Hspd1 (heat shock protein family D (Hsp60) member 1) - Rat Genome Database

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Gene: Hspd1 (heat shock protein family D (Hsp60) member 1) Rattus norvegicus
Analyze
Symbol: Hspd1
Name: heat shock protein family D (Hsp60) member 1
RGD ID: 621314
Description: Enables modification-dependent protein binding activity. Involved in several processes, including negative regulation of apoptotic process; positive regulation of cytokine production; and response to ischemia. Located in several cellular components, including mitochondrial crista; peroxisomal matrix; and zymogen granule. Used to study Alzheimer's disease and low tension glaucoma. Biomarker of several diseases, including artery disease (multiple); hydrocephalus; hyperglycemia; pulmonary fibrosis; and varicocele. Human ortholog(s) of this gene implicated in artery disease (multiple); autistic disorder; glucose intolerance; hereditary spastic paraplegia (multiple); and hypomyelinating leukodystrophy 4. Orthologous to human HSPD1 (heat shock protein family D (Hsp60) member 1); PARTICIPATES IN RNA degradation pathway; tuberculosis pathway; type 1 diabetes mellitus pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 1,1-dichloroethene; 1-bromopropane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: 60 kDa chaperonin; 60 kDa heat shock protein, mitochondrial; chaperonin 60; CPN60; heat shock 60kD protein 1 (chaperonin); heat shock 60kDa protein 1; heat shock protein 1 (chaperonin); heat shock protein 60 (liver); heat shock protein family D member 1; HSP-60; HSP-65; Hsp60; Hspd1-30p; mitochondrial matrix protein P1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Hspd1-ps1   Hspd1-ps10   Hspd1-ps11   Hspd1-ps12   Hspd1-ps13   Hspd1-ps14   Hspd1-ps15   Hspd1-ps16   Hspd1-ps17   Hspd1-ps18   Hspd1-ps19   Hspd1-ps2   Hspd1-ps20   Hspd1-ps21   Hspd1-ps22   Hspd1-ps23   Hspd1-ps25   Hspd1-ps26   Hspd1-ps27   Hspd1-ps28   Hspd1-ps29   Hspd1-ps3   Hspd1-ps31   Hspd1-ps32   Hspd1-ps4   Hspd1-ps5   Hspd1-ps6   Hspd1-ps7   Hspd1-ps8   Hspd1-ps9  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2956,579,195 - 56,590,011 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl956,579,201 - 56,589,662 (-)Ensembl
Rnor_6.0961,680,529 - 61,691,202 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl961,680,530 - 61,690,956 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0961,361,745 - 61,372,414 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4953,884,193 - 53,895,043 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1953,885,606 - 53,895,580 (-)NCBI
Celera954,060,669 - 54,071,096 (-)NCBICelera
Cytogenetic Map9q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,1-dichloroethene  (EXP)
1,2-dimethylhydrazine  (ISO)
1-bromopropane  (EXP)
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,2,2-tetramine  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrotoluene  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (ISO)
5-methyl-4-oxido-2-pyrazin-4-iumcarboxylic acid  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP,ISO)
7H-xanthine  (EXP)
9H-xanthine  (EXP)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
albendazole  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
amlodipine  (EXP)
ammonium chloride  (EXP)
amphibole asbestos  (ISO)
antimycin A  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
ATP  (EXP)
atrazine  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Brodifacoum  (EXP)
butyric acid  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
CCCP  (ISO)
chelerythrine  (EXP)
chloroacetic acid  (EXP)
chloropicrin  (ISO)
chromium trinitrate  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP)
clofibrate  (EXP,ISO)
clonidine  (EXP)
clonidine (amino form)  (EXP)
clonidine (imino form)  (EXP)
cocaine  (ISO)
colforsin daropate hydrochloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
curcumin  (EXP,ISO)
cyclophosphamide  (EXP)
cyclosporin A  (ISO)
cypermethrin  (EXP)
D-glucose  (ISO)
deguelin  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dichlorine  (EXP)
dicrotophos  (ISO)
dihydroxyacetone  (ISO)
dimethylarsinic acid  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
drospirenone  (ISO)
enzyme inhibitor  (ISO)
ethyl methanesulfonate  (ISO)
fenbuconazole  (ISO)
ferric ammonium citrate  (ISO)
ferric oxide  (ISO)
finasteride  (EXP)
flavone  (ISO)
flavonoids  (ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
formaldehyde  (ISO)
fructose  (EXP)
fulvestrant  (ISO)
Fusaric acid  (ISO)
geldanamycin  (ISO)
genistein  (EXP)
gentamycin  (EXP)
ginsenoside Re  (ISO)
glucose  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
graphite  (ISO)
hyaluronic acid  (EXP)
hydrogen peroxide  (EXP)
Indeno[1,2,3-cd]pyrene  (ISO)
indirubin  (ISO)
indometacin  (ISO)
isotretinoin  (ISO)
ivermectin  (ISO)
ketoconazole  (EXP)
kojic acid  (EXP)
lead diacetate  (ISO)
lead(II) chloride  (ISO)
limonene  (EXP)
lipopolysaccharide  (ISO)
liquiritigenin  (EXP,ISO)
liquiritin  (EXP,ISO)
lovastatin  (ISO)
mercury atom  (EXP)
mercury(0)  (EXP)
methamphetamine  (EXP)
methanol  (EXP)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
mevinphos  (EXP)
miconazole  (EXP)
minocycline  (EXP)
Mitotane  (EXP)
monocrotaline  (EXP,ISO)
motexafin gadolinium  (ISO)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-methylformamide  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosomorpholine  (EXP)
nefazodone  (EXP)
neomycin  (EXP)
nickel atom  (ISO)
nimesulide  (EXP)
nitroprusside  (ISO)
ochratoxin A  (EXP)
ouabain  (ISO)
ozone  (EXP)
p-chloromercuribenzoic acid  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (EXP,ISO)
paraquat  (EXP,ISO)
perfluorododecanoic acid  (EXP)
perfluorooctanoic acid  (EXP,ISO)
phenobarbital  (EXP)
phenytoin  (ISO)
PhIP  (EXP)
phlorizin  (ISO)
picolinic acid  (EXP)
picoxystrobin  (ISO)
pirinixic acid  (EXP,ISO)
poly(propylene imine) macromolecule  (ISO)
potassium chromate  (ISO)
potassium dichromate  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
Propiverine  (EXP)
quartz  (ISO)
quercetin  (ISO)
raloxifene  (EXP,ISO)
reactive oxygen species  (ISO)
Rebamipide  (EXP)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
rotenone  (EXP,ISO)
sarin  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium chromate  (ISO)
sodium dichromate  (EXP,ISO)
sodium fluoride  (EXP,ISO)
stavudine  (ISO)
streptozocin  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
T-2 toxin  (EXP)
tamoxifen  (EXP,ISO)
tanespimycin  (ISO)
tebufenpyrad  (ISO)
tenofovir disoproxil fumarate  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
tetraphene  (ISO)
thapsigargin  (ISO)
thiostrepton  (ISO)
trichloroethene  (EXP)
trimellitic anhydride  (ISO)
Triptolide  (EXP)
troglitazone  (ISO)
tunicamycin  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vincristine  (ISO)
vorinostat  (ISO)
warfarin  (ISO)
zidovudine  (ISO)
zinc acetate  (ISO)
zinc atom  (ISO)
zinc dichloride  (EXP)
zinc pyrithione  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
'de novo' protein folding  (IC)
activation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
adhesion of symbiont to host  (ISO)
apoptotic mitochondrial changes  (IBA,IMP)
B cell activation  (ISO)
B cell proliferation  (ISO)
biological process involved in interaction with symbiont  (ISO)
cellular response to heat  (IEP)
cellular response to interleukin-7  (ISO)
isotype switching to IgG isotypes  (ISO)
mitochondrial unfolded protein response  (IBA)
MyD88-dependent toll-like receptor signaling pathway  (ISO)
negative regulation of apoptotic process  (IMP,ISO)
negative regulation of apoptotic process in bone marrow cell  (IMP)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of reactive oxygen species biosynthetic process  (IMP)
positive regulation of apoptotic process  (ISO)
positive regulation of inflammatory response  (IDA)
positive regulation of interferon-alpha production  (IBA,ISO)
positive regulation of interferon-gamma production  (IBA,ISO)
positive regulation of interleukin-10 production  (ISO)
positive regulation of interleukin-12 production  (ISO)
positive regulation of interleukin-6 production  (IBA,IMP,ISO)
positive regulation of macrophage activation  (ISO)
positive regulation of T cell activation  (IBA,ISO)
positive regulation of T cell mediated immune response to tumor cell  (ISO)
positive regulation of tumor necrosis factor production  (IMP)
protein folding  (IBA)
protein import into mitochondrial intermembrane space  (IBA)
protein refolding  (ISO)
protein stabilization  (ISO)
response to activity  (IEP)
response to ATP  (IEP)
response to cocaine  (IEP)
response to cold  (ISS)
response to estrogen  (IEP)
response to glucocorticoid  (IEP)
response to heat  (IEP)
response to hydrogen peroxide  (IEP)
response to hypoxia  (IEP)
response to ischemia  (IEP)
response to lipopolysaccharide  (IEP)
response to organic cyclic compound  (IEP)
response to organic substance  (IEP)
response to unfolded protein  (ISO)
response to xenobiotic stimulus  (IEP)
T cell activation  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Additional References at PubMed
PMID:1348860   PMID:1516759   PMID:7904573   PMID:8101099   PMID:8824711   PMID:9243807   PMID:9867803   PMID:10205158   PMID:10663613   PMID:11027668   PMID:11050098   PMID:11445587  
PMID:11807771   PMID:12477932   PMID:12865426   PMID:12931191   PMID:12967636   PMID:12970367   PMID:14651853   PMID:15136728   PMID:15252132   PMID:15316393   PMID:15371451   PMID:15489334  
PMID:15616026   PMID:16148103   PMID:16708399   PMID:16854843   PMID:16959573   PMID:17164250   PMID:17307989   PMID:17634366   PMID:17675567   PMID:17823127   PMID:17923681   PMID:18086682  
PMID:18229457   PMID:18256040   PMID:18614015   PMID:18766470   PMID:19056867   PMID:19107191   PMID:19393246   PMID:19527807   PMID:19725078   PMID:19875724   PMID:19945465   PMID:19946888  
PMID:20080761   PMID:20193073   PMID:20458337   PMID:20507888   PMID:20633027   PMID:21245038   PMID:21266579   PMID:21276792   PMID:21328542   PMID:21391123   PMID:21753002   PMID:21874024  
PMID:22658674   PMID:23106098   PMID:23349634   PMID:23976951   PMID:23979707   PMID:24625528   PMID:24746669   PMID:25501148   PMID:25801186   PMID:25870185   PMID:26316108   PMID:26477505  
PMID:26767982   PMID:27056903   PMID:27818197   PMID:29476059   PMID:29581031   PMID:30196524   PMID:30896796   PMID:31802366   PMID:31904090   PMID:32357304   PMID:32892424   PMID:33219889  


Genomics

Comparative Map Data
Hspd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2956,579,195 - 56,590,011 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl956,579,201 - 56,589,662 (-)Ensembl
Rnor_6.0961,680,529 - 61,691,202 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl961,680,530 - 61,690,956 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0961,361,745 - 61,372,414 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4953,884,193 - 53,895,043 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1953,885,606 - 53,895,580 (-)NCBI
Celera954,060,669 - 54,071,096 (-)NCBICelera
Cytogenetic Map9q31NCBI
HSPD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2197,486,584 - 197,516,737 (-)EnsemblGRCh38hg38GRCh38
GRCh382197,486,584 - 197,500,274 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372198,351,308 - 198,364,998 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362198,059,553 - 198,073,243 (-)NCBINCBI36hg18NCBI36
Build 342198,176,815 - 198,190,504NCBI
Celera2192,107,181 - 192,120,871 (-)NCBI
Cytogenetic Map2q33.1NCBI
HuRef2190,203,711 - 190,217,402 (-)NCBIHuRef
CHM1_12198,357,144 - 198,370,838 (-)NCBICHM1_1
Hspd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39155,116,992 - 55,127,402 (-)NCBIGRCm39mm39
GRCm39 Ensembl155,116,994 - 55,127,402 (-)Ensembl
GRCm38155,077,833 - 55,088,243 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl155,077,835 - 55,088,243 (-)EnsemblGRCm38mm10GRCm38
MGSCv37155,134,678 - 55,144,776 (-)NCBIGRCm37mm9NCBIm37
MGSCv36155,022,380 - 55,032,390 (-)NCBImm8
Celera155,597,904 - 55,608,002 (-)NCBICelera
Cytogenetic Map1C1.2NCBI
Hspd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554033,063,133 - 3,073,419 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554033,062,724 - 3,073,419 (+)NCBIChiLan1.0ChiLan1.0
HSPD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B202,623,497 - 202,637,045 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B202,623,497 - 202,636,959 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B84,729,615 - 84,743,352 (-)NCBIMhudiblu_PPA_v0panPan3
HSPD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1377,010,421 - 7,025,912 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha377,956,566 - 7,967,852 (-)NCBI
ROS_Cfam_1.0376,900,931 - 6,911,990 (-)NCBI
ROS_Cfam_1.0 Ensembl376,900,933 - 6,911,980 (-)Ensembl
UMICH_Zoey_3.1376,899,765 - 6,910,835 (-)NCBI
UNSW_CanFamBas_1.0376,866,679 - 6,877,757 (-)NCBI
UU_Cfam_GSD_1.0376,889,830 - 6,900,900 (-)NCBI
Hspd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303155,150,440 - 155,160,005 (-)NCBI
SpeTri2.0NW_0049365061,678,069 - 1,687,632 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HSPD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15101,360,094 - 101,373,527 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115101,360,355 - 101,373,498 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215112,534,459 - 112,547,603 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HSPD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11083,003,266 - 83,017,397 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1083,003,717 - 83,017,363 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040116,426,692 - 116,441,017 (+)NCBIVero_WHO_p1.0
Hspd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248892,736,727 - 2,746,333 (+)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92043051965430519Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92207116986369743Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92207120067071200Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92375402458157242Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92375402461381613Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92375414483851531Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92526804479271759Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)92746863972468639Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93253550577535505Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93253550577535505Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)93696235977814038Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)93696235992058970Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94019418885194188Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94019418885194188Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94249534379271511Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94279151387976209Rat
11353951Bp394Blood pressure QTL 394arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94464992189649921Rat
12879506Pur33Proteinuria QTL 33total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)94464992189649921Rat
11353957Bmd92Bone mineral density QTL 920.01tibia mineral mass (VT:1000283)volumetric bone mineral density (CMO:0001553)94611419991114199Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94859825193598251Rat
1598849Memor17Memory QTL 172.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)94996854671098346Rat
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)95584784177026453Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:55
Count of miRNA genes:50
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000066589
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 4 20 6 6 2 4
Medium 3 39 43 35 19 35 8 11 72 35 37 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066589   ⟹   ENSRNOP00000063666
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl956,579,201 - 56,589,662 (-)Ensembl
Rnor_6.0 Ensembl961,680,530 - 61,690,956 (-)Ensembl
RefSeq Acc Id: NM_022229   ⟹   NP_071565
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2956,579,196 - 56,589,622 (-)NCBI
Rnor_6.0961,680,530 - 61,690,956 (-)NCBI
Rnor_5.0961,361,745 - 61,372,414 (-)NCBI
RGSC_v3.4953,884,193 - 53,895,043 (-)RGD
Celera954,060,669 - 54,071,096 (-)RGD
Sequence:
RefSeq Acc Id: XM_006244932   ⟹   XP_006244994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2956,579,195 - 56,590,011 (-)NCBI
Rnor_6.0961,680,529 - 61,691,202 (-)NCBI
Rnor_5.0961,361,745 - 61,372,414 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_071565   ⟸   NM_022229
- UniProtKB: P63039 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006244994   ⟸   XM_006244932
- Peptide Label: isoform X1
- UniProtKB: P63039 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063666   ⟸   ENSRNOT00000066589

Transcriptome

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

Promoters
RGD ID:13696671
Promoter ID:EPDNEW_R7195
Type:initiation region
Name:Hspd1_1
Description:heat shock protein family D member 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0961,690,958 - 61,691,018EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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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
LE/Stm (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
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)
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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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 61362288 61362289 C T snv NIG-III/Hok (KyushuU)
9 61362318 61362319 C G snv HTX/Kyo (KyushuU)
9 61371131 61371132 T G snv F344/Jcl (KyushuU)


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 61681102 61681103 C G snv CDR
9 61682192 61682193 T C snv FHL/EurMcwi (MCW)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 53885800 53885801 C G snv LE/Stm (KNAW)
9 53891577 53891578 G T snv LCR/2Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621314 AgrOrtholog
Ensembl Genes ENSRNOG00000014525 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000063666 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000066589 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.560.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.260.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.50.7.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7103955 IMAGE-MGC_LOAD
InterPro Chaperonin_Cpn60_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chaprnin_Cpn60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cpn60/TCP-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GroEL-like_apical_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GROEL-like_equatorial_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TCP-1-like_intermed_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:63868 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:91701 IMAGE-MGC_LOAD
NCBI Gene 63868 ENTREZGENE
Pfam Cpn60_TCP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hspd1 PhenoGen
PRINTS CHAPERONIN60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CHAPERONINS_CPN60 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48592 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52029 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54849 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs GroEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A482IDN3_RAT UniProtKB/TrEMBL
  CH60_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary P19226 UniProtKB/Swiss-Prot
  P19227 UniProtKB/Swiss-Prot
  P97602 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-10 Hspd1  heat shock protein family D (Hsp60) member 1  Hspd1  heat shock protein family D member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-25 Hspd1  heat shock protein family D member 1  Hspd1  heat shock protein 1 (chaperonin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-09-03 Hspd1  heat shock protein 1 (chaperonin)  Hspd1  heat shock 60kDa protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-08-12 Hspd1  heat shock 60kDa protein 1  Hspd1  heat shock protein 1 (chaperonin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Hspd1  heat shock protein 1 (chaperonin)  Hsp60  heat shock protein 60 (liver)  Symbol and Name updated 1299863 APPROVED
2002-08-07 Hsp60  heat shock protein 60 (liver)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction linked to Hspe1 by a region of 280 bp 633052