Mmp12 (matrix metallopeptidase 12) - Rat Genome Database

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Gene: Mmp12 (matrix metallopeptidase 12) Rattus norvegicus
Analyze
Symbol: Mmp12
Name: matrix metallopeptidase 12
RGD ID: 620195
Description: Predicted to enable several functions, including core promoter sequence-specific DNA binding activity; metal ion binding activity; and metalloendopeptidase activity. Involved in several processes, including positive regulation of epithelial cell proliferation; regulation of trophoblast cell migration; and response to hypoxia. Predicted to be located in cytoplasm; extracellular space; and nucleus. Used to study crescentic glomerulonephritis. Biomarker of anti-basement membrane glomerulonephritis and crescentic glomerulonephritis. Human ortholog(s) of this gene implicated in Barrett's esophagus; artery disease (multiple); coronary aneurysm; esophagus adenocarcinoma; and multiple sclerosis. Orthologous to human MMP12 (matrix metallopeptidase 12); INTERACTS WITH (R)-lipoic acid; 1,2-dimethylhydrazine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: macrophage metalloelastase; matrix metalloproteinase 12; matrix metalloproteinase-12; Mme; MMP-12
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Mmp12em1Soar   Mmp12em2Soar  
Genetic Models: SD-Mmp12em2Soar SD-Mmp12em1Soar
Is Marker For: Strains:   SD-Mmp12em1Soar  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.284,581,785 - 4,591,687 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl84,581,785 - 4,599,611 (+)Ensembl
Rnor_6.085,594,717 - 5,616,494 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,606,592 - 5,616,493 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.085,610,392 - 5,620,294 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,249,938 - 4,259,675 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.184,249,937 - 4,259,675 (+)NCBI
Celera86,141,589 - 6,151,491 (+)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-lipoic acid  (EXP)
1,2-dimethylhydrazine  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-nitroquinoline N-oxide  (ISO)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
acetohydroxamic acid  (ISO)
acrolein  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (EXP)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
aprepitant  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
barium sulfate  (EXP)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (EXP)
beta-hexachlorocyclohexane  (ISO)
beta-naphthoflavone  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
capsaicin  (ISO)
carbon atom  (ISO)
carbon nanotube  (EXP,ISO)
catechol  (ISO)
cefaloridine  (EXP)
ceric oxide  (EXP,ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cysteamine  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenziodolium  (ISO)
diclofenac  (ISO)
diethyl maleate  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
elemental carbon  (ISO)
Erionite  (ISO)
ethanol  (ISO)
fenbuconazole  (ISO)
ferric oxide  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (ISO)
graphite  (EXP)
indole-3-methanol  (EXP)
L-methionine  (ISO)
linuron  (ISO)
lipoic acid  (EXP)
lipopolysaccharide  (ISO)
LY294002  (ISO)
megestrol acetate  (EXP)
metacetamol  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
N-acetyl-L-cysteine  (ISO)
N-hydroxyacetimidic acid  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (ISO)
nickel sulfate  (ISO)
O-methyleugenol  (ISO)
octadecanoic acid  (ISO)
orphenadrine  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
PhIP  (EXP)
pioglitazone  (ISO)
prednisolone  (ISO)
progesterone  (ISO)
quartz  (EXP)
quercetin  (ISO)
raloxifene  (ISO)
rottlerin  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
simvastatin  (ISO)
sodium fluoride  (EXP)
succimer  (ISO)
T-2 toxin  (ISO)
tamoxifen  (ISO)
Tesaglitazar  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (EXP,ISO)
topotecan  (EXP)
tremolite asbestos  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
wortmannin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO)
extracellular matrix  (IEA)
extracellular space  (IEA,ISO)
nucleus  (IEA,ISO)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
1. Behmoaras J, etal., J Am Soc Nephrol. 2010 May 20.
2. Bradbury PA, etal., Carcinogenesis. 2009 May;30(5):793-8. doi: 10.1093/carcin/bgp065. Epub 2009 Mar 25.
3. Chakraborty D, etal., Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):E7212-E7221. Epub 2016 Nov 2.
4. Cheung C, etal., Cardiovasc Pathol. 2006 Mar-Apr;15(2):63-74.
5. Eriksson P, etal., Br J Surg. 2005 Nov;92(11):1372-6.
6. Fu JY, etal., Protein Expr Purif. 2001 Mar;21(2):268-74.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Hagemann T, etal., Eur J Cancer. 2001 Oct;37(15):1839-46.
9. Ikonomidis JS, etal., Circulation. 2006 Jul 4;114(1 Suppl):I365-70.
10. Johnson JL, etal., Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15575-80. Epub 2005 Oct 12.
11. Jormsjo S, etal., Circ Res. 2000 May 12;86(9):998-1003.
12. Kaneko Y, etal., J Immunol 2003 Mar 15;170(6):3377-85.
13. Kure M, etal., Mol Genet Metab. 2011 May;103(1):60-5. doi: 10.1016/j.ymgme.2011.01.001. Epub 2011 Jan 14.
14. Lamblin N, etal., J Am Coll Cardiol. 2002 Jul 3;40(1):43-8.
15. Lyu J and Joo CK, J Biol Chem. 2005 Jun 3;280(22):21653-60. Epub 2005 Mar 31.
16. MGD data from the GO Consortium
17. Mirowska-Guzel D, etal., J Neuroimmunol. 2009 Sep 29;214(1-2):113-7. doi: 10.1016/j.jneuroim.2009.06.014. Epub 2009 Jul 22.
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Okada S, etal., FASEB J. 2008 Oct;22(10):3672-84. doi: 10.1096/fj.08-111872. Epub 2008 Jul 7.
20. Power C, etal., Ann Neurol. 2003 Jun;53(6):731-42.
21. Rao VH, etal., Am J Pathol. 2006 Jul;169(1):32-46.
22. RGD automated data pipeline
23. RGD automated import pipeline for gene-chemical interactions
24. Ryan J, etal., Lab Invest. 2011 Dec;91(12):1727-38. doi: 10.1038/labinvest.2011.137. Epub 2011 Sep 5.
25. Verschuren L, etal., Antioxid Redox Signal. 2005 Sep-Oct;7(9-10):1195-202.
26. Wells JE, etal., Eur J Neurosci. 2005 Jan;21(1):187-96.
27. Xu L, etal., Chin Med J (Engl). 2004 Nov;117(11):1611-9.
28. Zhang B, etal., Stroke. 2001 Sep;32(9):2198-202.
Additional References at PubMed
PMID:11575928   PMID:12477932   PMID:15489334   PMID:19932771   PMID:22223197   PMID:22730688   PMID:23619615   PMID:24006456   PMID:24784232   PMID:24907602   PMID:25595645   PMID:25955565  
PMID:26534974   PMID:29101312   PMID:29428638  


Genomics

Comparative Map Data
Mmp12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.284,581,785 - 4,591,687 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl84,581,785 - 4,599,611 (+)Ensembl
Rnor_6.085,594,717 - 5,616,494 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,606,592 - 5,616,493 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.085,610,392 - 5,620,294 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,249,938 - 4,259,675 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.184,249,937 - 4,259,675 (+)NCBI
Celera86,141,589 - 6,151,491 (+)NCBICelera
Cytogenetic Map8q11NCBI
MMP12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11102,862,736 - 102,874,982 (-)EnsemblGRCh38hg38GRCh38
GRCh3811102,862,736 - 102,874,982 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711102,733,467 - 102,745,712 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611102,238,674 - 102,250,922 (-)NCBINCBI36hg18NCBI36
Build 3411102,238,685 - 102,250,889NCBI
Celera1199,895,056 - 99,907,358 (-)NCBI
Cytogenetic Map11q22.2NCBI
HuRef1198,661,485 - 98,673,788 (-)NCBIHuRef
CHM1_111102,616,439 - 102,628,740 (-)NCBICHM1_1
Mmp12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3997,344,397 - 7,360,461 (+)NCBIGRCm39mm39
GRCm39 Ensembl97,344,381 - 7,369,499 (+)Ensembl
GRCm3897,344,397 - 7,360,461 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl97,344,381 - 7,369,499 (+)EnsemblGRCm38mm10GRCm38
MGSCv3797,347,374 - 7,360,461 (+)NCBIGRCm37mm9NCBIm37
MGSCv3697,347,406 - 7,360,461 (+)NCBImm8
Celera94,747,651 - 4,760,738 (+)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Mmp12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554126,045,100 - 6,057,262 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554126,045,146 - 6,057,112 (-)NCBIChiLan1.0ChiLan1.0
MMP12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111101,294,469 - 101,306,762 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11101,294,475 - 101,306,762 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01197,809,644 - 97,822,063 (-)NCBIMhudiblu_PPA_v0panPan3
MMP12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1528,918,626 - 28,933,404 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl528,918,594 - 28,933,309 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha528,867,153 - 28,881,802 (+)NCBI
ROS_Cfam_1.0528,944,813 - 28,984,612 (+)NCBI
UMICH_Zoey_3.1529,004,848 - 29,019,524 (+)NCBI
UNSW_CanFamBas_1.0528,884,303 - 28,898,943 (+)NCBI
UU_Cfam_GSD_1.0529,059,239 - 29,073,925 (+)NCBI
Mmp12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494786,418,317 - 86,430,234 (-)NCBI
SpeTri2.0NW_0049365515,107,567 - 5,117,843 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MMP12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl933,473,085 - 33,483,679 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1933,473,625 - 33,483,630 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2937,421,192 - 37,431,173 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MMP12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1194,243,061 - 94,261,035 (-)NCBI
ChlSab1.1 Ensembl194,243,875 - 94,259,591 (-)Ensembl
Vero_WHO_p1.0NW_02366604331,622,735 - 31,635,226 (+)NCBI
Mmp12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248786,017 - 17,368 (+)NCBI


QTLs in Region (mRatBN7.2)
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)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat


Related Rat Strains
The following Strains have been annotated to Mmp12


Genetic Models
This gene Mmp12 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:37
Interacting mature miRNAs:43
Transcripts:ENSRNOT00000011727
Prediction methods:Miranda, Rnahybrid, 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 1 8 13 3 1
Low 1 9 10 5 6 5 14 4 10
Below cutoff 1 20 22 19 19 5 5 21 19 24 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011727   ⟹   ENSRNOP00000011727
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl84,581,785 - 4,591,686 (+)Ensembl
Rnor_6.0 Ensembl85,606,592 - 5,616,493 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106835   ⟹   ENSRNOP00000081814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl84,581,785 - 4,599,611 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109288   ⟹   ENSRNOP00000091196
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl84,582,892 - 4,591,686 (+)Ensembl
RefSeq Acc Id: NM_053963   ⟹   NP_446415
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.284,581,785 - 4,591,687 (+)NCBI
Rnor_6.085,606,592 - 5,616,494 (+)NCBI
Rnor_5.085,610,392 - 5,620,294 (+)NCBI
RGSC_v3.484,249,938 - 4,259,675 (+)RGD
Celera86,141,589 - 6,151,491 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446415 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88120 (Get FASTA)   NCBI Sequence Viewer  
  CAA67142 (Get FASTA)   NCBI Sequence Viewer  
  EDL78537 (Get FASTA)   NCBI Sequence Viewer  
  Q63341 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446415   ⟸   NM_053963
- Peptide Label: preproprotein
- UniProtKB: Q63341 (UniProtKB/Swiss-Prot),   R9PXT7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011727   ⟸   ENSRNOT00000011727
RefSeq Acc Id: ENSRNOP00000081814   ⟸   ENSRNOT00000106835
RefSeq Acc Id: ENSRNOP00000091196   ⟸   ENSRNOT00000109288
Protein Domains
ZnMc

Transcriptome

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

Promoters
RGD ID:13695732
Promoter ID:EPDNEW_R6256
Type:single initiation site
Name:Mmp12_1
Description:matrix metallopeptidase 12
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_6.085,606,581 - 5,606,641EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
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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)
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:620195 AgrOrtholog
Ensembl Genes ENSRNOG00000030187 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011727 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011727 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
IMAGE_CLONE IMAGE:7380302 IMAGE-MGC_LOAD
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
  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:117033 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:108621 IMAGE-MGC_LOAD
NCBI Gene 117033 ENTREZGENE
Pfam Hemopexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_M10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PG_binding_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Mmp12 PhenoGen
PIRSF Peptidase_M10A_matrix UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS MATRIXIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE 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 MMP12_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  R9PXT7 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q5I0P0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Mmp12  matrix metallopeptidase 12    matrix metalloproteinase 12  Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Mmp12  matrix metalloproteinase 12      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease may play a role in crescentic glomerulonephritis 737630
gene_expression highly expressed in kidneys on days 3 and 7 after the injection of anti-glomerular basement membrane antiserum 737630