Mmp7 (matrix metallopeptidase 7) - Rat Genome Database

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Gene: Mmp7 (matrix metallopeptidase 7) Rattus norvegicus
Analyze
Symbol: Mmp7
Name: matrix metallopeptidase 7
RGD ID: 3100
Description: Enables heparin binding activity. Involved in several processes, including cellular response to mechanical stimulus; estrous cycle; and maternal process involved in female pregnancy. Located in cell surface and extracellular space. Used to study hypertension and prostate carcinoma. Biomarker of bladder neck obstruction; coronary restenosis; hypertension; prostate cancer; and renal hypertension. Orthologous to human MMP7 (matrix metallopeptidase 7); PARTICIPATES IN syndecan signaling pathway; Wnt signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: matrilysin; matrin; matrix metalloproteinase 7; Matrix metalloproteinase 7 (matrilysin); matrix metalloproteinase-7; MMP-7; MPMM; pump-1 protease; uterine metalloproteinase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.284,848,186 - 4,855,908 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl84,848,186 - 4,855,902 (+)Ensembl
Rnor_6.085,893,253 - 5,900,965 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,893,249 - 5,901,049 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.085,895,393 - 5,903,105 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,526,018 - 4,533,730 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.184,526,033 - 4,533,729 (+)NCBI
Celera86,407,543 - 6,415,255 (+)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(E)-thiamethoxam  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3,7-dihydropurine-6-thione  (EXP)
3-[3-(tert-butylsulfanyl)-1-(4-chlorobenzyl)-5-(propan-2-yl)-1H-indol-2-yl]-2,2-dimethylpropanoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
7,12-dimethyltetraphene  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
aluminium atom  (ISO)
aluminium(0)  (ISO)
ammonium chloride  (EXP)
andrographolide  (ISO)
antimonite  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzyl isothiocyanate  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
BQ 123  (ISO)
butyric acid  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
caffeine  (ISO)
calcitriol  (ISO)
carbon nanotube  (EXP,ISO)
celastrol  (ISO)
chlordecone  (ISO)
choline  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clozapine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
Deguelin  (ISO)
delta-tocotrienol  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diallyl disulfide  (ISO)
Diallyl sulfide  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
ergosta-4,6,8(14),22-tetraen-3-one  (ISO)
ethanol  (ISO)
fenofibrate  (ISO)
ferric oxide  (ISO)
folic acid  (EXP,ISO)
furan  (EXP)
gallic acid  (ISO)
Garcinol  (ISO)
genistein  (ISO)
graphite  (EXP)
GW 4064  (ISO)
Honokiol  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
lithium chloride  (ISO)
losartan  (ISO)
mangiferin  (ISO)
mercaptopurine  (EXP)
methotrexate  (ISO)
mibolerone  (ISO)
mifepristone  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (ISO)
niclosamide  (EXP,ISO)
nicotine  (ISO)
nitroglycerin  (ISO)
nobiletin  (ISO)
Pachymic acid  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
permethrin  (EXP)
phenethyl isothiocyanate  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pinosylvin  (ISO)
pioglitazone  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
pterostilbene  (ISO)
purine-6-thiol  (EXP)
quercetin  (ISO)
resveratrol  (ISO)
riddelliine  (EXP)
salicylates  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
sulindac  (ISO)
sulindac sulfone  (ISO)
Tanshinone I  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thiamethoxam  (ISO)
thymoquinone  (ISO)
titanium dioxide  (EXP,ISO)
trans-pinosylvin  (ISO)
trichloroacetaldehyde  (ISO)
tyrphostin AG 1478  (ISO)
valproic acid  (ISO)
zearalenone  (EXP)
zinc dichloride  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Abramson SR, etal., J Biol Chem 1995 Jul 7;270(27):16016-22.
2. Anwaruddin S, etal., Am J Clin Pathol. 2005 Jan;123(1):140-5.
3. Asamoto M, etal., Cancer Res. 2001 Jun 15;61(12):4693-700.
4. Boixel C, etal., J Am Coll Cardiol. 2003 Jul 16;42(2):336-44.
5. Camp TM, etal., J Hypertens 2003 Sep;21(9):1719-27.
6. Chen G, etal., Am J Physiol Renal Physiol. 2007 Oct;293(4):F1272-81. Epub 2007 Aug 1.
7. Chieng-Yane P, etal., J Pharmacol Exp Ther. 2011 Mar;336(3):643-51. doi: 10.1124/jpet.110.175182. Epub 2010 Dec 7.
8. Feng J, etal., J Reprod Fertil. 1998 Nov;114(2):347-50.
9. Flogel U, etal., FASEB J. 2004 Jul;18(10):1156-8. Epub 2004 May 7.
10. Gantus MA, etal., Brain Res. 2006 Nov 29;1122(1):36-46. Epub 2006 Oct 6.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. Giannocco G, etal., Mol Cell Endocrinol. 2004 Oct 29;226(1-2):19-26.
13. GOA data from the GO Consortium
14. Hu BH, etal., J Neurosci. 2012 Oct 24;32(43):14927-41. doi: 10.1523/JNEUROSCI.1588-12.2012.
15. Ji J, etal., Transplantation. 2010 Apr 27;89(8):945-53. doi: 10.1097/TP.0b013e3181d05aa7.
16. Jovanovic V, etal., J Immunol. 2008 Feb 1;180(3):1317-25.
17. Kieseier BC, etal., Ann Neurol. 1998 Apr;43(4):427-34.
18. Kieseier BC, etal., Brain. 1998 Jan;121 ( Pt 1):159-66.
19. Lin PC, etal., J Physiol. 2006 Oct 12;.
20. Lindsey ML, etal., Circulation. 2006 Jun 27;113(25):2919-28. Epub 2006 Jun 12.
21. Lu PC, etal., Invest Ophthalmol Vis Sci. 1999 Jan;40(1):20-7.
22. Lynch CC, etal., Cancer Cell. 2005 May;7(5):485-96.
23. MGD data from the GO Consortium
24. Nakano A, etal., J Neurosurg. 1995 Aug;83(2):298-307.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. Obokata A, etal., Anticancer Res. 2007 Jan-Feb;27(1A):95-105.
27. Okumura N, etal., Proteomics. 2005 Jul;5(11):2896-906.
28. Pipeline to import KEGG annotations from KEGG into RGD
29. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
30. Rechtman MP, etal., J Reprod Fertil. 1999 Sep;117(1):169-77.
31. RGD automated data pipeline
32. RGD automated import pipeline for gene-chemical interactions
33. Rudolph-Owen LA, etal., Cancer Res. 1998 Dec 1;58(23):5500-6.
34. Safranek J, etal., Anticancer Res. 2009 Jul;29(7):2513-7.
35. Schroder A, etal., J Urol. 2013 Jun;189(6):2377-84. doi: 10.1016/j.juro.2012.12.110. Epub 2013 Jan 9.
36. Seiyama A Dyn Med. 2006 Jan 24;5:3.
37. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
38. Tanasijevic MJ J Thromb Thrombolysis. 2005 Feb;19(1):21-4.
39. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
40. Villar J, etal., Intensive Care Med. 2011 Jul;37(7):1201-9. doi: 10.1007/s00134-011-2234-0. Epub 2011 May 13.
41. Villar J, etal., PLoS One. 2011;6(9):e23914. doi: 10.1371/journal.pone.0023914. Epub 2011 Sep 15.
42. Wang X, etal., Circulation. 2009 May 12;119(18):2480-9. doi: 10.1161/CIRCULATIONAHA.108.835488. Epub 2009 Apr 27.
43. Yang HM, etal., Zhongguo Wei Zhong Bing Ji Jiu Yi Xue. 2004 Jun;16(6):345-7.
44. Yerrapureddy A, etal., Cell Physiol Biochem. 2010;25(1):113-22. doi: 10.1159/000272056. Epub 2009 Dec 22.
45. Yu WH and Woessner JF Jr, J Biol Chem. 2000 Feb 11;275(6):4183-91.
46. Yuan Q, etal., Zhongguo Gu Shang. 2012 Sep;25(9):761-5.
Additional References at PubMed
PMID:9037065   PMID:11248802   PMID:14656925   PMID:15297466   PMID:15489334   PMID:17554258   PMID:18644839   PMID:20056603   PMID:20655064   PMID:22238106   PMID:23376485   PMID:23533145  
PMID:23845380   PMID:23870463   PMID:26482249   PMID:28626073   PMID:31493243   PMID:31791378  


Genomics

Comparative Map Data
Mmp7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.284,848,186 - 4,855,908 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl84,848,186 - 4,855,902 (+)Ensembl
Rnor_6.085,893,253 - 5,900,965 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,893,249 - 5,901,049 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.085,895,393 - 5,903,105 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,526,018 - 4,533,730 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.184,526,033 - 4,533,729 (+)NCBI
Celera86,407,543 - 6,415,255 (+)NCBICelera
Cytogenetic Map8q11NCBI
MMP7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11102,520,508 - 102,530,750 (-)EnsemblGRCh38hg38GRCh38
GRCh3811102,520,508 - 102,530,747 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711102,391,239 - 102,401,478 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611101,896,449 - 101,906,688 (-)NCBINCBI36hg18NCBI36
Build 3411101,896,448 - 101,906,688NCBI
Celera1199,552,782 - 99,563,021 (-)NCBI
Cytogenetic Map11q22.2NCBI
HuRef1198,318,241 - 98,328,480 (-)NCBIHuRef
CHM1_111102,274,287 - 102,284,528 (-)NCBICHM1_1
Mmp7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3997,692,091 - 7,699,586 (+)NCBIGRCm39mm39
GRCm39 Ensembl97,692,091 - 7,699,586 (+)Ensembl
GRCm3897,692,090 - 7,699,585 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl97,692,090 - 7,699,585 (+)EnsemblGRCm38mm10GRCm38
MGSCv3797,692,111 - 7,699,416 (+)NCBIGRCm37mm9NCBIm37
MGSCv3697,692,097 - 7,699,255 (+)NCBImm8
Celera95,082,790 - 5,090,191 (+)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Mmp7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554125,778,502 - 5,792,445 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554125,780,772 - 5,792,485 (-)NCBIChiLan1.0ChiLan1.0
MMP7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111100,960,107 - 100,970,355 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11100,960,032 - 100,971,099 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01197,467,037 - 97,477,305 (-)NCBIMhudiblu_PPA_v0panPan3
MMP7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1529,187,902 - 29,196,157 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl529,187,851 - 29,196,153 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha529,135,576 - 29,143,842 (+)NCBI
ROS_Cfam_1.0529,239,121 - 29,247,375 (+)NCBI
UMICH_Zoey_3.1529,273,927 - 29,282,176 (+)NCBI
UNSW_CanFamBas_1.0529,153,310 - 29,161,571 (+)NCBI
UU_Cfam_GSD_1.0529,328,802 - 29,337,062 (+)NCBI
Mmp7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494786,138,756 - 86,148,072 (-)NCBI
SpeTri2.0NW_0049365515,388,456 - 5,395,071 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MMP7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl933,214,594 - 33,225,080 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1933,214,590 - 33,225,080 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2937,133,037 - 37,143,432 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MMP7
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1193,889,189 - 93,901,077 (-)NCBI
ChlSab1.1 Ensembl193,889,198 - 93,899,587 (-)Ensembl
Vero_WHO_p1.0NW_02366604331,959,442 - 31,969,839 (+)NCBI
Mmp7
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624878345,038 - 364,986 (+)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
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:30
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000014041
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 1
Medium 1 4 1
Low 1 11 14 1 1 1 13 3 1
Below cutoff 1 5 28 24 5 24 4 4 6 10 15 5 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014041   ⟹   ENSRNOP00000014041
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl84,848,186 - 4,855,902 (+)Ensembl
Rnor_6.0 Ensembl85,893,249 - 5,901,049 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000100430   ⟹   ENSRNOP00000079054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl84,848,186 - 4,854,256 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109262   ⟹   ENSRNOP00000091123
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl84,848,186 - 4,854,275 (+)Ensembl
RefSeq Acc Id: NM_012864   ⟹   NP_036996
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.284,848,186 - 4,855,908 (+)NCBI
Rnor_6.085,893,253 - 5,900,965 (+)NCBI
Rnor_5.085,895,393 - 5,903,105 (+)NCBI
RGSC_v3.484,526,018 - 4,533,730 (+)RGD
Celera86,407,543 - 6,415,255 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036996 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA99432 (Get FASTA)   NCBI Sequence Viewer  
  AAH64657 (Get FASTA)   NCBI Sequence Viewer  
  EDL78525 (Get FASTA)   NCBI Sequence Viewer  
  P50280 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036996   ⟸   NM_012864
- Peptide Label: precursor
- UniProtKB: P50280 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000014041   ⟸   ENSRNOT00000014041
RefSeq Acc Id: ENSRNOP00000091123   ⟸   ENSRNOT00000109262
RefSeq Acc Id: ENSRNOP00000079054   ⟸   ENSRNOT00000100430

Transcriptome

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

Promoters
RGD ID:13695735
Promoter ID:EPDNEW_R6260
Type:single initiation site
Name:Mmp7_1
Description:matrix metallopeptidase 7
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_6.085,893,240 - 5,893,300EPDNEW

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)
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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
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)
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
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)
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
F344/DuCrl (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/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
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)
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
F344/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
FHH/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
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
FXLE16/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
FXLE18/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
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/FarMcwi (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
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)
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
HXB2/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
HXB20/IpcvMcwi (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
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)
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
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)
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
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)
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
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)
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
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)
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
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)
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
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)
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
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:3100 AgrOrtholog
Ensembl Genes ENSRNOG00000010507 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000014041 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000014041 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.390.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5623517 IMAGE-MGC_LOAD
InterPro M10A_MMP UniProtKB/Swiss-Prot
  Matrilysin UniProtKB/Swiss-Prot
  MetalloPept_cat_dom_sf UniProtKB/Swiss-Prot
  Pept_M10_metallopeptidase UniProtKB/Swiss-Prot
  Pept_M10A UniProtKB/Swiss-Prot
  Pept_M10A_Zn_BS UniProtKB/Swiss-Prot
  Peptidase_Metallo UniProtKB/Swiss-Prot
  Peptidoglycan-bd-like UniProtKB/Swiss-Prot
  PGBD-like_sf UniProtKB/Swiss-Prot
KEGG Report rno:25335 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72527 IMAGE-MGC_LOAD
NCBI Gene 25335 ENTREZGENE
PANTHER PTHR10201:SF143 UniProtKB/Swiss-Prot
Pfam Peptidase_M10 UniProtKB/Swiss-Prot
  PG_binding_1 UniProtKB/Swiss-Prot
PhenoGen Mmp7 PhenoGen
PRINTS MATRIXIN UniProtKB/Swiss-Prot
PROSITE CYSTEINE_SWITCH UniProtKB/Swiss-Prot
  ZINC_PROTEASE UniProtKB/Swiss-Prot
SMART ZnMc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47090 UniProtKB/Swiss-Prot
TIGR TC209815
UniProt MMP7_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Mmp7  matrix metallopeptidase 7    matrix metalloproteinase 7  Name updated 1299863 APPROVED
2002-06-10 Mmp7  Matrix metalloproteinase 7 (matrilysin)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_function cleaves and activates latent human interstitial collagenase 1 728999