Hsf1 (heat shock transcription factor 1) - Rat Genome Database

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Gene: Hsf1 (heat shock transcription factor 1) Rattus norvegicus
Analyze
Symbol: Hsf1
Name: heat shock transcription factor 1
RGD ID: 620913
Description: Enables several functions, including STAT family protein binding activity; promoter-specific chromatin binding activity; and sequence-specific single stranded DNA binding activity. Involved in several processes, including cellular response to lipid; positive regulation of macromolecule metabolic process; and regulation of inclusion body assembly. Located in chromatin; cytoplasm; and nucleus. Used to study Parkinson's disease; muscular atrophy; and transient cerebral ischemia. Biomarker of Alzheimer's disease; Parkinson's disease; congestive heart failure; cryptorchidism; and transient cerebral ischemia. Human ortholog(s) of this gene implicated in Huntington's disease. Orthologous to human HSF1 (heat shock transcription factor 1); INTERACTS WITH (+)-schisandrin B; (R)-adrenaline; (Z)-ligustilide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: heat shock factor protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27108,196,040 - 108,223,011 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7108,196,056 - 108,223,011 (+)Ensembl
Rnor_6.07117,538,523 - 117,565,478 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,538,523 - 117,565,478 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,526,154 - 117,553,109 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,524,211 - 114,551,166 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17114,580,681 - 114,585,056 (+)NCBI
Celera7104,547,683 - 104,574,508 (+)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(20S)-ginsenoside Rg3  (ISO)
(R)-adrenaline  (EXP)
(R,S)-Scoulerine  (ISO)
(Z)-ligustilide  (EXP)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
1-naphthyl isothiocyanate  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-nitrofluorene  (EXP)
2-tert-butylhydroquinone  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (ISO)
7H-xanthine  (EXP)
9H-xanthine  (EXP)
acetate ester  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (EXP,ISO)
albendazole  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
allyl alcohol  (ISO)
alpha-D-galactose  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphibole asbestos  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
apratoxin A  (ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
Aurin  (ISO)
azathioprine  (ISO)
Bardoxolone methyl  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
C.I. Natural Red 20  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfate  (ISO)
Calcimycin  (ISO)
capsaicin  (EXP)
carbamazepine  (ISO)
carbonyl cyanide p-trifluoromethoxyphenylhydrazone  (ISO)
ceftazidime pentahydrate  (ISO)
celastrol  (EXP,ISO)
chelidonine  (ISO)
chlorphenamine  (ISO)
cisplatin  (ISO)
clotrimazole  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP)
curcumin  (EXP,ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
cyproheptadine  (ISO)
D-glucose  (ISO)
dactolisib  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (EXP,ISO)
diltiazem  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
ebselen  (ISO)
elesclomol  (ISO)
epoxomicin  (ISO)
etacrynic acid  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenbendazole  (ISO)
fenofibrate  (EXP)
fipronil  (EXP)
flavonoids  (EXP)
formaldehyde  (ISO)
fotemustine  (ISO)
fulvestrant  (ISO)
furosemide  (ISO)
galactose  (ISO)
geldanamycin  (ISO)
geneticin  (ISO)
gentamycin  (EXP,ISO)
glucose  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
hemin  (ISO)
homocysteic acid  (EXP)
hydrogen chloride  (ISO)
hydrogen peroxide  (EXP,ISO)
ibuprofen  (ISO)
imipramine  (ISO)
indole-3-methanol  (ISO)
indometacin  (ISO)
L-serine  (ISO)
lactacystin  (ISO)
lead diacetate  (ISO)
linalool  (ISO)
LY294002  (ISO)
maneb  (ISO)
melatonin  (ISO)
menadione  (ISO)
mercury atom  (ISO)
mercury dichloride  (ISO)
mercury(0)  (ISO)
mesalamine  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
mifepristone  (ISO)
mometasone furoate  (ISO)
monohexyl phthalate  (ISO)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nickel sulfate  (ISO)
nifedipine  (ISO)
nimesulide  (ISO)
nitrofurantoin  (ISO)
oxaprozin  (ISO)
oxyphenbutazone  (ISO)
ozone  (ISO)
papaverine  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
parthenolide  (ISO)
PD 0325901  (ISO)
pevonedistat  (ISO)
Phenoxybenzamine  (ISO)
phenprocoumon  (ISO)
phosphocholine  (ISO)
phosphorylcholine chloride  (ISO)
piperidones  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
PLX-4720  (ISO)
promegestone  (ISO)
promethazine  (ISO)
pyocyanine  (EXP)
pyridine  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rivastigmine  (ISO)
rotenone  (ISO)
SB 203580  (EXP)
Securinine  (ISO)
senecionine  (ISO)
Shikonin  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
silver(1+) nitrate  (ISO)
simvastatin  (ISO)
sirolimus  (ISO)
sodium arsenite  (ISO)
Sodium salicylate  (ISO)
solanesol  (ISO)
sphingosine 1-phosphate  (ISO)
sulforaphane  (ISO)
sulindac  (ISO)
sunitinib  (ISO)
tanespimycin  (ISO)
teprenone  (ISO)
teriflunomide  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP)
thalidomide  (ISO)
thiazoles  (ISO)
thioacetamide  (EXP)
thiopental  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)
withaferin A  (ISO)
wortmannin  (ISO)
zinc atom  (ISO)
zinc oxide  (ISO)
zinc pyrithione  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular protein-containing complex assembly  (ISO)
cellular response to amino acid stimulus  (IDA,IEP)
cellular response to angiotensin  (IDA)
cellular response to cadmium ion  (ISO)
cellular response to copper ion  (ISO)
cellular response to diamide  (ISO)
cellular response to estradiol stimulus  (IDA)
cellular response to gamma radiation  (ISO)
cellular response to heat  (IMP,ISO)
cellular response to hydrogen peroxide  (IMP)
cellular response to L-glutamine  (IEP)
cellular response to lipopolysaccharide  (IEP)
cellular response to nitroglycerin  (IEP)
cellular response to organic cyclic compound  (IDA)
cellular response to potassium ion  (IEP)
cellular response to radiation  (IDA)
cellular response to sodium arsenite  (ISO)
cellular response to unfolded protein  (ISO)
cellular response to xenobiotic stimulus  (IEP)
defense response  (IDA)
embryonic placenta development  (ISO)
embryonic process involved in female pregnancy  (ISO)
female meiotic nuclear division  (ISO)
in utero embryonic development  (ISO)
MAPK cascade  (ISO)
mRNA transcription  (ISO)
negative regulation of cardiac muscle cell apoptotic process  (IMP)
negative regulation of cell population proliferation  (ISO)
negative regulation of double-strand break repair via nonhomologous end joining  (ISO)
negative regulation of gene expression  (IMP)
negative regulation of inclusion body assembly  (IMP)
negative regulation of neuron death  (IMP)
negative regulation of protein-containing complex assembly  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
negative regulation of tumor necrosis factor production  (ISO)
positive regulation of apoptotic DNA fragmentation  (IMP)
positive regulation of cell population proliferation  (ISO)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  (IMP)
positive regulation of DNA-binding transcription factor activity  (ISO)
positive regulation of gene expression  (IMP,ISO)
positive regulation of inclusion body assembly  (IMP)
positive regulation of macrophage differentiation  (ISO)
positive regulation of microtubule binding  (IMP)
positive regulation of mitotic cell cycle  (ISO)
positive regulation of mRNA polyadenylation  (ISO)
positive regulation of multicellular organism growth  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription from RNA polymerase II promoter in response to heat stress  (ISO)
positive regulation of tyrosine phosphorylation of STAT protein  (IMP)
protein phosphorylation  (ISO)
regulation of cellular response to heat  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (TAS)
response to activity  (IEP)
response to amino acid  (IEP)
response to estradiol  (IDA)
response to heat  (IDA,ISO)
response to hypobaric hypoxia  (IEP)
response to lipopolysaccharide  (ISO)
response to nutrient  (IEP)
response to organic cyclic compound  (IEP)
response to organonitrogen compound  (IEP)
response to peptide  (IEP)
response to psychosocial stress  (IEP)
response to testosterone  (IDA)
spermatogenesis  (ISO)

Cellular Component

References

References - curated
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10. GOA data from the GO Consortium
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Additional References at PubMed
PMID:7760831   PMID:7935471   PMID:8455624   PMID:8926278   PMID:9222587   PMID:9341107   PMID:9499401   PMID:9727490   PMID:10359787   PMID:10413683   PMID:10545106   PMID:10561509  
PMID:10747973   PMID:11032181   PMID:11514557   PMID:11583998   PMID:12659875   PMID:12665592   PMID:12917326   PMID:14707147   PMID:14766729   PMID:14994269   PMID:15016915   PMID:15483628  
PMID:15877948   PMID:16278218   PMID:16554823   PMID:16889897   PMID:16990482   PMID:17095722   PMID:17536178   PMID:17589386   PMID:17785525   PMID:17897941   PMID:18242848   PMID:18398426  
PMID:18434628   PMID:18755693   PMID:18794143   PMID:19910575   PMID:20426530   PMID:21085490   PMID:21098017   PMID:21597468   PMID:21690297   PMID:22246807   PMID:23587726   PMID:23769970  
PMID:23902977   PMID:24065656   PMID:25109347   PMID:25963659   PMID:26159920   PMID:26251235   PMID:26359349   PMID:26436502   PMID:26719858   PMID:26727490   PMID:26754925   PMID:27216364  
PMID:28383811   PMID:29257252   PMID:29997244   PMID:30143534   PMID:30467350   PMID:31522994   PMID:32457290   PMID:33989081  


Genomics

Comparative Map Data
Hsf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27108,196,040 - 108,223,011 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl7108,196,056 - 108,223,011 (+)Ensembl
Rnor_6.07117,538,523 - 117,565,478 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,538,523 - 117,565,478 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,526,154 - 117,553,109 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,524,211 - 114,551,166 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17114,580,681 - 114,585,056 (+)NCBI
Celera7104,547,683 - 104,574,508 (+)NCBICelera
Cytogenetic Map7q34NCBI
HSF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8144,291,591 - 144,314,720 (+)EnsemblGRCh38hg38GRCh38
GRCh388144,291,603 - 144,314,720 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh378145,515,286 - 145,538,383 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 368145,486,078 - 145,509,193 (+)NCBINCBI36hg18NCBI36
Build 348145,486,090 - 145,509,187NCBI
Celera8141,707,360 - 141,713,153 (+)NCBI
Cytogenetic Map8q24.3NCBI
HuRef8140,629,839 - 140,652,904 (+)NCBIHuRef
CHM1_18145,553,452 - 145,576,661 (+)NCBICHM1_1
Hsf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391576,361,562 - 76,385,355 (+)NCBIGRCm39mm39
GRCm39 Ensembl1576,361,622 - 76,386,113 (+)Ensembl
GRCm381576,477,362 - 76,501,155 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1576,477,422 - 76,501,913 (+)EnsemblGRCm38mm10GRCm38
MGSCv371576,307,875 - 76,331,402 (+)NCBIGRCm37mm9NCBIm37
MGSCv361576,304,700 - 76,328,227 (+)NCBImm8
Celera1577,977,956 - 78,001,512 (+)NCBICelera
Cytogenetic Map15D3NCBI
cM Map1535.95NCBI
Hsf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554542,907,265 - 2,932,351 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554542,907,265 - 2,932,352 (+)NCBIChiLan1.0ChiLan1.0
HSF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.18144,062,137 - 144,067,725 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl8144,062,137 - 144,067,866 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v08141,055,310 - 141,078,360 (+)NCBIMhudiblu_PPA_v0panPan3
HSF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11337,724,741 - 37,745,259 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1337,724,759 - 37,745,252 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1337,688,336 - 37,708,839 (+)NCBI
ROS_Cfam_1.01338,200,982 - 38,221,480 (+)NCBI
UMICH_Zoey_3.11337,893,218 - 37,913,632 (+)NCBI
UNSW_CanFamBas_1.01338,001,763 - 38,022,270 (+)NCBI
UU_Cfam_GSD_1.01338,478,086 - 38,498,596 (+)NCBI
Hsf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303501,635 - 524,700 (-)NCBI
SpeTri2.0NW_0049364707,927,734 - 7,950,805 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HSF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4461,559 - 486,473 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14463,531 - 486,483 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24610,323 - 633,482 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HSF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.18138,503,836 - 138,529,562 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl8138,503,831 - 138,529,165 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660391,334,097 - 1,360,855 (-)NCBIVero_WHO_p1.0
Hsf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473512,536,818 - 12,562,643 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
Hsf1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27108,220,039 - 108,220,337 (+)MAPPERmRatBN7.2
Rnor_6.07117,562,507 - 117,562,804NCBIRnor6.0
Rnor_5.07117,550,138 - 117,550,435UniSTSRnor5.0
Celera7104,571,538 - 104,571,835UniSTS
Cytogenetic Map7q34UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)784257275129257275Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7103146217116738842Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)780221299124373579Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)780221299112308525Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)780221299125221299Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)791412594129807172Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)780221299109401111Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)784257275129257275Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)783153392128153392Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)794811326116294265Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)781737938126737938Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)794811085116738842Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:60
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000050108
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
Medium 3 35 32 19 18 19 5 8 66 29 40 11 5
Low 8 25 22 1 22 3 3 8 6 1 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000050108   ⟹   ENSRNOP00000047030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7108,196,056 - 108,223,011 (+)Ensembl
Rnor_6.0 Ensembl7117,538,523 - 117,565,478 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098804   ⟹   ENSRNOP00000091032
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7108,196,056 - 108,222,720 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101096   ⟹   ENSRNOP00000090341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7108,196,056 - 108,223,011 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106601   ⟹   ENSRNOP00000076751
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7108,217,511 - 108,223,011 (+)Ensembl
RefSeq Acc Id: NM_024393   ⟹   NP_077369
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27108,196,056 - 108,223,011 (+)NCBI
Rnor_6.07117,538,523 - 117,565,478 (+)NCBI
Rnor_5.07117,526,154 - 117,553,109 (+)NCBI
RGSC_v3.47114,524,211 - 114,551,166 (+)RGD
Celera7104,547,683 - 104,574,508 (+)RGD
Sequence:
RefSeq Acc Id: XM_006241888   ⟹   XP_006241950
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27108,196,042 - 108,222,779 (+)NCBI
Rnor_6.07117,538,538 - 117,565,246 (+)NCBI
Rnor_5.07117,526,154 - 117,553,109 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241889   ⟹   XP_006241951
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27108,196,040 - 108,222,671 (+)NCBI
Rnor_6.07117,538,537 - 117,565,246 (+)NCBI
Rnor_5.07117,526,154 - 117,553,109 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241890   ⟹   XP_006241952
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27108,196,042 - 108,222,779 (+)NCBI
Rnor_6.07117,538,538 - 117,565,246 (+)NCBI
Rnor_5.07117,526,154 - 117,553,109 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006241891   ⟹   XP_006241953
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27108,196,043 - 108,222,779 (+)NCBI
Rnor_6.07117,538,539 - 117,565,246 (+)NCBI
Rnor_5.07117,526,154 - 117,553,109 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039079940   ⟹   XP_038935868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27108,196,041 - 108,222,671 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_077369   ⟸   NM_024393
- UniProtKB: F1MAF1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241951   ⟸   XM_006241889
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006241950   ⟸   XM_006241888
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006241952   ⟸   XM_006241890
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006241953   ⟸   XM_006241891
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: ENSRNOP00000047030   ⟸   ENSRNOT00000050108
RefSeq Acc Id: XP_038935868   ⟸   XM_039079940
- Peptide Label: isoform X5
RefSeq Acc Id: ENSRNOP00000090341   ⟸   ENSRNOT00000101096
RefSeq Acc Id: ENSRNOP00000091032   ⟸   ENSRNOT00000098804
RefSeq Acc Id: ENSRNOP00000076751   ⟸   ENSRNOT00000106601
Protein Domains
HSF_DOMAIN   Vert_HS_TF

Transcriptome

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

Promoters
RGD ID:13695425
Promoter ID:EPDNEW_R5948
Type:initiation region
Name:Hsf1_1
Description:heat shock transcription factor 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_6.07117,538,570 - 117,538,630EPDNEW

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)
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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)
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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)
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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/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)
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)
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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)
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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:620913 AgrOrtholog
Ensembl Genes ENSRNOG00000021732 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000047030 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050108 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro HSF_DNA-bd UniProtKB/TrEMBL
  HSF_fam UniProtKB/TrEMBL
  Vert_HS_TF UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:79245 UniProtKB/TrEMBL
NCBI Gene 79245 ENTREZGENE
PANTHER PTHR10015 UniProtKB/TrEMBL
Pfam HSF_DNA-bind UniProtKB/TrEMBL
  Vert_HS_TF UniProtKB/TrEMBL
PhenoGen Hsf1 PhenoGen
PRINTS HSFDOMAIN UniProtKB/TrEMBL
PROSITE HSF_DOMAIN UniProtKB/TrEMBL
SMART HSF UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt F1MAF1 ENTREZGENE, UniProtKB/TrEMBL
  Q63717_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-02-26 Hsf1  heat shock transcription factor 1      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Hsf1  heat shock transcription factor 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation activated by hyperphosphorylation following heat shock 708322
gene_regulation heat shock and exercise promotes Hsf1-heat shock element (HSE) DNA binding in the myocardium in the absence of changes in reduced glutathione (GSH) 625653