Hspa5 (heat shock protein family A (Hsp70) member 5) - Rat Genome Database

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Gene: Hspa5 (heat shock protein family A (Hsp70) member 5) Rattus norvegicus
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Symbol: Hspa5
Name: heat shock protein family A (Hsp70) member 5
RGD ID: 2843
Description: Enables unfolded protein binding activity. Involved in several processes, including cellular response to cAMP; cellular response to gamma radiation; and cellular response to metal ion. Acts upstream of or within response to endoplasmic reticulum stress. Located in mitochondrion and smooth endoplasmic reticulum. Biomarker of fatty liver disease; post-traumatic stress disorder; transient cerebral ischemia; ureteral obstruction; and visual epilepsy. Human ortholog(s) of this gene implicated in dopamine beta-hydroxylase deficiency. Orthologous to human HSPA5 (heat shock protein family A (Hsp70) member 5); PARTICIPATES IN codeine and morphine pharmacodynamics pathway; codeine and morphine pharmacokinetics pathway; etoposide pharmacodynamics pathway; INTERACTS WITH (+)-pilocarpine; (+)-schisandrin B; (R)-adrenaline.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 78 kDa glucose-regulated protein; BIP; endoplasmic reticulum chaperone BiP; GRP 78; GRP-78; GRP78; heat shock 70 kDa protein 5; Heat shock 70kD protein 5; heat shock 70kDa protein 5 (glucose-regulated protein); heat shock protein 5; heat shock protein 70 family protein 5; heat shock protein family A member 5; HSP70 family protein 5; immunoglobulin heavy chain-binding protein; steroidogenesis-activator polypeptide
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
mRatBN7.2318,055,507 - 18,059,969 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl318,055,405 - 18,059,891 (+)Ensembl
Rnor_6.0313,838,304 - 13,842,763 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl313,838,304 - 13,842,762 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0319,157,874 - 19,162,333 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4313,783,825 - 13,788,022 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1313,680,196 - 13,684,394 (+)NCBI
Celera312,776,654 - 12,781,113 (+)NCBICelera
RH 3.4 Map3151.7RGD
Cytogenetic Map3p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(+)-schisandrin B  (EXP)
(+)-Tetrandrine  (ISO)
(-)-anisomycin  (ISO)
(-)-gambogic acid  (ISO)
(E)-thiamethoxam  (ISO)
(R)-adrenaline  (EXP)
(R)-lipoic acid  (EXP,ISO)
(R)-noradrenaline  (EXP)
(R,S)-Scoulerine  (ISO)
(S)-colchicine  (ISO)
(S)-nicotine  (EXP,ISO)
(Z)-3-butylidenephthalide  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1,3-dinitrobenzene  (EXP)
1,4-dithiothreitol  (EXP,ISO)
1-bromopropane  (EXP,ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
1-nitropyrene  (ISO)
15-acetyldeoxynivalenol  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,2,2-tetramine  (EXP)
2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,4,6-trinitrotoluene  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2,4-dichlorophenol  (ISO)
2,4-dinitrotoluene  (ISO)
2-amino-2-deoxy-D-galactopyranose  (EXP)
2-amino-2-deoxy-D-glucopyranose  (EXP,ISO)
2-arachidonoylglycerol  (ISO)
2-deoxy-D-glucose  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methyl-6-(phenylethynyl)pyridine  (EXP)
2-tert-butylhydroquinone  (ISO)
20-hydroxyecdysone  (ISO)
3'-amino-3'-deoxy-N(6),N(6)-dimethyladenosine  (EXP)
3,3'-diindolylmethane  (ISO)
3-acetyldeoxynivalenol  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-methyladenine  (ISO)
3H-1,2-dithiole-3-thione  (EXP,ISO)
4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid  (ISO)
4-Hydroxy-TEMPO  (ISO)
4-hydroxynon-2-enal  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutylamine  (ISO)
4-phenylbutyric acid  (EXP,ISO)
5-(N,N-hexamethylene)amiloride  (ISO)
5-fluorouracil  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
7,12-dimethyltetraphene  (EXP)
7H-xanthine  (EXP)
8-Br-cAMP  (ISO)
9H-xanthine  (EXP)
acetylsalicylic acid  (ISO)
acrolein  (EXP,ISO)
acrylamide  (EXP)
actinomycin D  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP,ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinal  (ISO)
all-trans-retinoic acid  (EXP,ISO)
allopurinol  (ISO)
alloxan  (ISO)
Aloe emodin  (ISO)
alpha-(methylamino)isobutyric acid  (ISO)
alpha-D-galactose  (ISO)
amiloride  (ISO)
ammonium chloride  (EXP)
amosite asbestos  (ISO)
amphibole asbestos  (ISO)
aniline  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
antimycin A  (EXP,ISO)
apigenin  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP,ISO)
atazanavir sulfate  (ISO)
ATP  (ISO)
atrazine  (ISO)
BAPTA  (ISO)
beauvericin  (ISO)
benomyl  (ISO)
benzalkonium chloride  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-cyclodextrin  (ISO)
beta-D-glucosamine  (EXP,ISO)
beta-naphthoflavone  (ISO)
bifenthrin  (ISO)
bilirubin IXalpha  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (EXP)
boric acid  (ISO)
bortezomib  (ISO)
brefeldin A  (ISO)
bromobenzene  (EXP)
bufalin  (ISO)
bupropion  (ISO)
buspirone  (EXP)
Butylparaben  (ISO)
butyric acid  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfate  (ISO)
Calcimycin  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
calix[6]arene  (ISO)
Candesartan cilexetil  (EXP)
cannabidiol  (ISO)
cantharidin  (ISO)
capsaicin  (ISO)
carbaryl  (ISO)
carbon atom  (ISO)
carbon nanotube  (ISO)
carboplatin  (EXP)
casticin  (ISO)
celastrol  (ISO)
celecoxib  (ISO)
ceruletide  (EXP)
chenodeoxycholic acid  (ISO)
Chikusetsusaponin-V  (ISO)
chlordecone  (ISO)
chlorhexidine  (ISO)
chloroacetaldehyde  (ISO)
chloroacetic acid  (ISO)
chlorobenzene  (ISO)
chloroethene  (ISO)
chloropicrin  (ISO)
chloroquine  (EXP)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
chromium(6+)  (EXP,ISO)
chrysazin  (ISO)
cidofovir anhydrous  (ISO)
cimetidine  (ISO)
cisplatin  (EXP,ISO)
clofibrate  (EXP,ISO)
cobalt dichloride  (EXP)
cobicistat  (ISO)
cocaine  (EXP,ISO)
colforsin daropate hydrochloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (EXP)
copper(II) sulfate  (EXP,ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cycloheximide  (EXP,ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (EXP,ISO)
cylindrospermopsin  (ISO)
cypermethrin  (ISO)
cytochalasin B  (EXP)
D-glucose  (EXP,ISO)
D-mannopyranose  (ISO)
D-penicillamine  (ISO)
dantrolene  (ISO)
DDT  (EXP,ISO)
demethoxycurcumin  (ISO)
deoxycholic acid  (ISO)
deoxynivalenol  (ISO)
diallyl trisulfide  (ISO)
diamminedichloroplatinum  (ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP,ISO)
dichlorine  (EXP)
diclofenac  (EXP,ISO)
dicoumarol  (ISO)
Dienochlor  (ISO)
diethyl maleate  (ISO)
dihydrocapsaicin  (ISO)
dimethylarsinic acid  (EXP)
Dinitramine  (ISO)
dioscin  (EXP,ISO)
dioxygen  (EXP,ISO)
disodium selenite  (ISO)
diuron  (EXP)
dizocilpine maleate  (EXP)
dopamine  (ISO)
dorsomorphin  (EXP)
doxorubicin  (EXP,ISO)
edaravone  (EXP)
elemental carbon  (ISO)
emodin  (EXP)
endosulfan  (EXP,ISO)
enniatin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
ethylbenzene  (ISO)
fangchinoline  (ISO)
fenofibrate  (EXP)
fenvalerate  (EXP)
fisetin  (ISO)
flavokawain B  (ISO)
fluoranthene  (ISO)
fluorescein 5-isothiocyanate  (ISO)
folic acid  (ISO)
formetanate  (ISO)
fructose  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
furan  (EXP)
Fusarenone X  (ISO)
gadolinium atom  (ISO)
gadolinium trichloride  (EXP)
galactose  (ISO)
gedunin  (ISO)
geldanamycin  (ISO)
gemcitabine  (ISO)
gentamycin  (EXP,ISO)
ginsenoside Rg1  (ISO)
glafenine  (EXP)
glucose  (EXP,ISO)
glutathione  (ISO)
glycine  (ISO)
glycine betaine  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glyphosate  (EXP)
graphene oxide  (ISO)
graphite  (ISO)
Guanabenz  (EXP,ISO)
GW 4064  (ISO)
hexadecanoic acid  (EXP,ISO)
homocysteine  (ISO)
hyaluronic acid  (EXP)
hydralazine  (ISO)
hydrazine  (EXP)
hydrogen peroxide  (EXP,ISO)
hydroxytyrosol  (EXP)
ibuprofen  (EXP,ISO)
Ibutilide  (EXP)
icosanoid  (EXP)
imidacloprid  (ISO)
indinavir  (ISO)
indometacin  (EXP,ISO)
indoxyl sulfate  (ISO)
iodide salt  (EXP)
ionomycin  (ISO)
iprodione  (ISO)
isoflavones  (EXP)
isoprenaline  (EXP,ISO)
ivermectin  (ISO)
ketamine  (EXP)
KN-93  (EXP)
kojic acid  (EXP)
L-1,4-dithiothreitol  (EXP,ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lactacystin  (ISO)
lanthanum atom  (ISO)
lead diacetate  (EXP)
lead nitrate  (ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
lead(II) chloride  (EXP,ISO)
linagliptin  (ISO)
linoleic acid  (ISO)
lipoic acid  (EXP,ISO)
lipopolysaccharide  (EXP,ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
losartan  (EXP)
luteolin  (ISO)
LY294002  (EXP,ISO)
lycopene  (EXP)
maneb  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP)
meglumine amidotrizoate  (EXP)
melatonin  (EXP)
menadione  (ISO)
menaquinone  (ISO)
mercury atom  (EXP)
mercury dichloride  (EXP,ISO)
mercury(0)  (EXP)
metformin  (EXP,ISO)
methamphetamine  (EXP,ISO)
methapyrilene  (EXP)
methomyl  (ISO)
methyl beta-cyclodextrin  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
methylseleninic acid  (ISO)
metyrapone  (ISO)
microcystin  (EXP)
microcystin RR  (ISO)
microcystin-LR  (ISO)
minocycline  (EXP)
mithramycin  (ISO)
Monobutylphthalate  (ISO)
monosodium L-glutamate  (EXP)
morusin  (ISO)
mycophenolic acid  (ISO)
myriocin  (ISO)
N,N-dimethylformamide  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-hexadecanoylsphingosine  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methylnicotinate  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
naloxone  (ISO)
naltrexone  (ISO)
naphthalene  (ISO)
nefazodone  (ISO)
nelfinavir  (ISO)
nickel atom  (EXP)
nickel sulfate  (EXP)
nicotine  (EXP,ISO)
nifedipine  (EXP)
nilotinib  (ISO)
nitric oxide  (ISO)
Nivalenol  (ISO)
nocodazole  (EXP)
Nodularin  (ISO)
Nonidet P-40  (ISO)
nonivamide  (ISO)
Nonylphenol  (EXP)
Norbinaltorphimine  (ISO)
obeticholic acid  (ISO)
ochratoxin A  (ISO)
okadaic acid  (EXP)
oleanolic acid  (ISO)
oleic acid  (EXP,ISO)
oleuropein  (EXP)
orlistat  (ISO)
ouabain  (ISO)
oxaliplatin  (EXP)
oxidopamine  (EXP)
oxycodone  (EXP,ISO)
ozone  (EXP,ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
patulin  (ISO)
perfluorodecanoic acid  (EXP)
perfluorododecanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (ISO)
PhIP  (EXP)
phlorizin  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirimicarb  (ISO)
pirinixic acid  (ISO)
platycodin D  (ISO)
plumbagin  (ISO)
poly(guanylic acid)  (EXP)
potassium dichromate  (EXP,ISO)
potassium iodide  (ISO)
proanthocyanidin  (EXP)
procymidone  (EXP)
progesterone  (ISO)
propiconazole  (ISO)
pterostilbene  (ISO)
pyrazinecarboxamide  (EXP,ISO)
pyrrolidine dithiocarbamate  (EXP)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (EXP,ISO)
Riluzole  (ISO)
rimonabant  (ISO)
Roridin A  (ISO)
rotenone  (EXP,ISO)
rottlerin  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
salubrinal  (EXP,ISO)
salvianolic acid B  (EXP)
saquinavir  (ISO)
SB 203580  (ISO)
SCH 23390  (EXP)
selenomethionine  (EXP)
serpentine asbestos  (ISO)
silicon dioxide  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sirolimus  (EXP,ISO)
SKF-96365 hydrochloride  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (EXP,ISO)
sorafenib  (ISO)
SR 144528  (ISO)
streptozocin  (EXP,ISO)
sulforaphane  (ISO)
sulfur dioxide  (EXP,ISO)
sunitinib  (ISO)
T-2 toxin  (EXP,ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (EXP,ISO)
tanespimycin  (ISO)
tauroursodeoxycholic acid  (EXP,ISO)
tebufenpyrad  (ISO)
telmisartan  (EXP)
TEMPO  (EXP)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (EXP,ISO)
thiamethoxam  (ISO)
thioacetamide  (EXP)
thiostrepton  (ISO)
thymoquinone  (ISO)
Tiron  (ISO)
titanium dioxide  (ISO)
toluene  (EXP,ISO)
transplatin  (ISO)
triadimefon  (EXP)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclocarban  (ISO)
triphenylstannane  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
troglitazone  (EXP,ISO)
tunicamycin  (EXP,ISO)
U-73122  (ISO)
uranium atom  (ISO)
ursodeoxycholic acid  (ISO)
ursolic acid  (ISO)
usnic acid  (ISO)
valproic acid  (EXP,ISO)
vemurafenib  (ISO)
vinclozolin  (EXP)
vincristine  (EXP)
vitamin E  (ISO)
vitexin  (ISO)
vorinostat  (ISO)
wortmannin  (ISO)
xylitol  (ISO)
Z-Val-Phe-H  (ISO)
zearalenone  (ISO)
zinc atom  (EXP,ISO)
zinc oxide  (ISO)
zinc pyrithione  (ISO)
zinc(0)  (EXP,ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cellular response to antibiotic  (IEP)
cellular response to calcium ion  (IEP)
cellular response to cAMP  (IEP)
cellular response to gamma radiation  (IEP)
cellular response to glucose starvation  (ISO)
cellular response to interleukin-4  (ISO)
cellular response to manganese ion  (IEP)
cellular response to nerve growth factor stimulus  (IEP)
cellular response to unfolded protein  (IBA)
cellular response to xenobiotic stimulus  (IEP)
cerebellar Purkinje cell layer development  (ISO)
cerebellum structural organization  (ISO)
chaperone cofactor-dependent protein refolding  (IBA)
endoplasmic reticulum unfolded protein response  (IBA,ISO)
ER overload response  (ISO)
IRE1-mediated unfolded protein response  (ISO)
luteolysis  (IEP)
maintenance of protein localization in endoplasmic reticulum  (ISO,ISS)
negative regulation of apoptotic process  (ISO)
negative regulation of IRE1-mediated unfolded protein response  (ISS)
negative regulation of protein-containing complex assembly  (ISS)
negative regulation of transforming growth factor beta receptor signaling pathway  (ISO)
neuron apoptotic process  (IEP)
neuron differentiation  (IEP)
positive regulation of cell migration  (ISO,ISS)
positive regulation of neuron projection development  (IMP)
positive regulation of protein ubiquitination  (ISO)
posttranslational protein targeting to membrane, translocation  (ISO,ISS)
protein refolding  (IBA)
proteolysis involved in cellular protein catabolic process  (ISO)
response to cocaine  (IEP)
response to endoplasmic reticulum stress  (IDA,IEP)
response to methamphetamine hydrochloride  (IEP)
response to radiation  (IEP)
stress response to metal ion  (IEP)
substantia nigra development  (ISO)
toxin transport  (ISO)
ubiquitin-dependent ERAD pathway  (IBA)

References

References - curated
1. Ahn SM, etal., Psychopharmacology (Berl). 2007 Dec;195(3):407-14. Epub 2007 Sep 13.
2. Aoki T, etal., J Biochem. 1997 Jan;121(1):122-7.
3. Blass S, etal., Arthritis Rheum. 2001 Apr;44(4):761-71.
4. Chen HL, etal., Zhen Ci Yan Jiu. 2014 Dec;39(6):431-6.
5. Cho YM, etal., Exp Mol Med. 2009 Jun 30;41(6):440-52. doi: 10.3858/emm.2009.41.6.049.
6. Chouchani ET, etal., Biochem J. 2010 Aug 15;430(1):49-59. doi: 10.1042/BJ20100633.
7. Croci S, etal., Proteomics. 2010 Nov;10(21):3835-53.
8. Deuring JJ, etal., Biochem J. 2012 Jan 1;441(1):87-93.
9. Falahatpisheh H, etal., Cell Stress Chaperones. 2007 Autumn;12(3):209-18.
10. Faure JJ, etal., Metab Brain Dis. 2009 Dec;24(4):685-700. doi: 10.1007/s11011-009-9167-0. Epub 2009 Oct 14.
11. Fu Q, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2014 Jan;34(1):92-5.
12. Galizzi G, etal., Neurosci Lett. 2011 Jan 25;488(3):258-62. Epub 2010 Nov 19.
13. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
14. GOA data from the GO Consortium
15. Hayashi T and Su TP, Cell. 2007 Nov 2;131(3):596-610.
16. Inokuchi Y, etal., Invest Ophthalmol Vis Sci. 2009 Jan;50(1):334-44. doi: 10.1167/iovs.08-2123. Epub 2008 Aug 29.
17. Jansen G, etal., Mol Cell Proteomics. 2012 Sep;11(9):710-23. doi: 10.1074/mcp.M111.016550. Epub 2012 Jun 4.
18. Kim CH, etal., J Biol Chem. 2011 Mar 18;286(11):9196-204. Epub 2011 Jan 5.
19. Kuznetsov G, etal., J Biol Chem. 1994 Sep 16;269(37):22990-5.
20. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
21. Li SS, etal., Ren Fail. 2015 Jun;37(5):890-5. doi: 10.3109/0886022X.2015.1015427. Epub 2015 Feb 24.
22. Lu JF, etal., Fa Yi Xue Za Zhi. 2018 Aug;34(4):347-351. doi: 10.12116/j.issn.1004-5619.2018.04.001. Epub 2018 Aug 25.
23. Mande PV, etal., Reproduction. 2011 Dec 5.
24. Mantuano E, etal., J Neurosci. 2011 Sep 21;31(38):13376-85.
25. MGD data from the GO Consortium
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34. Pipeline to import SMPDB annotations from SMPDB into RGD
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38. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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Additional References at PubMed
PMID:3468506   PMID:3563495   PMID:7679955   PMID:8666824   PMID:8889548   PMID:9006956   PMID:9798653   PMID:10085239   PMID:10760948   PMID:11181571   PMID:11854325   PMID:11943137  
PMID:12065409   PMID:12411443   PMID:12475965   PMID:12646573   PMID:12665508   PMID:12826667   PMID:14960307   PMID:15166316   PMID:15294975   PMID:15308636   PMID:15452145   PMID:15489334  
PMID:15665855   PMID:15838258   PMID:16223484   PMID:16433633   PMID:16906134   PMID:17634366   PMID:17854840   PMID:17991893   PMID:18400946   PMID:18787714   PMID:18850735   PMID:18923430  
PMID:18953869   PMID:19056867   PMID:19103594   PMID:19199708   PMID:19218986   PMID:19363290   PMID:19411306   PMID:19503733   PMID:19720107   PMID:19769458   PMID:19816510   PMID:19946888  
PMID:20167237   PMID:20235454   PMID:20335166   PMID:20458337   PMID:21187406   PMID:21289099   PMID:21423176   PMID:21429313   PMID:21494687   PMID:21630459   PMID:21970967   PMID:22083547  
PMID:22206666   PMID:22342161   PMID:22460328   PMID:22589549   PMID:22640899   PMID:22689054   PMID:22783020   PMID:22837305   PMID:22926577   PMID:23106098   PMID:23174603   PMID:23175774  
PMID:23215692   PMID:23349634   PMID:23376485   PMID:23716698   PMID:23787763   PMID:23816873   PMID:23913443   PMID:23921388   PMID:23926254   PMID:23975754   PMID:23979707   PMID:23990668  
PMID:24030972   PMID:24334118   PMID:24475200   PMID:24508390   PMID:24625528   PMID:24643222   PMID:24768185   PMID:24880098   PMID:25279841   PMID:25468996   PMID:25863526   PMID:25885223  
PMID:26088419   PMID:26316108   PMID:26376412   PMID:26438849   PMID:26464674   PMID:26582200   PMID:26655470   PMID:26729625   PMID:27905509   PMID:28275724   PMID:28951310   PMID:29476059  
PMID:29719251   PMID:29958740   PMID:30155775   PMID:30217942   PMID:30431062   PMID:30486828   PMID:30895947   PMID:31904090   PMID:32357304   PMID:32657424   PMID:32794050  


Genomics

Comparative Map Data
Hspa5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2318,055,507 - 18,059,969 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl318,055,405 - 18,059,891 (+)Ensembl
Rnor_6.0313,838,304 - 13,842,763 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl313,838,304 - 13,842,762 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0319,157,874 - 19,162,333 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4313,783,825 - 13,788,022 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1313,680,196 - 13,684,394 (+)NCBI
Celera312,776,654 - 12,781,113 (+)NCBICelera
RH 3.4 Map3151.7RGD
Cytogenetic Map3p11NCBI
HSPA5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9125,234,853 - 125,241,382 (-)EnsemblGRCh38hg38GRCh38
GRCh389125,234,853 - 125,241,343 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379127,997,132 - 128,003,622 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369127,036,953 - 127,043,430 (-)NCBINCBI36hg18NCBI36
Build 349125,076,687 - 125,083,163NCBI
Celera998,645,114 - 98,651,649 (-)NCBI
Cytogenetic Map9q33.3NCBI
HuRef997,609,713 - 97,616,253 (-)NCBIHuRef
CHM1_19128,146,874 - 128,153,413 (-)NCBICHM1_1
Hspa5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39234,662,102 - 34,666,541 (+)NCBIGRCm39mm39
GRCm39 Ensembl234,661,982 - 34,667,559 (+)Ensembl
GRCm38234,772,090 - 34,776,529 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl234,771,970 - 34,777,547 (+)EnsemblGRCm38mm10GRCm38
MGSCv37234,627,610 - 34,632,049 (+)NCBIGRCm37mm9NCBIm37
MGSCv36234,594,104 - 34,598,466 (+)NCBImm8
Celera234,472,567 - 34,477,006 (+)NCBICelera
Cytogenetic Map2BNCBI
cM Map222.94NCBI
Hspa5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554193,055,420 - 3,062,131 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554193,055,420 - 3,060,208 (+)NCBIChiLan1.0ChiLan1.0
HSPA5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19124,865,211 - 124,870,458 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9124,865,211 - 124,870,458 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0996,351,645 - 96,356,761 (-)NCBIMhudiblu_PPA_v0panPan3
HSPA5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1957,850,870 - 57,855,607 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl957,850,922 - 57,855,257 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha957,050,544 - 57,055,478 (+)NCBI
ROS_Cfam_1.0958,771,363 - 58,776,290 (+)NCBI
UMICH_Zoey_3.1957,529,524 - 57,534,454 (+)NCBI
UNSW_CanFamBas_1.0957,846,243 - 57,851,163 (+)NCBI
UU_Cfam_GSD_1.0957,936,913 - 57,941,842 (+)NCBI
Hspa5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947193,579,938 - 193,584,190 (-)NCBI
SpeTri2.0NW_00493648713,348,465 - 13,352,717 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HSPA5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1265,930,045 - 265,934,904 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11265,930,044 - 265,934,959 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21299,754,103 - 299,758,617 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap1q2.10-q2.13NCBI
HSPA5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11212,920,705 - 12,925,888 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1212,920,710 - 12,927,431 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660793,184,743 - 3,190,031 (-)NCBIVero_WHO_p1.0
Hspa5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247609,986,529 - 9,991,261 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D2Wsu141e  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2318,059,686 - 18,059,895 (+)MAPPERmRatBN7.2
Rnor_6.0313,842,481 - 13,842,689NCBIRnor6.0
Rnor_5.0319,162,051 - 19,162,259UniSTSRnor5.0
RGSC_v3.4313,787,796 - 13,788,004UniSTSRGSC3.4
Celera312,780,831 - 12,781,039UniSTS
Cytogenetic Map3p11UniSTS
RH94472  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2318,059,718 - 18,059,876 (+)MAPPERmRatBN7.2
Rnor_6.0313,842,513 - 13,842,670NCBIRnor6.0
Rnor_5.0319,162,083 - 19,162,240UniSTSRnor5.0
RGSC_v3.4313,787,828 - 13,787,985UniSTSRGSC3.4
Celera312,780,863 - 12,781,020UniSTS
RH 3.4 Map3151.7UniSTS
Cytogenetic Map3p11UniSTS
D2Wsu17e  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2318,059,658 - 18,059,863 (+)MAPPERmRatBN7.2
Rnor_6.0313,842,453 - 13,842,657NCBIRnor6.0
Rnor_5.0319,162,023 - 19,162,227UniSTSRnor5.0
RGSC_v3.4313,787,768 - 13,787,972UniSTSRGSC3.4
Celera312,780,803 - 12,781,007UniSTS
Cytogenetic Map3p11UniSTS
Hspa5  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2318,059,672 - 18,059,805 (+)MAPPERmRatBN7.2
Rnor_6.0313,842,467 - 13,842,599NCBIRnor6.0
Rnor_5.0319,162,037 - 19,162,169UniSTSRnor5.0
RGSC_v3.4313,787,782 - 13,787,914UniSTSRGSC3.4
Celera312,780,817 - 12,780,949UniSTS
Cytogenetic Map3p11UniSTS
RH125368  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2318,059,164 - 18,059,437 (+)MAPPERmRatBN7.2
Rnor_6.0313,841,959 - 13,842,231NCBIRnor6.0
Rnor_5.0319,161,529 - 19,161,801UniSTSRnor5.0
RGSC_v3.4313,787,274 - 13,787,546UniSTSRGSC3.4
Celera312,780,309 - 12,780,581UniSTS
Cytogenetic Map3p11UniSTS
UniSTS:259180  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2318,056,171 - 18,056,705 (+)MAPPERmRatBN7.2
Rnor_6.0313,838,969 - 13,839,502NCBIRnor6.0
Rnor_5.0319,158,539 - 19,159,072UniSTSRnor5.0
RGSC_v3.4313,784,284 - 13,784,817UniSTSRGSC3.4
Celera312,777,319 - 12,777,852UniSTS
Cytogenetic Map3p11UniSTS
HSPA5_988  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2318,059,084 - 18,059,880 (+)MAPPERmRatBN7.2
Rnor_6.0313,841,879 - 13,842,674NCBIRnor6.0
Rnor_5.0319,161,449 - 19,162,244UniSTSRnor5.0
RGSC_v3.4313,787,194 - 13,787,989UniSTSRGSC3.4
Celera312,780,229 - 12,781,024UniSTS
Cytogenetic Map3p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31737470335528639Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31737470335528639Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)31737470335528639Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)31737470335528639Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)heart rate (CMO:0000002)31737470335528639Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)heart rate (CMO:0000002)31737470335528639Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)body weight (CMO:0000012)31737470335528639Rat
634306Bp140Blood pressure QTL 1403.30.0013arterial blood pressure trait (VT:2000000)body weight (CMO:0000012)31737470335528639Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:70
Count of miRNA genes:48
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000025067
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 13 6 6 2
Medium 3 43 51 35 19 35 8 11 74 33 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025067   ⟹   ENSRNOP00000025064
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl318,055,405 - 18,059,891 (+)Ensembl
Rnor_6.0 Ensembl313,838,304 - 13,842,762 (+)Ensembl
RefSeq Acc Id: NM_013083   ⟹   NP_037215
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2318,055,507 - 18,059,969 (+)NCBI
Rnor_6.0313,838,304 - 13,842,763 (+)NCBI
Rnor_5.0319,157,874 - 19,162,333 (+)NCBI
RGSC_v3.4313,783,825 - 13,788,022 (+)RGD
Celera312,776,654 - 12,781,113 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_037215   ⟸   NM_013083
- Peptide Label: precursor
- UniProtKB: P06761 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025064   ⟸   ENSRNOT00000025067

Transcriptome

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

Promoters
RGD ID:13692006
Promoter ID:EPDNEW_R2531
Type:single initiation site
Name:Hspa5_1
Description:heat shock protein family A member 5
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_6.0313,838,329 - 13,838,389EPDNEW

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