Prkn (parkin RBR E3 ubiquitin protein ligase) - Rat Genome Database

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Gene: Prkn (parkin RBR E3 ubiquitin protein ligase) Rattus norvegicus
Analyze
Symbol: Prkn
Name: parkin RBR E3 ubiquitin protein ligase
RGD ID: 61797
Description: Enables protein kinase binding activity. Involved in several processes, including cellular response to amino acid stimulus; negative regulation of neuron death; and negative regulation of synaptic transmission. Located in several cellular components, including bounding membrane of organelle; membrane raft; and postsynaptic density. Colocalizes with mitochondrion. Used to study Parkinson's disease. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Parkinson's disease; Parkinson's disease 2; and ovarian cancer. Orthologous to human PRKN (parkin RBR E3 ubiquitin protein ligase); PARTICIPATES IN altered mitochondrial autophagy pathway; mitochondrial autophagy pathway; Parkinson's disease pathway; INTERACTS WITH 4-Hydroxy-TEMPO; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: E3 ubiquitin-protein ligase parkin; Park; Park2; parkin; parkin RBR E3 ubiquitin protein ligase 2; parkin variant SV5DEL; Parkinson disease (autosomal recessive, juvenile) 2, parkin; parkinson protein 2, E3 ubiquitin protein ligase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Prknem1Sage  
Genetic Models: LE-Prknem1Sage-/- LE-Prknem1Sage
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2148,688,651 - 49,882,520 (-)NCBImRatBN7.2
Rnor_6.0148,880,015 - 50,069,998 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0149,684,308 - 50,875,397 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4143,151,265 - 44,374,470 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1143,154,209 - 44,377,415 (-)NCBI
Celera144,478,407 - 45,666,902 (-)NCBICelera
Cytogenetic Map1q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-selegiline  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3-BROMO-7-NITROINDAZOLE  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-Hydroxy-TEMPO  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (ISO)
androgen antagonist  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (EXP,ISO)
atrazine  (EXP)
azoxystrobin  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Butylparaben  (EXP)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (ISO)
carnosic acid  (ISO)
CCCP  (EXP,ISO)
chloroquine  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
cinnarizine  (ISO)
cisplatin  (EXP)
coenzyme Q10  (ISO)
curcumin  (EXP)
cyclosporin A  (ISO)
DDE  (EXP)
diarsenic trioxide  (EXP,ISO)
diazinon  (EXP)
dibutyl phthalate  (EXP)
dieldrin  (ISO)
dioxygen  (ISO)
dopamine  (ISO)
doxorubicin  (EXP,ISO)
emtricitabine  (ISO)
enzacamene  (EXP)
epoxiconazole  (EXP)
epoxomicin  (EXP,ISO)
ethanol  (ISO)
fenpyroximate  (ISO)
folic acid  (ISO)
furan  (EXP)
furosemide  (EXP)
Genipin  (ISO)
glutathione  (ISO)
hydrogen peroxide  (EXP,ISO)
indole-3-methanol  (EXP)
indometacin  (ISO)
iodixanol  (EXP)
ketoconazole  (EXP)
Lasiocarpine  (ISO)
lead diacetate  (ISO)
linsidomine  (ISO)
linuron  (EXP)
lipopolysaccharide  (EXP)
luteolin  (ISO)
maneb  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP,ISO)
melatonin  (EXP)
methamphetamine  (EXP,ISO)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
miconazole  (EXP)
minocycline  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP,ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-Nitrosopyrrolidine  (ISO)
nicotine  (ISO)
O-acetyl-L-carnitine  (ISO)
O-methyleugenol  (ISO)
oligomycin A  (ISO)
oxidopamine  (EXP,ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
picoxystrobin  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
pyrimidifen  (ISO)
quercetin 3-O-beta-D-glucofuranoside  (EXP)
quercetin 3-O-beta-D-glucopyranoside  (EXP)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
rimonabant  (EXP,ISO)
rotenone  (EXP,ISO)
rutin  (EXP)
S-nitrosoglutathione  (ISO)
silicon dioxide  (EXP)
sirolimus  (EXP,ISO)
sirtinol  (ISO)
sodium arsenite  (EXP,ISO)
sorafenib  (ISO)
sunitinib  (ISO)
T-2 toxin  (EXP)
taurine  (EXP)
tebufenpyrad  (ISO)
tenofovir disoproxil fumarate  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
Tiron  (EXP,ISO)
titanium dioxide  (ISO)
trans-piceid  (ISO)
trifloxystrobin  (ISO)
trifluoperazine  (ISO)
trimellitic anhydride  (ISO)
tubocurarine  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult locomotory behavior  (ISO,ISS)
aggresome assembly  (ISO,ISS)
autophagy of mitochondrion  (IBA,IDA,ISO,ISS)
brain development  (IEP)
cellular protein catabolic process  (ISO)
cellular response to hydrogen sulfide  (IDA)
cellular response to L-glutamate  (IDA)
cellular response to L-glutamine  (IEP)
cellular response to manganese ion  (IEP)
cellular response to toxic substance  (ISO,ISS)
dopamine metabolic process  (ISO)
dopamine uptake involved in synaptic transmission  (ISO)
free ubiquitin chain polymerization  (ISO)
learning  (ISO)
locomotory behavior  (ISO)
mitochondrial fission  (ISS)
mitochondrial fragmentation involved in apoptotic process  (IMP)
mitochondrion localization  (IDA)
mitochondrion organization  (ISS)
mitochondrion to lysosome transport  (ISO)
mitophagy  (ISO)
modulation of chemical synaptic transmission  (ISO)
negative regulation by host of viral genome replication  (ISO)
negative regulation of actin filament bundle assembly  (ISO)
negative regulation of canonical Wnt signaling pathway  (ISO)
negative regulation of cell death  (ISO)
negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway  (ISO,ISS)
negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway  (ISO)
negative regulation of excitatory postsynaptic potential  (IMP)
negative regulation of exosomal secretion  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of glucokinase activity  (ISO,ISS)
negative regulation of insulin secretion  (ISO,ISS)
negative regulation of intralumenal vesicle formation  (ISO)
negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator  (ISO)
negative regulation of JNK cascade  (ISS)
negative regulation of mitochondrial fission  (IMP)
negative regulation of mitochondrial fusion  (ISS)
negative regulation of neuron apoptotic process  (IMP,ISO,ISS)
negative regulation of neuron death  (IGI,ISO)
negative regulation of oxidative stress-induced neuron death  (IGI)
negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway  (ISO,ISS)
negative regulation of primary amine oxidase activity  (ISO)
negative regulation of protein phosphorylation  (IBA,ISO,ISS)
negative regulation of reactive oxygen species biosynthetic process  (IMP)
negative regulation of reactive oxygen species metabolic process  (ISO,ISS)
negative regulation of release of cytochrome c from mitochondria  (ISO,ISS)
negative regulation of spontaneous neurotransmitter secretion  (ISO)
negative regulation of synaptic transmission, glutamatergic  (IMP)
negative regulation of transcription by RNA polymerase II  (ISO)
neuron cellular homeostasis  (ISS)
norepinephrine metabolic process  (ISO)
parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization  (ISO)
positive regulation of apoptotic process  (IMP)
positive regulation of ATP biosynthetic process  (IMP)
positive regulation of autophagy of mitochondrion  (ISO)
positive regulation of dendrite extension  (ISO)
positive regulation of DNA binding  (ISO,ISS)
positive regulation of gene expression  (ISO)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO,ISS)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (IMP)
positive regulation of mitochondrial fission  (ISS)
positive regulation of mitochondrial fusion  (ISO,ISS)
positive regulation of mitochondrial membrane potential  (IMP)
positive regulation of mitophagy  (IMP)
positive regulation of mitophagy in response to mitochondrial depolarization  (ISO)
positive regulation of neurotransmitter uptake  (ISO)
positive regulation of proteasomal protein catabolic process  (ISO)
positive regulation of proteasomal ubiquitin-dependent protein catabolic process  (IBA,ISO)
positive regulation of protein binding  (ISO)
positive regulation of protein linear polyubiquitination  (ISO)
positive regulation of protein localization to membrane  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO,ISS)
positive regulation of tumor necrosis factor-mediated signaling pathway  (ISO,ISS)
proteasomal protein catabolic process  (ISO)
proteasome-mediated ubiquitin-dependent protein catabolic process  (ISO,ISS)
protein autoubiquitination  (ISO,ISS)
protein destabilization  (ISO,ISS)
protein K11-linked ubiquitination  (ISO,ISS)
protein K48-linked ubiquitination  (ISO,ISS)
protein K6-linked ubiquitination  (ISO,ISS)
protein K63-linked ubiquitination  (ISO,ISS)
protein localization to mitochondrion  (IDA,ISO,ISS)
protein metabolic process  (ISO)
protein monoubiquitination  (ISO,ISS)
protein polyubiquitination  (IBA,ISO,ISS)
protein stabilization  (ISO)
protein ubiquitination  (IDA,ISO,ISS)
regulation of apoptotic process  (IBA)
regulation of autophagy  (ISO,ISS)
regulation of cellular response to oxidative stress  (IBA,ISO,ISS)
regulation of dopamine metabolic process  (ISO)
regulation of gene expression  (IMP)
regulation of mitochondrial membrane potential  (ISO)
regulation of mitochondrion organization  (IBA,ISO,ISS)
regulation of neurotransmitter secretion  (ISO)
regulation of protein stability  (ISO)
regulation of protein ubiquitination  (ISO)
regulation of reactive oxygen species metabolic process  (ISO)
response to corticosterone  (IEP)
response to curcumin  (IEP)
response to endoplasmic reticulum stress  (IEP,ISO)
response to muscle activity  (IEP)
response to oxidative stress  (ISS)
response to unfolded protein  (IEP)
response to xenobiotic stimulus  (IEP)
startle response  (ISO)
synaptic transmission, dopaminergic  (ISO)
synaptic transmission, glutamatergic  (ISO)
ubiquitin-dependent protein catabolic process  (IBA,ISO,ISS)
zinc ion homeostasis  (ISS)

References

References - curated
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Additional References at PubMed
PMID:10973942   PMID:11078524   PMID:11439185   PMID:11675120   PMID:12628165   PMID:12915482   PMID:12930822   PMID:14530399   PMID:14645198   PMID:14985362   PMID:15249681   PMID:15252205  
PMID:15453267   PMID:15576511   PMID:15603737   PMID:15684050   PMID:15728840   PMID:15882845   PMID:15987638   PMID:16174552   PMID:16227987   PMID:16352719   PMID:16554120   PMID:16905117  
PMID:16955485   PMID:17097639   PMID:17116640   PMID:17314283   PMID:17327227   PMID:17512523   PMID:17553932   PMID:17873367   PMID:17883392   PMID:18190519   PMID:18195004   PMID:18346797  
PMID:18541373   PMID:19029340   PMID:19229105   PMID:19279012   PMID:19339245   PMID:19591802   PMID:19725078   PMID:19880420   PMID:20064468   PMID:20798600   PMID:20871098   PMID:20889974  
PMID:21113145   PMID:21376232   PMID:21466165   PMID:21508222   PMID:21532592   PMID:21613270   PMID:21694720   PMID:21753002   PMID:21890690   PMID:22314364   PMID:22511790   PMID:22792159  
PMID:23152496   PMID:23212910   PMID:23258539   PMID:23393160   PMID:23453807   PMID:23661642   PMID:23858059   PMID:23933751   PMID:23985028   PMID:24063750   PMID:24187134   PMID:24337465  
PMID:24386307   PMID:24446486   PMID:24660806   PMID:24784582   PMID:24896179   PMID:24898855   PMID:24949970   PMID:25101677   PMID:25244949   PMID:25583483   PMID:25621951   PMID:26224857  
PMID:26260794   PMID:26310625   PMID:26364802   PMID:26465230   PMID:26911690   PMID:26935412   PMID:27284007   PMID:27601173   PMID:27797717   PMID:27841025   PMID:27903732   PMID:28063983  
PMID:28254618   PMID:28724963   PMID:29311685   PMID:29367643   PMID:29367744   PMID:29475881   PMID:29538088   PMID:30250268   PMID:30387846   PMID:30796971   PMID:31406131   PMID:32173525  
PMID:32392329   PMID:32900550   PMID:33125104   PMID:33296434   PMID:34001858  


Genomics

Comparative Map Data
Prkn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2148,688,651 - 49,882,520 (-)NCBImRatBN7.2
Rnor_6.0148,880,015 - 50,069,998 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0149,684,308 - 50,875,397 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4143,151,265 - 44,374,470 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1143,154,209 - 44,377,415 (-)NCBI
Celera144,478,407 - 45,666,902 (-)NCBICelera
Cytogenetic Map1q11NCBI
PRKN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6161,347,417 - 162,727,775 (-)EnsemblGRCh38hg38GRCh38
GRCh386161,347,417 - 162,727,802 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376161,768,449 - 163,148,798 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366161,689,661 - 163,068,793 (-)NCBINCBI36hg18NCBI36
Build 346161,740,081 - 163,119,211NCBI
Celera6162,497,923 - 163,878,436 (-)NCBI
Cytogenetic Map6q26NCBI
HuRef6159,224,034 - 160,600,983 (-)NCBIHuRef
CHM1_16162,031,091 - 163,411,071 (-)NCBICHM1_1
Prkn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391711,059,227 - 12,282,257 (+)NCBIGRCm39mm39
GRCm39 Ensembl1711,059,271 - 12,282,248 (+)Ensembl
GRCm381710,840,359 - 12,063,370 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1710,840,384 - 12,063,361 (+)EnsemblGRCm38mm10GRCm38
MGSCv371711,033,250 - 12,256,227 (+)NCBIGRCm37mm9NCBIm37
MGSCv361710,683,742 - 11,906,719 (+)NCBImm8
Celera1710,880,667 - 12,092,859 (+)NCBICelera
Cytogenetic Map17A1NCBI
cM Map177.8NCBI
Prkn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543918,664,379 - 19,951,152 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543918,664,230 - 19,953,358 (+)NCBIChiLan1.0ChiLan1.0
PRKN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16164,498,420 - 165,678,904 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6164,314,990 - 165,678,770 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06159,293,016 - 160,679,106 (-)NCBIMhudiblu_PPA_v0panPan3
PRKN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1149,886,887 - 51,201,930 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl149,889,005 - 51,201,764 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha150,729,328 - 52,042,064 (-)NCBI
ROS_Cfam_1.0150,071,882 - 51,381,593 (-)NCBI
UMICH_Zoey_3.1149,954,154 - 51,268,026 (-)NCBI
UNSW_CanFamBas_1.0149,824,568 - 51,126,809 (-)NCBI
UU_Cfam_GSD_1.0150,440,798 - 51,751,574 (-)NCBI
Prkn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946144,866,545 - 145,855,394 (-)NCBI
SpeTri2.0NW_00493648912,118,538 - 12,913,664 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PRKN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15,465,511 - 6,730,881 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115,698,508 - 6,731,132 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.217,649,954 - 8,260,243 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Sscrofa10.217,197,051 - 7,562,040 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PRKN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11388,856,056 - 90,329,379 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604061,183,625 - 62,136,281 (-)NCBIVero_WHO_p1.0
Prkn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624855430,148 - 1,992,121 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Mit9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,361,465 - 49,361,612 (+)MAPPERmRatBN7.2
Rnor_6.0149,547,328 - 49,547,474NCBIRnor6.0
Rnor_5.0150,204,369 - 50,204,515UniSTSRnor5.0
RGSC_v3.4143,840,481 - 43,840,628RGDRGSC3.4
RGSC_v3.4143,840,482 - 43,840,628UniSTSRGSC3.4
RGSC_v3.1143,843,426 - 43,843,573RGD
Celera145,146,244 - 45,146,390UniSTS
RH 3.4 Map1575.1UniSTS
RH 3.4 Map1575.1RGD
RH 2.0 Map1291.4RGD
SHRSP x BN Map123.8RGD
Cytogenetic Map1q11UniSTS
D1Mgh4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2148,963,584 - 48,963,799 (+)MAPPERmRatBN7.2
Rnor_6.0149,147,799 - 49,148,011NCBIRnor6.0
Rnor_5.0150,601,428 - 50,601,640UniSTSRnor5.0
RGSC_v3.4143,426,139 - 43,426,354RGDRGSC3.4
RGSC_v3.4143,426,140 - 43,426,354UniSTSRGSC3.4
RGSC_v3.1143,429,085 - 43,429,299RGD
RH 3.4 Map1574.4RGD
RH 3.4 Map1574.4UniSTS
RH 2.0 Map1287.8RGD
SHRSP x BN Map123.88RGD
Cytogenetic Map1q11UniSTS
D1Rat18  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,268,362 - 49,268,520 (+)MAPPERmRatBN7.2
Rnor_6.0149,454,221 - 49,454,378NCBIRnor6.0
Rnor_5.0150,297,465 - 50,297,622UniSTSRnor5.0
RGSC_v3.4143,747,375 - 43,747,532UniSTSRGSC3.4
RGSC_v3.4143,747,374 - 43,747,532RGDRGSC3.4
RGSC_v3.1143,750,320 - 43,750,477RGD
Celera145,054,420 - 45,054,577UniSTS
RH 3.4 Map1575.2RGD
RH 3.4 Map1575.2UniSTS
RH 2.0 Map1291.4RGD
SHRSP x BN Map123.88RGD
Cytogenetic Map1q11UniSTS
D1Rat19  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,393,172 - 49,393,289 (+)MAPPERmRatBN7.2
Rnor_6.0149,578,577 - 49,578,693NCBIRnor6.0
Rnor_5.0150,173,150 - 50,173,266UniSTSRnor5.0
RGSC_v3.4143,872,710 - 43,872,827RGDRGSC3.4
RGSC_v3.4143,872,711 - 43,872,827UniSTSRGSC3.4
RGSC_v3.1143,875,655 - 43,875,772RGD
Celera145,177,968 - 45,178,100UniSTS
RH 3.4 Map1573.5RGD
RH 3.4 Map1573.5UniSTS
SHRSP x BN Map123.8UniSTS
SHRSP x BN Map123.8RGD
Cytogenetic Map1q11UniSTS
D1Rat17  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,648,235 - 49,648,371 (+)MAPPERmRatBN7.2
Rnor_6.0149,835,153 - 49,835,288NCBIRnor6.0
Rnor_5.0149,918,738 - 49,918,873UniSTSRnor5.0
RGSC_v3.4144,137,014 - 44,137,149UniSTSRGSC3.4
RGSC_v3.4144,136,888 - 44,137,155RGDRGSC3.4
RGSC_v3.1144,139,959 - 44,140,094RGD
Celera145,432,877 - 45,433,012UniSTS
RH 3.4 Map1579.5RGD
RH 3.4 Map1579.5UniSTS
RH 2.0 Map1295.3RGD
SHRSP x BN Map123.8399RGD
Cytogenetic Map1q11UniSTS
D1Rat143  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,176,688 - 49,176,934 (+)MAPPERmRatBN7.2
Rnor_6.0149,361,976 - 49,362,221NCBIRnor6.0
Rnor_5.0150,389,523 - 50,389,768UniSTSRnor5.0
RGSC_v3.4143,655,630 - 43,655,876RGDRGSC3.4
RGSC_v3.4143,655,631 - 43,655,876UniSTSRGSC3.4
RGSC_v3.1143,658,576 - 43,658,821RGD
Celera144,962,761 - 44,963,008UniSTS
RH 3.4 Map21132.8UniSTS
RH 3.4 Map21132.8RGD
SHRSP x BN Map123.88UniSTS
SHRSP x BN Map123.88RGD
Cytogenetic Map1q11UniSTS
D1Rat191  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2148,963,584 - 48,963,811 (+)MAPPERmRatBN7.2
Rnor_6.0149,147,799 - 49,148,023NCBIRnor6.0
Rnor_5.0150,601,416 - 50,601,640UniSTSRnor5.0
RGSC_v3.4143,426,139 - 43,426,366RGDRGSC3.4
RGSC_v3.4143,426,140 - 43,426,366UniSTSRGSC3.4
RGSC_v3.1143,429,085 - 43,429,311RGD
RH 3.4 Map1574.3RGD
RH 3.4 Map1574.3UniSTS
SHRSP x BN Map124.95UniSTS
SHRSP x BN Map124.95RGD
Cytogenetic Map1q11UniSTS
D1Rat228  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,342,028 - 49,342,260 (+)MAPPERmRatBN7.2
Rnor_6.0149,527,891 - 49,528,122NCBIRnor6.0
Rnor_5.0150,223,721 - 50,223,952UniSTSRnor5.0
RGSC_v3.4143,821,045 - 43,821,276UniSTSRGSC3.4
RGSC_v3.4143,820,945 - 43,821,344RGDRGSC3.4
RGSC_v3.1143,823,990 - 43,824,221RGD
Celera145,126,810 - 45,127,041UniSTS
RH 3.4 Map1575.1RGD
RH 3.4 Map1575.1UniSTS
RH 2.0 Map1291.4RGD
SHRSP x BN Map124.95RGD
Cytogenetic Map1q11UniSTS
D1Got61  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,218,171 - 49,218,412 (+)MAPPERmRatBN7.2
Rnor_6.0149,403,457 - 49,403,697NCBIRnor6.0
Rnor_5.0150,348,047 - 50,348,287UniSTSRnor5.0
RGSC_v3.4143,697,167 - 43,697,408RGDRGSC3.4
RGSC_v3.4143,697,168 - 43,697,408UniSTSRGSC3.4
RGSC_v3.1143,700,113 - 43,700,353RGD
Celera145,004,275 - 45,004,503UniSTS
RH 3.4 Map1574.2UniSTS
RH 3.4 Map1574.2RGD
RH 2.0 Map1291.0RGD
Cytogenetic Map1q11UniSTS
RH134081  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,580,043 - 49,580,226 (+)MAPPERmRatBN7.2
Rnor_6.0149,765,013 - 49,765,195NCBIRnor6.0
Rnor_5.0149,987,414 - 49,987,596UniSTSRnor5.0
RGSC_v3.4144,068,411 - 44,068,593UniSTSRGSC3.4
Celera145,364,623 - 45,364,805UniSTS
RH 3.4 Map1574.9UniSTS
Cytogenetic Map1q11UniSTS
BE097220  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2148,961,574 - 48,961,782 (+)MAPPERmRatBN7.2
Rnor_6.0149,145,789 - 49,145,996NCBIRnor6.0
Rnor_5.0150,603,443 - 50,603,650UniSTSRnor5.0
RGSC_v3.4143,424,130 - 43,424,337UniSTSRGSC3.4
Celera144,748,614 - 44,748,821UniSTS
RH 3.4 Map1573.6UniSTS
Cytogenetic Map1q11UniSTS
BE107128  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2179,180,875 - 79,181,012 (-)MAPPERmRatBN7.2
mRatBN7.2179,180,875 - 79,181,012 (+)MAPPERmRatBN7.2
mRatBN7.2149,826,424 - 49,826,561 (-)MAPPERmRatBN7.2
mRatBN7.2149,826,424 - 49,826,561 (+)MAPPERmRatBN7.2
Rnor_6.0150,014,365 - 50,014,501NCBIRnor6.0
Rnor_6.0180,439,800 - 80,439,936NCBIRnor6.0
Rnor_5.0149,739,855 - 49,739,991UniSTSRnor5.0
Rnor_5.0181,705,821 - 81,705,957UniSTSRnor5.0
RGSC_v3.4178,884,493 - 78,884,629UniSTSRGSC3.4
RGSC_v3.4144,315,802 - 44,315,938UniSTSRGSC3.4
Celera145,610,880 - 45,611,016UniSTS
Celera173,640,456 - 73,640,592UniSTS
RH 3.4 Map1589.6UniSTS
Cytogenetic Map1q11UniSTS
Cytogenetic Map1q21UniSTS
BE120978  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,044,400 - 49,044,610 (+)MAPPERmRatBN7.2
Rnor_6.0149,227,529 - 49,227,738NCBIRnor6.0
Rnor_5.0150,522,152 - 50,522,361UniSTSRnor5.0
RGSC_v3.4143,507,299 - 43,507,508UniSTSRGSC3.4
Celera144,831,334 - 44,831,543UniSTS
RH 3.4 Map1572.3UniSTS
Cytogenetic Map1q11UniSTS
AI171223  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2148,889,265 - 48,889,408 (+)MAPPERmRatBN7.2
Rnor_6.0149,073,451 - 49,073,593NCBIRnor6.0
Rnor_5.0150,675,094 - 50,675,236UniSTSRnor5.0
RGSC_v3.4143,351,829 - 43,351,971UniSTSRGSC3.4
Celera144,676,562 - 44,676,704UniSTS
RH 3.4 Map1573.9UniSTS
Cytogenetic Map1q11UniSTS
AU048432  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2149,777,511 - 49,777,655 (+)MAPPERmRatBN7.2
Rnor_6.0149,965,368 - 49,965,511NCBIRnor6.0
Rnor_5.0149,788,592 - 49,788,735UniSTSRnor5.0
RGSC_v3.4144,267,128 - 44,267,271UniSTSRGSC3.4
Celera145,562,063 - 45,562,206UniSTS
Cytogenetic Map1q11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11620621049268520Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat


Genetic Models
This gene Prkn is modified in the following models/strains

Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_020093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088712 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088719 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB039878 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC135026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF168004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF210434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF257234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF343574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF343575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF381277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF381278 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF381279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF381280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF381281 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF381285 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU322017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU322019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU322363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU322364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU345835 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU345836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC774169 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC774170 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC774172 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC774173 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC774174 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC774175 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC774176 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KC774177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC156097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: NM_020093   ⟹   NP_064478
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,690,481 - 49,882,447 (-)NCBI
Rnor_6.0148,880,015 - 50,069,998 (-)NCBI
Rnor_5.0149,684,308 - 50,875,397 (+)NCBI
RGSC_v3.4143,151,265 - 44,374,470 (-)RGD
Celera144,478,407 - 45,666,902 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088710   ⟹   XP_038944638
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,882,511 (-)NCBI
RefSeq Acc Id: XM_039088712   ⟹   XP_038944640
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,882,509 (-)NCBI
RefSeq Acc Id: XM_039088713   ⟹   XP_038944641
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,723,571 (-)NCBI
RefSeq Acc Id: XM_039088714   ⟹   XP_038944642
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,882,508 (-)NCBI
RefSeq Acc Id: XM_039088717   ⟹   XP_038944645
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,882,508 (-)NCBI
RefSeq Acc Id: XM_039088718   ⟹   XP_038944646
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,496,788 (-)NCBI
RefSeq Acc Id: XM_039088719   ⟹   XP_038944647
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,882,024 (-)NCBI
RefSeq Acc Id: XM_039088723   ⟹   XP_038944651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,241,230 (-)NCBI
RefSeq Acc Id: XM_039088724   ⟹   XP_038944652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,882,347 (-)NCBI
RefSeq Acc Id: XM_039088725   ⟹   XP_038944653
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2148,688,651 - 49,882,504 (-)NCBI
RefSeq Acc Id: XM_039088727   ⟹   XP_038944655
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2149,303,859 - 49,882,520 (-)NCBI
Protein Sequences
Protein RefSeqs NP_064478 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944638 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944640 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944641 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944642 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944645 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944646 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944647 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944651 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944652 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944653 (Get FASTA)   NCBI Sequence Viewer  
  XP_038944655 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF34874 (Get FASTA)   NCBI Sequence Viewer  
  AAF68666 (Get FASTA)   NCBI Sequence Viewer  
  AAG37013 (Get FASTA)   NCBI Sequence Viewer  
  AAL73348 (Get FASTA)   NCBI Sequence Viewer  
  AAL73349 (Get FASTA)   NCBI Sequence Viewer  
  AAM21452 (Get FASTA)   NCBI Sequence Viewer  
  AAM21453 (Get FASTA)   NCBI Sequence Viewer  
  AAM21454 (Get FASTA)   NCBI Sequence Viewer  
  AAM21455 (Get FASTA)   NCBI Sequence Viewer  
  AAM21456 (Get FASTA)   NCBI Sequence Viewer  
  AAM21460 (Get FASTA)   NCBI Sequence Viewer  
  ADB77772 (Get FASTA)   NCBI Sequence Viewer  
  ADB77773 (Get FASTA)   NCBI Sequence Viewer  
  ADB90267 (Get FASTA)   NCBI Sequence Viewer  
  ADB90268 (Get FASTA)   NCBI Sequence Viewer  
  ADB96018 (Get FASTA)   NCBI Sequence Viewer  
  ADB96019 (Get FASTA)   NCBI Sequence Viewer  
  AGP25364 (Get FASTA)   NCBI Sequence Viewer  
  AGP25365 (Get FASTA)   NCBI Sequence Viewer  
  AGP25367 (Get FASTA)   NCBI Sequence Viewer  
  AGP25368 (Get FASTA)   NCBI Sequence Viewer  
  AGP25369 (Get FASTA)   NCBI Sequence Viewer  
  AGP25370 (Get FASTA)   NCBI Sequence Viewer  
  AGP25371 (Get FASTA)   NCBI Sequence Viewer  
  AGP25372 (Get FASTA)   NCBI Sequence Viewer  
  BAA92431 (Get FASTA)   NCBI Sequence Viewer  
  BAX00771 (Get FASTA)   NCBI Sequence Viewer  
  EDL83078 (Get FASTA)   NCBI Sequence Viewer  
  EDL83079 (Get FASTA)   NCBI Sequence Viewer  
  EDL83080 (Get FASTA)   NCBI Sequence Viewer  
  EDL83081 (Get FASTA)   NCBI Sequence Viewer  
  EDL83082 (Get FASTA)   NCBI Sequence Viewer  
  EDL83083 (Get FASTA)   NCBI Sequence Viewer  
  EDL83084 (Get FASTA)   NCBI Sequence Viewer  
  EDL83085 (Get FASTA)   NCBI Sequence Viewer  
  Q9JK66 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_064478   ⟸   NM_020093
- UniProtKB: Q9JK66 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_038944638   ⟸   XM_039088710
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944640   ⟸   XM_039088712
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944645   ⟸   XM_039088717
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038944642   ⟸   XM_039088714
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038944653   ⟸   XM_039088725
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038944652   ⟸   XM_039088724
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038944647   ⟸   XM_039088719
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038944641   ⟸   XM_039088713
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944646   ⟸   XM_039088718
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038944651   ⟸   XM_039088723
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038944655   ⟸   XM_039088727
- Peptide Label: isoform X10
Protein Domains
Ubiquitin-like


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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
BBDP/Wor (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
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)
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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 (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
BN/SsN (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
BN/SsN (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
BUF/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
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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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
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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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
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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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
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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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
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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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
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)
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)
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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)
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)
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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)
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)
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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