Ngfr (nerve growth factor receptor) - Rat Genome Database

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Gene: Ngfr (nerve growth factor receptor) Rattus norvegicus
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Symbol: Ngfr
Name: nerve growth factor receptor
RGD ID: 3177
Description: Enables several functions, including amyloid-beta binding activity; nerve growth factor binding activity; and neurotrophin TRKA receptor binding activity. Involved in several processes, including positive regulation of cell communication; regulation of neuron death; and regulation of neuron projection development. Located in several cellular components, including dendrite membrane; neuronal cell body membrane; and perikaryon. Used to study degenerative disc disease; glaucoma; hypertension; and middle cerebral artery infarction. Biomarker of several diseases, including brain disease (multiple); neuropathy (multiple); polycystic ovary syndrome; portal hypertension; and respiratory syncytial virus infectious disease. Human ortholog(s) of this gene implicated in Alzheimer's disease and mental depression. Orthologous to human NGFR (nerve growth factor receptor); PARTICIPATES IN cytokine mediated signaling pathway; neurotrophic factor signaling pathway; INTERACTS WITH (+)-pilocarpine; (+)-schisandrin B; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: gp80-LNGFR; LNGFR; low affinity nerve growth factor receptor; low affinity nerve growth factor receptor precursor; low affinity neurotrophin receptor p75NTR; low-affinity nerve growth factor receptor; nerve growth factor receptor (TNFR superfamily, member 16); Nerve growth factor receptor fast; Nerve growth factor receptor, fast; NGF receptor; p75; p75 ICD; p75NTR; RNNGFRR; Tnfrsf16; tumor necrosis factor receptor superfamily member 16
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: QTLs:   Bp134   Cm44   Cm75   Bw102  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21080,515,287 - 80,533,518 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1080,515,299 - 80,533,518 (-)Ensembl
Rnor_6.01083,389,828 - 83,408,061 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1083,389,847 - 83,408,061 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01083,198,396 - 83,216,629 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41084,262,804 - 84,281,006 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11084,277,173 - 84,295,376 (-)NCBI
Celera1079,287,338 - 79,305,497 (-)NCBICelera
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP,ISO)
(+)-schisandrin B  (EXP)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (EXP,ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
aristolochic acid  (ISO)
benzo[a]pyrene  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
Butylbenzyl phthalate  (EXP)
butyric acid  (EXP)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
calcitriol  (EXP,ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
cefaloridine  (EXP)
celecoxib  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cisplatin  (ISO)
clothianidin  (ISO)
clozapine  (EXP,ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
diazinon  (EXP)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP)
diethyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
diisononyl phthalate  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethanol  (ISO)
fenarimol  (EXP)
fenoprofen  (ISO)
fenvalerate  (EXP)
fluoxetine  (ISO)
flurbiprofen  (ISO)
flusilazole  (EXP)
folic acid  (ISO)
fonofos  (ISO)
fructose  (EXP)
Fusarenone X  (ISO)
Geniposide pentaacetate  (EXP)
genistein  (ISO)
ginsenoside Rd  (ISO)
ginsenoside Re  (ISO)
glyceollin  (ISO)
haloperidol  (EXP)
ibuprofen  (ISO)
indometacin  (ISO)
ketoconazole  (EXP)
ketoprofen  (ISO)
L-methionine  (ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
Licochalcone B  (ISO)
manganese(II) chloride  (ISO)
masoprocol  (EXP)
mercury atom  (EXP)
mercury(0)  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
N-[2-[4-(2-methoxyphenyl)-1-piperazinyl]ethyl]-N-(2-pyridinyl)cyclohexanecarboxamide  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-Nitrosopyrrolidine  (ISO)
naproxen  (EXP,ISO)
nicotine  (ISO)
nitrofen  (EXP)
O-methyleugenol  (ISO)
oxaprozin  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP)
parathion  (ISO)
pentanal  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
propanal  (ISO)
propiconazole  (EXP,ISO)
pyrrolidine dithiocarbamate  (EXP)
quetiapine fumarate  (EXP)
resveratrol  (ISO)
risperidone  (EXP)
rotenone  (ISO)
SB 203580  (EXP)
SB 431542  (ISO)
sevoflurane  (EXP)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sulindac sulfone  (ISO)
sumatriptan  (EXP)
tebuconazole  (EXP)
terbufos  (ISO)
tetrachloromethane  (EXP)
titanium dioxide  (ISO)
toluene  (ISO)
trametinib  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of cysteine-type endopeptidase activity involved in apoptotic process  (IEA,ISO)
axon guidance  (IEA,ISO)
cellular glucose homeostasis  (IEA,ISO,ISS)
cellular response to amyloid-beta  (IEA,ISO)
cellular response to oxidative stress  (IMP)
central nervous system development  (IEA,ISO)
circadian regulation of gene expression  (IEA,ISO,ISS)
circadian rhythm  (ISO)
detection of temperature stimulus  (IEA,ISO)
dorsal aorta development  (IEA,ISO)
glucose homeostasis  (ISO,ISS)
hair follicle morphogenesis  (IEA,ISO)
intracellular protein transport  (IEA,ISO,ISS)
negative regulation of angiogenesis  (IMP)
negative regulation of apoptotic process  (IMP)
negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis  (IEA,ISO)
negative regulation of cell migration  (IEA,ISO)
negative regulation of dendritic spine development  (IMP)
negative regulation of fibroblast growth factor receptor signaling pathway  (IEA,ISO)
negative regulation of hair follicle development  (IEA,ISO)
negative regulation of mitochondrial depolarization  (IMP)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of neuron projection development  (IDA)
nerve development  (IEA,ISO)
neuron apoptotic process  (IEA,ISO)
positive regulation of apoptotic process  (IMP)
positive regulation of apoptotic signaling pathway  (IEA,ISO)
positive regulation of excitatory postsynaptic potential  (IMP)
positive regulation of fibroblast proliferation  (IEA,ISO)
positive regulation of MAPK cascade  (IDA)
positive regulation of myelination  (IMP)
positive regulation of neural precursor cell proliferation  (IMP)
positive regulation of neuron death  (IDA)
positive regulation of neuron differentiation  (IDA)
positive regulation of neuron projection development  (IMP)
positive regulation of odontogenesis of dentin-containing tooth  (IEA,ISO)
positive regulation of pri-miRNA transcription by RNA polymerase II  (IEA,ISO)
positive regulation of protein kinase B signaling  (IDA)
positive regulation of protein localization to nucleus  (IEA,ISO)
positive regulation of Rho protein signal transduction  (IDA)
positive regulation of synaptic transmission, cholinergic  (IMP)
positive regulation of synaptic transmission, glutamatergic  (IMP)
regulation of cell death  (IDA)
regulation of gene expression  (ISO)
regulation of reactive oxygen species metabolic process  (IMP)
response to lipopolysaccharide  (IEP)
response to wounding  (IMP)
Rho protein signal transduction  (IBA,IEA,ISO)
sensory perception of pain  (IMP)
signal transduction  (IDA)
skeletal muscle cell differentiation  (IEP)
skin development  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:1317267   PMID:1446821   PMID:7812786   PMID:9268129   PMID:9305641   PMID:10021336   PMID:10536054   PMID:10588868   PMID:10985348   PMID:11279055   PMID:11559852   PMID:11727563  
PMID:11927634   PMID:11978834   PMID:12034707   PMID:12097334   PMID:12376548   PMID:12727325   PMID:12849738   PMID:12860969   PMID:12876432   PMID:12882321   PMID:12882335   PMID:12884521  
PMID:12902347   PMID:12944916   PMID:14623136   PMID:15056278   PMID:15277529   PMID:15337528   PMID:15496412   PMID:15507485   PMID:15525274   PMID:15606485   PMID:15609087   PMID:15694322  
PMID:15701642   PMID:15737741   PMID:15737746   PMID:15754321   PMID:15866043   PMID:15878242   PMID:15911341   PMID:16118792   PMID:16195501   PMID:16246731   PMID:16356734   PMID:16480956  
PMID:16644033   PMID:16690703   PMID:16712417   PMID:16849393   PMID:16877354   PMID:16887120   PMID:17082460   PMID:17108171   PMID:17174281   PMID:17215246   PMID:17217411   PMID:17287525  
PMID:17355907   PMID:17394529   PMID:17494700   PMID:17524373   PMID:17543952   PMID:17639781   PMID:17640868   PMID:17671845   PMID:17696763   PMID:17870109   PMID:17952852   PMID:17997040  
PMID:18090258   PMID:18182498   PMID:18191823   PMID:18400893   PMID:18450779   PMID:18466900   PMID:18511024   PMID:18511210   PMID:18606199   PMID:18625710   PMID:18639597   PMID:18751719  
PMID:18817846   PMID:18842820   PMID:18930116   PMID:19114034   PMID:19138744   PMID:19141250   PMID:19146958   PMID:19156869   PMID:19229990   PMID:19295126   PMID:19376068   PMID:19403809  
PMID:19429059   PMID:19565663   PMID:19585233   PMID:19701634   PMID:19706676   PMID:19762468   PMID:19818769   PMID:19953569   PMID:20022966   PMID:20083190   PMID:20333303   PMID:20530577  
PMID:20559810   PMID:20659559   PMID:20890994   PMID:21150695   PMID:21238591   PMID:21295348   PMID:21300049   PMID:21358016   PMID:21411748   PMID:21569322   PMID:21658451   PMID:21674565  
PMID:22183269   PMID:22238106   PMID:22460790   PMID:23105112   PMID:23260665   PMID:23615109   PMID:23643896   PMID:23785138   PMID:23809594   PMID:23842744   PMID:23973667   PMID:24069373  
PMID:24095693   PMID:24914971   PMID:24939843   PMID:24997497   PMID:25329094   PMID:25394381   PMID:25433207   PMID:25527128   PMID:25665281   PMID:25708205   PMID:26071990   PMID:26212415  
PMID:26268439   PMID:26287629   PMID:26864466   PMID:27038014   PMID:27494324   PMID:27683907   PMID:27726026   PMID:27830679   PMID:27913431   PMID:28380447   PMID:28821608   PMID:28887537  
PMID:29202822   PMID:29226516   PMID:29425916   PMID:30081046   PMID:30357966   PMID:30415068   PMID:31924125   PMID:32685448   PMID:32792564   PMID:33191703  


Genomics

Comparative Map Data
Ngfr
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21080,515,287 - 80,533,518 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1080,515,299 - 80,533,518 (-)Ensembl
Rnor_6.01083,389,828 - 83,408,061 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1083,389,847 - 83,408,061 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01083,198,396 - 83,216,629 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41084,262,804 - 84,281,006 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11084,277,173 - 84,295,376 (-)NCBI
Celera1079,287,338 - 79,305,497 (-)NCBICelera
Cytogenetic Map10q26NCBI
NGFR
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1749,495,293 - 49,515,008 (+)EnsemblGRCh38hg38GRCh38
GRCh381749,495,293 - 49,515,008 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371747,572,655 - 47,592,370 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361744,927,666 - 44,947,360 (+)NCBINCBI36hg18NCBI36
Build 341744,927,665 - 44,947,360NCBI
Celera1744,027,660 - 44,047,391 (+)NCBI
Cytogenetic Map17q21.33NCBI
HuRef1742,937,638 - 42,957,366 (+)NCBIHuRef
CHM1_11747,637,800 - 47,657,550 (+)NCBICHM1_1
Ngfr
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391195,459,644 - 95,478,524 (-)NCBIGRCm39mm39
GRCm39 Ensembl1195,459,644 - 95,478,561 (-)Ensembl
GRCm381195,568,818 - 95,587,698 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1195,568,818 - 95,587,735 (-)EnsemblGRCm38mm10GRCm38
MGSCv371195,430,132 - 95,449,012 (-)NCBIGRCm37mm9NCBIm37
MGSCv361195,384,908 - 95,403,788 (-)NCBImm8
Celera11105,207,524 - 105,226,387 (-)NCBICelera
Cytogenetic Map11DNCBI
cM Map1159.01NCBI
Ngfr
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545112,030,252 - 12,047,305 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545112,030,303 - 12,047,305 (-)NCBIChiLan1.0ChiLan1.0
NGFR
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1178,075,301 - 8,094,966 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl178,075,316 - 8,094,966 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0178,089,600 - 8,109,361 (-)NCBIMhudiblu_PPA_v0panPan3
NGFR
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1925,598,468 - 25,621,021 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl925,601,074 - 25,623,274 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha925,057,204 - 25,079,762 (+)NCBI
ROS_Cfam_1.0926,393,929 - 26,416,386 (+)NCBI
UMICH_Zoey_3.1925,161,801 - 25,184,255 (+)NCBI
UNSW_CanFamBas_1.0925,420,950 - 25,443,499 (+)NCBI
UU_Cfam_GSD_1.0925,550,245 - 25,572,703 (+)NCBI
Ngfr
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560225,017,882 - 25,037,009 (+)NCBI
SpeTri2.0NW_00493649012,038,500 - 12,057,257 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NGFR
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1225,699,427 - 25,720,357 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11225,699,410 - 25,720,355 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21225,702,140 - 25,722,387 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NGFR
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11669,894,000 - 69,914,209 (+)NCBI
ChlSab1.1 Ensembl1669,894,139 - 69,912,189 (+)Ensembl
Vero_WHO_p1.0NW_02366607740,998,497 - 41,018,701 (+)NCBI
Ngfr
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247955,623,686 - 5,639,545 (+)NCBI

Position Markers
D10Wox16  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21080,516,125 - 80,516,250 (+)MAPPERmRatBN7.2
Rnor_6.01083,390,674 - 83,390,798NCBIRnor6.0
Rnor_5.01083,199,242 - 83,199,366UniSTSRnor5.0
RGSC_v3.41084,263,627 - 84,263,752RGDRGSC3.4
RGSC_v3.41084,263,628 - 84,263,752UniSTSRGSC3.4
RGSC_v3.11084,277,997 - 84,278,122RGD
RH 3.4 Map10735.2UniSTS
RH 3.4 Map10735.2RGD
RH 2.0 Map10905.1RGD
Cytogenetic Map10q31UniSTS
D10Arb21  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21080,516,147 - 80,516,346 (+)MAPPERmRatBN7.2
Rnor_6.01083,390,696 - 83,390,894NCBIRnor6.0
Rnor_5.01083,199,264 - 83,199,462UniSTSRnor5.0
RGSC_v3.41084,263,649 - 84,263,848RGDRGSC3.4
RGSC_v3.41084,263,650 - 84,263,848UniSTSRGSC3.4
RGSC_v3.11084,278,019 - 84,278,218RGD
Celera1079,288,199 - 79,288,361UniSTS
FHH x ACI Map1064.75UniSTS
FHH x ACI Map1064.75RGD
Cytogenetic Map10q31UniSTS
D10Mit13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21080,516,134 - 80,516,299 (+)MAPPERmRatBN7.2
Rnor_6.01083,390,683 - 83,390,847NCBIRnor6.0
Rnor_5.01083,199,251 - 83,199,415UniSTSRnor5.0
RGSC_v3.41084,263,636 - 84,263,800RGDRGSC3.4
RGSC_v3.41084,263,637 - 84,263,801UniSTSRGSC3.4
RGSC_v3.11084,278,006 - 84,278,170RGD
Cytogenetic Map10q31UniSTS
D10Arb31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21080,516,021 - 80,516,335 (+)MAPPERmRatBN7.2
Rnor_6.01083,390,570 - 83,390,883NCBIRnor6.0
Rnor_5.01083,199,138 - 83,199,451UniSTSRnor5.0
RGSC_v3.41084,263,524 - 84,263,837UniSTSRGSC3.4
RGSC_v3.11084,277,893 - 84,278,207RGD
Celera1079,288,073 - 79,288,350UniSTS
Cytogenetic Map10q31UniSTS
D10Hmgc1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21080,516,124 - 80,516,311 (+)MAPPERmRatBN7.2
Rnor_6.01083,390,673 - 83,390,859NCBIRnor6.0
Rnor_5.01083,199,241 - 83,199,427UniSTSRnor5.0
RGSC_v3.41084,262,803 - 84,263,813RGDRGSC3.4
RGSC_v3.41084,263,627 - 84,263,813UniSTSRGSC3.4
RH 3.4 Map10745.1UniSTS
RH 3.4 Map10745.1RGD
Cytogenetic Map10q31UniSTS
AW534168  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21080,516,564 - 80,516,716 (+)MAPPERmRatBN7.2
Rnor_6.01083,391,113 - 83,391,264NCBIRnor6.0
Rnor_5.01083,199,681 - 83,199,832UniSTSRnor5.0
RGSC_v3.41084,264,067 - 84,264,218UniSTSRGSC3.4
Celera1079,288,580 - 79,288,731UniSTS
RH 3.4 Map10737.2UniSTS
Cytogenetic Map10q31UniSTS
PMC26408P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21080,523,968 - 80,524,128 (+)MAPPERmRatBN7.2
Rnor_6.01083,398,517 - 83,398,676NCBIRnor6.0
Rnor_5.01083,207,085 - 83,207,244UniSTSRnor5.0
RGSC_v3.41084,271,471 - 84,271,630UniSTSRGSC3.4
Celera1079,295,984 - 79,296,143UniSTS
Cytogenetic Map10q31UniSTS
UniSTS:464682  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21080,517,306 - 80,517,427 (+)MAPPERmRatBN7.2
Rnor_6.01083,391,855 - 83,391,975NCBIRnor6.0
Rnor_5.01083,200,423 - 83,200,543UniSTSRnor5.0
RGSC_v3.41084,264,809 - 84,264,929UniSTSRGSC3.4
Celera1079,289,322 - 79,289,442UniSTS
Cytogenetic Map10q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
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
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
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
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
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
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
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
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106134527681714865Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106134541382564856Rat
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
2298481Eau9Experimental allergic uveoretinitis QTL 90.0169uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)106592723382565079Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
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
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
12880053Cm104Cardiac mass QTL 1040.009heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)107345299283463334Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
12880050Am10Aortic mass QTL 100.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)107437208484007272Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107563188787055282Rat
2325836Bp346Blood pressure QTL 3460.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608584007272Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
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
724516Uae17Urinary albumin excretion QTL 173.6urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)107821062285220348Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)107889965587307728Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)107981378985160854Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:431
Count of miRNA genes:241
Interacting mature miRNAs:280
Transcripts:ENSRNOT00000007268
Prediction methods:Microtar, Miranda, Rnahybrid
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 4 4 4 4 39 14 26
Low 3 32 36 20 19 20 2 2 35 20 14 11 2
Below cutoff 7 17 17 17 6 9 1 1 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000007268   ⟹   ENSRNOP00000007268
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1080,515,299 - 80,533,518 (-)Ensembl
Rnor_6.0 Ensembl1083,389,847 - 83,408,061 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000107122   ⟹   ENSRNOP00000084438
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1080,515,299 - 80,527,405 (-)Ensembl
RefSeq Acc Id: NM_012610   ⟹   NP_036742
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21080,515,287 - 80,533,518 (-)NCBI
Rnor_6.01083,389,835 - 83,408,061 (-)NCBI
Rnor_5.01083,198,396 - 83,216,629 (-)NCBI
RGSC_v3.41084,262,804 - 84,281,006 (-)RGD
Celera1079,287,338 - 79,305,497 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_036742 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB60486 (Get FASTA)   NCBI Sequence Viewer  
  CAA28783 (Get FASTA)   NCBI Sequence Viewer  
  EDM05760 (Get FASTA)   NCBI Sequence Viewer  
  P07174 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036742   ⟸   NM_012610
- Peptide Label: precursor
- UniProtKB: P07174 (UniProtKB/Swiss-Prot),   G3V6P1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000007268   ⟸   ENSRNOT00000007268
RefSeq Acc Id: ENSRNOP00000084438   ⟸   ENSRNOT00000107122
Protein Domains
Death   TNFR-Cys

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)
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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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3177 AgrOrtholog
Ensembl Genes ENSRNOG00000005392 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000007268 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007268 ENTREZGENE, UniProtKB/TrEMBL
InterPro DEATH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Death_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR/NGFR_Cys_rich_reg UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR16_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFRSF16_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24596 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 24596 ENTREZGENE
Pfam Death UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_16_TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_c6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ngfr PhenoGen
PRINTS TNFACTORR16 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE DEATH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_NGFR_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR_NGFR_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DEATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TNFR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47986 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228469
UniProt G3V6P1 ENTREZGENE, UniProtKB/TrEMBL
  P07174 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-28 Ngfr  nerve growth factor receptor  Ngfr  nerve growth factor receptor (TNFR superfamily, member 16)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Ngfr  nerve growth factor receptor (TNFR superfamily, member 16)    nerve growth factor receptor  Name updated 625702 APPROVED
2002-06-10 Ngfr  nerve growth factor receptor      Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction interacts with necdin and MAGE-H1 729117
gene_process mediates oligodendrocyte cell death following spinal cord injury 625697
gene_regulation induced in dying neurons following seizure, ischemia, excitotoxic agents, axotomy, and in cortical neurons following experimental allergic encephalomyelitis 625697
gene_regulation induced by the unprocessed NGF precursor(proNGF) 625697