0531,810,279 - 31,810,446NCBIRnor6.0
Rnor_5.0536,479,498 - 36,479,665UniSTSRnor5.0
RGSC_v3.4532,586,264 - 32,586,431UniSTSRGSC3.4
Celera530,710,610 - 30,710,777UniSTS
RH 3.4 Map5162.82UniSTS
Cytogenetic Map5q13UniSTS
MMP16_920  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2531,546,930 - 31,547,841 (+)MAPPER
Rnor_6.0531,809,029 - 31,809,937NCBIRnor6.0
Rnor_5.0536,478,248 - 36,479,156UniSTSRnor5.0
RGSC_v3.4532,585,014 - 32,585,922UniSTSRGSC3.4
Celera530,709,360 - 30,710,268UniSTS
Cytogenetic Map5q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51328888858288888Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51884791363847913Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51884791376608178Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52190436366904363Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52495621244747071Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52907889974078899Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52907889974078899Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52964166174641661Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52964166174641661Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:583
Count of miRNA genes:265
Interacting mature miRNAs:342
Transcripts:ENSRNOT00000050137
Prediction methods:Microtar, Miranda, Targetscan
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 2 2 2 72 12 28 9
Low 3 37 54 39 18 39 7 7 2 12 13 2 7
Below cutoff 6 1 1 1 4 11 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050137   ⟹   ENSRNOP00000040229
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl531,568,419 - 31,810,484 (+)Ensembl
RefSeq Acc Id: NM_080776   ⟹   NP_542954
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2531,312,280 - 31,556,276 (+)NCBI
Rnor_6.0531,568,419 - 31,810,484 (+)NCBI
Rnor_5.0536,239,463 - 36,484,341 (+)NCBI
RGSC_v3.4532,352,311 - 32,586,469 (+)RGD
Celera530,477,009 - 30,710,815 (+)RGD
Sequence:
RefSeq Acc Id: XM_039110732   ⟹   XP_038966660
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2531,468,802 - 31,556,274 (+)NCBI
Protein Sequences
Protein RefSeqs NP_542954 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966660 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA22223 (Get FASTA)   NCBI Sequence Viewer  
  EDL98489 (Get FASTA)   NCBI Sequence Viewer  
  EDL98490 (Get FASTA)   NCBI Sequence Viewer  
  O35548 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_542954   ⟸   NM_080776
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSRNOP00000040229   ⟸   ENSRNOT00000050137
RefSeq Acc Id: XP_038966660   ⟸   XM_039110732
- Peptide Label: isoform X1
Protein Domains
ZnMc

Transcriptome

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

Promoters
RGD ID:13693583
Promoter ID:EPDNEW_R4108
Type:initiation region
Name:Mmp16_1
Description:matrix metallopeptidase 16
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_6.0531,568,431 - 31,568,491EPDNEW

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)
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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:620199 AgrOrtholog
Ensembl Genes ENSRNOG00000005708 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040229 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050137 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
  MMP16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_M10_metallopeptidase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_M10A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Pept_M10A_metallopeptidase_C UniProtKB/Swiss-Prot
  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
KEGG Report rno:65205 UniProtKB/Swiss-Prot
NCBI Gene 65205 ENTREZGENE
PANTHER PTHR10201:SF26 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF3377 UniProtKB/Swiss-Prot
  Hemopexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_M10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PG_binding_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Mmp16 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 F1M7F5_RAT UniProtKB/TrEMBL
  MMP16_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary O35541 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-22 Mmp16  matrix metallopeptidase 16  Mmp16  matrix metalloproteinase 16  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Mmp16  matrix metalloproteinase 16      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Mmp16        Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_function cleaves endogenous progelatinase A to its mature form 729074
gene_protein 607 amino acids 729074