Timp2 (TIMP metallopeptidase inhibitor 2) - Rat Genome Database

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Gene: Timp2 (TIMP metallopeptidase inhibitor 2) Rattus norvegicus
Analyze
Symbol: Timp2
Name: TIMP metallopeptidase inhibitor 2
RGD ID: 61312
Description: Enables integrin binding activity and metalloendopeptidase inhibitor activity. Involved in several processes, including positive regulation of adenylate cyclase activity; positive regulation of neuron differentiation; and regulation of intracellular signal transduction. Located in several cellular components, including cell surface; growth cone; and neuronal cell body. Used to study portal hypertension. Biomarker of cardiomyopathy; congestive heart failure; and intracranial aneurysm. Human ortholog(s) of this gene implicated in Moyamoya disease. Orthologous to human TIMP2 (TIMP metallopeptidase inhibitor 2); INTERACTS WITH (+)-pilocarpine; (R)-noradrenaline; 1,3,5-trinitro-1,3,5-triazinane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: metalloproteinase inhibitor 2; MGC105282; TIMP-2; tissue inhibitor of metalloproteinase 2; tissue inhibitor of metalloproteinases 2
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
mRatBN7.210103,541,199 - 103,590,611 (-)NCBImRatBN7.2
Rnor_6.010107,338,465 - 107,386,072 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10107,338,465 - 107,386,072 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010106,973,463 - 107,021,070 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410108,310,473 - 108,358,821 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110108,324,976 - 108,373,325 (-)NCBI
Celera10102,103,187 - 102,150,797 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(R)-noradrenaline  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
1-naphthyl isothiocyanate  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-hydroxypropanoic acid  (ISO)
24,25-Dihydroxyvitamin D  (ISO)
3,4-dihydrocoumarin  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acetaldehyde  (EXP)
acetylsalicylic acid  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
ambroxol  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic acid  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
benazepril  (EXP)
benomyl  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-D-glucosamine  (EXP)
beta-naphthoflavone  (ISO)
betulin  (EXP)
betulinic acid  (EXP)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisdemethoxycurcumin  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
C60 fullerene  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
candesartan  (EXP)
capsaicin  (EXP)
carbamazepine  (ISO)
carbendazim  (ISO)
carbon nanotube  (ISO)
casticin  (ISO)
celecoxib  (EXP)
chloroquine  (ISO)
choline  (ISO)
cisplatin  (EXP,ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (EXP,ISO)
cyclosporin A  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
Deguelin  (ISO)
demethoxycurcumin  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diallyl disulfide  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
diisononyl phthalate  (ISO)
dimethyl sulfoxide  (EXP)
dioxygen  (EXP)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
ethanol  (EXP,ISO)
eugenol  (EXP)
fenofibrate  (ISO)
fenvalerate  (EXP)
ferric oxide  (ISO)
Fexofenadine hydrochloride  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
furosemide  (EXP)
gallic acid  (EXP)
Geniposide pentaacetate  (EXP)
genistein  (ISO)
glucose  (ISO)
Gly-His-Lys  (EXP)
graphene oxide  (ISO)
HET0016  (ISO)
hexachlorobenzene  (EXP)
hinokiflavone  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (EXP,ISO)
indinavir  (ISO)
indometacin  (EXP)
Isoangustone A  (ISO)
juglone  (ISO)
L-cysteine  (EXP)
L-methionine  (EXP,ISO)
lamivudine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
losartan  (EXP)
LY294002  (ISO)
melatonin  (EXP)
menadione  (ISO)
mesalamine  (ISO)
methamphetamine  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
metoprolol  (EXP)
mono(2-ethylhexyl) phthalate  (EXP,ISO)
N-acetyl-L-cysteine  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
naproxen  (EXP)
nickel sulfate  (ISO)
niclosamide  (ISO)
nitric oxide  (ISO)
nitrofen  (EXP)
obeticholic acid  (EXP)
ochratoxin A  (ISO)
okadaic acid  (ISO)
omeprazole  (EXP)
oroxylin A  (ISO)
oxaliplatin  (EXP)
oxidopamine  (ISO)
ozone  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
pentane-2,3-dione  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
potassium dichromate  (ISO)
pravastatin  (EXP)
prazosin  (EXP)
progesterone  (ISO)
propanal  (ISO)
pyrrolidine dithiocarbamate  (EXP)
quercetin  (ISO)
rac-lactic acid  (ISO)
radon atom  (ISO)
radon(0)  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
S-adenosyl-L-homocysteine  (ISO)
saquinavir  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
simvastatin  (EXP)
solasodine  (ISO)
Soman  (EXP)
streptozocin  (EXP)
sulfapyridine  (ISO)
sulfasalazine  (ISO)
sulforaphane  (ISO)
sumatriptan  (EXP)
sunitinib  (ISO)
T-2 toxin  (ISO)
tebuconazole  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
thalidomide  (EXP)
thioacetamide  (EXP,ISO)
thymoquinone  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triclosan  (ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
wortmannin  (ISO)
zidovudine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
1. Aoki T, etal., Stroke. 2007 Aug;38(8):2337-45. Epub 2007 Jun 14.
2. Branca M, etal., Anticancer Res. 2006 Mar-Apr;26(2B):1543-56.
3. Briest W, etal., Cardiovasc Res 2001 Nov;52(2):265-73.
4. Cook TF, etal., Arch Biochem Biophys 1994 Jun;311(2):313-20.
5. Curry TE Jr and Wheeler SE, Biol Reprod 2002 Dec;67(6):1943-51.
6. Dahlman I, etal., Eur J Immunol 1998 Jul;28(7):2188-96
7. Ding HL, etal., Rev Diabet Stud. 2005 Winter;2(4):216-20. Epub 2006 Feb 10.
8. Eissa S, etal., Eur Urol. 2007 Nov;52(5):1388-96. Epub 2007 Apr 10.
9. Fager N and Jaworski DM, Mech Dev. 2000 Nov;98(1-2):105-9.
10. Florys B, etal., Endokrynol Diabetol Chor Przemiany Materii Wieku Rozw. 2006;12(3):184-9.
11. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
12. Gipson TS, etal., J Immunol. 1999 Mar 15;162(6):3653-62.
13. GOA data from the GO Consortium
14. Graesslin O, etal., Int J Gynecol Cancer. 2006 Sep-Oct;16(5):1911-7.
15. Grima J, etal., J Androl 1996 May-Jun;17(3):263-75.
16. Hatori K, etal., Anat Rec A Discov Mol Cell Evol Biol 2004 Apr;277(2):262-71.
17. Hu YB, etal., J Gene Med. 2007 Mar;9(3):217-29.
18. Ikonomidis JS, etal., Circulation. 2006 Jul 4;114(1 Suppl):I365-70.
19. Jaworski DM Glia. 2000 Apr;30(2):199-208.
20. Jinga D, etal., Roum Arch Microbiol Immunol. 2004 Jul-Dec;63(3-4):141-58.
21. Kang HS, etal., Neurosurgery. 2006 Jun;58(6):1074-80; discussion 1074-80.
22. Kawata N, etal., Urology. 2007 Jun;69(6):1049-53.
23. Krizanac-Bengez L, etal., Am J Physiol Cell Physiol. 2006 Oct;291(4):C740-9. Epub 2006 May 17.
24. Li H, etal., Cardiovasc Res. 2000 May;46(2):298-306.
25. Li Q, etal., Acta Cardiol. 2007 Oct;62(5):485-91.
26. Longin J and Le Magueresse-Battistoni B, Mol Cell Endocrinol 2002 Mar 28;189(1-2):25-35.
27. Lorenzl S, etal., J Neurol Sci. 2003 Mar 15;207(1-2):71-6.
28. Mendes O, etal., Clin Exp Metastasis. 2007;24(5):341-51. Epub 2007 May 16.
29. MGD data from the GO Consortium
30. NCBI rat LocusLink and RefSeq merged data July 26, 2002
31. Nie QH, etal., World J Gastroenterol. 2004 Jan;10(1):86-90.
32. Noji Y, etal., Circ J. 2004 Apr;68(4):355-60.
33. Peihong S and Perry F, Ethiop Med J. 2007 Jan;45(1):79-83.
34. Perez-Martinez L and Jaworski DM, J Neurosci. 2005 May 18;25(20):4917-29.
35. Pulukuri SM, etal., Oncogene. 2007 Aug 9;26(36):5229-37. Epub 2007 Feb 26.
36. Remmers EF, etal., Nat Genet 1996 Sep;14(1):82-5
37. RGD automated data pipeline
38. RGD automated import pipeline for gene-chemical interactions
39. Salzmann J, etal., Br J Ophthalmol. 2000 Oct;84(10):1091-6.
40. Santoro M, etal., Exp Cell Res 1994 Aug;213(2):398-403.
41. Shuo T, etal., J Neurochem. 2007 Sep;102(5):1561-8. Epub 2007 May 26.
42. Slongo ML, etal., Biol Chem 2002 Jan;383(1):235-9.
43. Staack A, etal., BMC Urol. 2006 Aug 10;6:19.
44. Struckmann K, etal., Verh Dtsch Ges Pathol. 2005;89:178-83.
45. Takahashi I, etal., J Mol Histol. 2005 Jun;36(5):355-66. Epub 2005 Oct 6.
46. Trudel D, etal., Hum Pathol. 2008 Mar 7;.
47. Vasala K and Turpeenniemi-Hujanen T, Clin Biochem. 2007 Jun;40(9-10):640-4. Epub 2007 Feb 8.
48. von Moers A, etal., Acta Neuropathol (Berl). 2005 Mar;109(3):285-93. Epub 2004 Dec 23.
49. Xue AM, etal., Zhonghua Bing Li Xue Za Zhi. 2007 Jun;36(6):405-9.
50. Zhang X, etal., J Neurosci Res. 2006 Aug 1;84(2):278-90.
51. Zhao YG, etal., Cancer Res. 2004 Jan 15;64(2):590-8.
52. Zhao YG, etal., Mol Reprod Dev 2002 Jun;62(2):149-58.
53. Zhao ZJ, etal., Beijing Da Xue Xue Bao. 2008 Feb 18;40(1):101-104.
Additional References at PubMed
PMID:1309971   PMID:9573338   PMID:10827175   PMID:10827176   PMID:11869290   PMID:12477932   PMID:12950084   PMID:12970340   PMID:15489334   PMID:18000599   PMID:18415800   PMID:18558556  
PMID:18675881   PMID:18935914   PMID:18983773   PMID:19184368   PMID:20103929   PMID:20226641   PMID:21141515   PMID:21782897   PMID:22045123   PMID:22092673   PMID:22110735   PMID:22974613  
PMID:23376485   PMID:23383440   PMID:23886643   PMID:23979707   PMID:24006456   PMID:24073280   PMID:24685074   PMID:24970341   PMID:25028660   PMID:26047379   PMID:26258010   PMID:26601648  
PMID:27322513   PMID:27323108   PMID:29075637   PMID:29302675   PMID:29308554   PMID:29955613   PMID:31392726  


Genomics

Candidate Gene Status
Timp2 is a candidate Gene for QTL Cia5
Comparative Map Data
Timp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210103,541,199 - 103,590,611 (-)NCBImRatBN7.2
Rnor_6.010107,338,465 - 107,386,072 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10107,338,465 - 107,386,072 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010106,973,463 - 107,021,070 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410108,310,473 - 108,358,821 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110108,324,976 - 108,373,325 (-)NCBI
Celera10102,103,187 - 102,150,797 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
TIMP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1778,852,977 - 78,925,387 (-)EnsemblGRCh38hg38GRCh38
GRCh381778,852,977 - 78,925,387 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371776,849,059 - 76,921,469 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361774,360,654 - 74,433,067 (-)NCBINCBI36hg18NCBI36
Build 341774,360,655 - 74,433,067NCBI
Celera1773,446,776 - 73,467,725 (-)NCBI
Cytogenetic Map17q25.3NCBI
HuRef1772,271,475 - 72,343,528 (-)NCBIHuRef
CHM1_11776,912,998 - 76,985,403 (-)NCBICHM1_1
Timp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911118,191,887 - 118,246,237 (-)NCBIGRCm39mm39
GRCm39 Ensembl11118,191,895 - 118,246,566 (-)Ensembl
GRCm3811118,301,061 - 118,355,411 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11118,301,069 - 118,355,740 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711118,162,375 - 118,216,725 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611118,117,151 - 118,171,501 (-)NCBImm8
Celera11130,046,014 - 130,100,382 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1183.09NCBI
Timp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555063,768,646 - 3,813,820 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555063,769,113 - 3,812,896 (+)NCBIChiLan1.0ChiLan1.0
TIMP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11778,476,807 - 78,495,885 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1778,476,807 - 78,495,649 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01772,928,692 - 73,001,892 (-)NCBIMhudiblu_PPA_v0panPan3
TIMP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.192,521,882 - 2,533,883 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl92,521,882 - 2,533,989 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha93,159,531 - 3,168,419 (+)NCBI
Dog10K_Boxer_Tasha93,146,850 - 3,191,997 (+)NCBI
ROS_Cfam_1.093,140,666 - 3,188,540 (+)NCBI
UMICH_Zoey_3.193,175,669 - 3,184,556 (+)NCBI
UMICH_Zoey_3.193,162,992 - 3,208,134 (+)NCBI
UNSW_CanFamBas_1.093,288,768 - 3,333,886 (+)NCBI
UNSW_CanFamBas_1.093,301,440 - 3,310,326 (+)NCBI
UU_Cfam_GSD_1.093,369,678 - 3,414,817 (+)NCBI
Timp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056023,160,813 - 3,179,526 (+)NCBI
SpeTri2.0NW_0049365943,232,433 - 3,244,241 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TIMP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl123,254,493 - 3,300,835 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1123,254,794 - 3,300,835 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2123,294,254 - 3,340,447 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TIMP2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11670,819,591 - 70,850,471 (-)NCBI
ChlSab1.1 Ensembl1670,819,139 - 70,850,471 (-)Ensembl
Vero_WHO_p1.0NW_02366607741,956,134 - 42,029,058 (-)NCBI
Timp2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248018,228,618 - 8,270,606 (-)NCBI

Position Markers
Timp2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210103,590,354 - 103,590,484 (+)MAPPERmRatBN7.2
Rnor_6.010107,385,816 - 107,385,945NCBIRnor6.0
Rnor_5.010107,020,814 - 107,020,943UniSTSRnor5.0
Celera10102,150,541 - 102,150,670UniSTS
Cytogenetic Map10q32.3UniSTS
Ddc8  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210103,568,065 - 103,568,480 (+)MAPPERmRatBN7.2
Rnor_6.010107,363,534 - 107,363,948NCBIRnor6.0
Rnor_5.010106,998,532 - 106,998,946UniSTSRnor5.0
Celera10102,128,259 - 102,128,673UniSTS
Cytogenetic Map10q32.3UniSTS
Timp2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210103,553,466 - 103,553,573 (+)MAPPERmRatBN7.2
Rnor_6.010107,348,935 - 107,349,041NCBIRnor6.0
Rnor_5.010106,983,933 - 106,984,039UniSTSRnor5.0
Celera10102,113,660 - 102,113,766UniSTS
Cytogenetic Map10q32.3UniSTS
Timp2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210103,556,030 - 103,556,135 (+)MAPPERmRatBN7.2
Rnor_6.010107,351,499 - 107,351,603NCBIRnor6.0
Rnor_5.010106,986,497 - 106,986,601UniSTSRnor5.0
Celera10102,116,224 - 102,116,328UniSTS
Cytogenetic Map10q32.3UniSTS
Timp2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210103,545,903 - 103,546,023 (+)MAPPERmRatBN7.2
mRatBN7.23163,247,412 - 163,248,931 (+)MAPPERmRatBN7.2
Rnor_6.010107,341,373 - 107,341,492NCBIRnor6.0
Rnor_6.03172,549,698 - 172,551,216NCBIRnor6.0
Rnor_5.010106,976,371 - 106,976,490UniSTSRnor5.0
Rnor_5.03178,596,824 - 178,598,342UniSTSRnor5.0
Celera10102,106,097 - 102,106,216UniSTS
Celera3162,420,887 - 162,422,405UniSTS
Cytogenetic Map10q32.3UniSTS
Timp2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.210103,543,868 - 103,544,040 (+)MAPPERmRatBN7.2
Rnor_6.010107,339,340 - 107,339,511NCBIRnor6.0
Rnor_5.010106,974,338 - 106,974,509UniSTSRnor5.0
Celera10102,104,062 - 102,104,233UniSTS
Cytogenetic Map10q32.3UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1090910316107211142Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091228102104060283Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)1096703043107057807Rat
631539Oia6Oil induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1097010147104670812Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:329
Count of miRNA genes:191
Interacting mature miRNAs:216
Transcripts:ENSRNOT00000004290
Prediction methods:Microtar, 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 3 43 41 25 19 25 8 11 74 35 41 11 8
Low 16 16 16
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004290   ⟹   ENSRNOP00000004290
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl10107,338,465 - 107,386,072 (-)Ensembl
RefSeq Acc Id: NM_021989   ⟹   NP_068824
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210103,542,994 - 103,590,611 (-)NCBI
Rnor_6.010107,338,465 - 107,386,072 (-)NCBI
Rnor_5.010106,973,463 - 107,021,070 (-)NCBI
RGSC_v3.410108,310,473 - 108,358,821 (-)RGD
Celera10102,103,187 - 102,150,797 (-)RGD
Sequence:
RefSeq Acc Id: XM_039085773   ⟹   XP_038941701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210103,541,199 - 103,577,752 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_068824   ⟸   NM_021989
- Peptide Label: precursor
- UniProtKB: P30121 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004290   ⟸   ENSRNOT00000004290
RefSeq Acc Id: XP_038941701   ⟸   XM_039085773
- Peptide Label: isoform X1
Protein Domains
NTR

Transcriptome

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


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)
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)
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)
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)
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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)
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)
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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)
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)
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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)
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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
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)
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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
LEXF2B/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
LEXF3/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
LEXF4/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
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
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)
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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/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
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
LN/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
M520/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
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
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)
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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 (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
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
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)
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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
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
SHR/OlalpcvMcwi (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
SHRSP/A3NCrl (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
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 (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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
WAG/RijCrl (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: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (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
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 (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
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)
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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 (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
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:61312 AgrOrtholog
Ensembl Genes ENSRNOG00000003148 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000004290 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004290 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.40.50.120 UniProtKB/Swiss-Prot
  3.90.370.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7303706 IMAGE-MGC_LOAD
InterPro Netrin_domain UniProtKB/Swiss-Prot
  TIMP UniProtKB/Swiss-Prot
  TIMP-like_OB-fold UniProtKB/Swiss-Prot
  TIMP2 UniProtKB/Swiss-Prot
  TIMP_C UniProtKB/Swiss-Prot
  TIMP_CS UniProtKB/Swiss-Prot
KEGG Report rno:29543 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105282 IMAGE-MGC_LOAD
NCBI Gene 29543 ENTREZGENE
PANTHER PTHR11844 UniProtKB/Swiss-Prot
  PTHR11844:SF24 UniProtKB/Swiss-Prot
Pfam TIMP UniProtKB/Swiss-Prot
PhenoGen Timp2 PhenoGen
PROSITE NTR UniProtKB/Swiss-Prot
  TIMP UniProtKB/Swiss-Prot
SMART NTR UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50242 UniProtKB/Swiss-Prot
UniProt P30121 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q546J4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Timp2  TIMP metallopeptidase inhibitor 2  Timp2  tissue inhibitor of metalloproteinase 2   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Timp2  tissue inhibitor of metalloproteinase 2       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in testis Sertoli and Leydig cells 730126