Sqstm1 (sequestosome 1) - Rat Genome Database
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Gene: Sqstm1 (sequestosome 1) Rattus norvegicus
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Symbol: Sqstm1
Name: sequestosome 1
RGD ID: 69287
Description: Exhibits identical protein binding activity and protein kinase C binding activity. Involved in positive regulation of protein phosphorylation and response to ischemia. Localizes to Lewy body and mitochondrion. Biomarker of glaucoma and hypertension. Human ortholog(s) of this gene implicated in GNE myopathy; Paget's disease of bone; and frontotemporal dementia and/or amyotrophic lateral sclerosis-3. Orthologous to human SQSTM1 (sequestosome 1); PARTICIPATES IN interleukin-1 signaling pathway; mitochondrial autophagy pathway; nuclear factor, erythroid 2 like 2 signaling pathway; INTERACTS WITH (+)-schisandrin B; (-)-anisomycin; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: induced oxidative stress-like; Osi; oxidative stress induced; PKC-zeta-interacting protein; protein kinase C-zeta-interacting protein; sequestosome-1; ubiquitin-binding protein p62; ZIP; ZIP3
Orthologs:
Homo sapiens (human) : SQSTM1 (sequestosome 1)  HGNC  Alliance
Mus musculus (house mouse) : Sqstm1 (sequestosome 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Sqstm1 (sequestosome 1)
Pan paniscus (bonobo/pygmy chimpanzee) : SQSTM1 (sequestosome 1)
Canis lupus familiaris (dog) : SQSTM1 (sequestosome 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Sqstm1 (sequestosome 1)
Sus scrofa (pig) : SQSTM1 (sequestosome 1)
Chlorocebus sabaeus (African green monkey) : SQSTM1 (sequestosome 1)
Heterocephalus glaber (naked mole-rat) : Sqstm1 (sequestosome 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: suggests misassembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01035,704,728 - 35,716,316 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1035,704,730 - 35,716,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01035,463,172 - 35,474,754 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41035,751,300 - 35,762,630 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11035,752,706 - 35,763,676 (-)NCBI
Celera1033,874,680 - 33,885,832 (-)NCBICelera
Cytogenetic Map10q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(+)-Tetrandrine  (ISO)
(-)-anisomycin  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-benzothiazole-2-thiol  (ISO)
1,4-benzoquinone  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-(chloromethyl)pyridine  (ISO)
2-butoxyethanol  (ISO)
2-deoxy-D-glucose  (ISO)
2-hydroxyethyl methacrylate  (ISO)
2-hydroxypropanoic acid  (ISO)
2-methoxyethanol  (EXP)
2-tert-butylhydroquinone  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (EXP,ISO)
3-phenylprop-2-enal  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4'-epidoxorubicin  (EXP)
4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid  (ISO)
4,4'-methylene-bis-(2-chloroaniline)  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (ISO)
4-nitro-1,2-phenylenediamine  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
7beta-aminocephalosporanic acid  (ISO)
abamectin  (ISO)
acarbose  (ISO)
acrolein  (ISO)
actinomycin D  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
aloxistatin  (ISO)
alpha,alpha-trehalose  (ISO)
alpha-D-galactose  (EXP,ISO)
amiodarone  (ISO)
ammonium chloride  (EXP,ISO)
ammonium hexachloroplatinate  (ISO)
andrographolide  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (EXP,ISO)
artesunate  (ISO)
astemizole  (EXP)
astragaloside IV  (EXP)
atazanavir sulfate  (ISO)
avobenzone  (ISO)
azathioprine  (ISO)
bafilomycin A1  (EXP,ISO)
benzidine  (ISO)
benzo[a]pyrene  (EXP,ISO)
beta-naphthoflavone  (ISO)
beta-thujaplicin  (ISO)
bexarotene  (EXP)
bicalutamide  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (EXP,ISO)
brazilin  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP,ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
camptothecin  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbon disulfide  (EXP,ISO)
carbon nanotube  (ISO)
carglumic acid  (ISO)
CCCP  (ISO)
celastrol  (EXP)
celecoxib  (ISO)
cerium trichloride  (ISO)
chenodeoxycholic acid  (ISO)
CHIR 99021  (ISO)
chloroacetaldehyde  (ISO)
chlorogenic acid  (ISO)
chloropicrin  (ISO)
chloroquine  (EXP,ISO)
cholesterol  (ISO)
cholic acid  (ISO)
chromium(6+)  (ISO)
ciglitazone  (ISO)
ciprofibrate  (ISO)
cisplatin  (EXP,ISO)
Citreoviridin  (EXP,ISO)
clofibrate  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP,ISO)
cocaine  (ISO)
Colforsin dapropate hydrochloride  (ISO)
colistin  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
Corynoxine B  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
Cryptotanshinone  (ISO)
cucurbitacin E  (ISO)
cyclosporin A  (EXP,ISO)
cylindrospermopsin  (ISO)
cypermethrin  (ISO)
D-glucose  (EXP,ISO)
dactolisib  (ISO)
DDT  (ISO)
deoxycholic acid  (ISO)
deoxynivalenol  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (EXP,ISO)
dibenzofuran  (ISO)
dibutyl phthalate  (ISO)
dieldrin  (EXP)
diethyl maleate  (ISO)
dinitrogen  (ISO)
dioxygen  (EXP,ISO)
disodium selenite  (EXP,ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (EXP)
embelin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
epichlorohydrin  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
eugenol  (ISO)
excitatory amino acid agonist  (EXP)
fenofibrate  (EXP)
fingolimod hydrochloride  (ISO)
flavokawain B  (ISO)
fluoxetine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
furosemide  (EXP)
Fusaric acid  (ISO)
galactose  (EXP,ISO)
gamma-hexachlorocyclohexane  (ISO)
gefitinib  (ISO)
Genipin  (ISO)
genistein  (ISO)
geraniol  (ISO)
glucose  (EXP,ISO)
glutathione  (ISO)
glycerol 2-phosphate  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glycyrrhizinic acid  (EXP)
gossypetin  (ISO)
graphene oxide  (ISO)
graphite  (EXP,ISO)
GW 4064  (ISO)
hexadecanoic acid  (EXP,ISO)
hexamethylene diisocyanate  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
hydroxychloroquine  (ISO)
hypochlorous acid  (ISO)
ifosfamide  (ISO)
indometacin  (ISO)
iodixanol  (EXP)
iohexol  (EXP)
iron atom  (ISO)
iron(0)  (ISO)
iron(III) citrate  (ISO)
isoflavones  (ISO)
isoprenaline  (ISO)
kainic acid  (EXP)
L-ascorbic acid  (ISO)
L-leucine  (ISO)
lactulose  (EXP)
lead diacetate  (ISO)
lead nitrate  (EXP,ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
leflunomide  (EXP,ISO)
liquiritigenin  (EXP)
liquiritin  (EXP)
lithium chloride  (ISO)
LY294002  (ISO)
manganese(II) chloride  (EXP,ISO)
Matrine  (ISO)
melatonin  (EXP)
menadione  (ISO)
mercury dibromide  (ISO)
metformin  (EXP,ISO)
methamphetamine  (EXP,ISO)
methotrexate  (ISO)
methoxyacetic acid  (EXP)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP,ISO)
methylmercury(1+)  (EXP)
Monobutylphthalate  (EXP)
monocrotaline  (EXP)
morusin  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-methylformamide  (ISO)
N-methylnicotinate  (ISO)
N-nitrosodiethylamine  (ISO)
NADP zwitterion  (EXP)
NADP(+)  (EXP)
nefazodone  (EXP,ISO)
nickel dichloride  (EXP)
nicotinamide  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
Nonidet P-40  (ISO)
obeticholic acid  (ISO)
ochratoxin A  (ISO)
oligomycin A  (ISO)
organoselenium compound  (ISO)
osimertinib  (ISO)
oxaliplatin  (EXP)
oxidopamine  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
p-cresol  (ISO)
Paeonol  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
patulin  (ISO)
pepstatin A  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
phenol  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
PhIP  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
plumbagin  (ISO)
potassium bromate  (ISO)
potassium chromate  (ISO)
potassium iodide  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
prodigiosin  (ISO)
progesterone  (ISO)
promethazine  (ISO)
puerarin  (EXP)
Pyridostigmine bromide  (EXP)
pyrovalerone  (ISO)
quercetin  (ISO)
quinolinic acid  (EXP)
rac-lactic acid  (ISO)
raloxifene  (EXP)
reserpine  (ISO)
resveratrol  (EXP,ISO)
retinyl acetate  (ISO)
Rhein  (ISO)
rifampicin  (ISO)
Riluzole  (ISO)
Ro 31-8220  (ISO)
rotenone  (EXP,ISO)
salubrinal  (ISO)
SB 431542  (ISO)
SB-239063  (EXP)
Securinine  (ISO)
selenium atom  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sirolimus  (EXP,ISO)
sirtinol  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP,ISO)
sodium fluoride  (EXP,ISO)
Soman  (EXP)
sorafenib  (ISO)
stilbenoid  (ISO)
streptozocin  (ISO)
succimer  (ISO)
sulforaphane  (ISO)
sulindac  (ISO)
sulindac sulfide  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
taurine  (EXP,ISO)
taurocholic acid  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
thiamine(1+) chloride  (EXP,ISO)
thiram  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triacsin C  (ISO)
trichloroethene  (ISO)
trimethyltin  (EXP)
troglitazone  (ISO)
Tungsten carbide  (ISO)
tunicamycin  (ISO)
urethane  (ISO)
usnic acid  (ISO)
valproic acid  (ISO)
venlafaxine hydrochloride  (EXP)
vincristine  (ISO)
vitamin D  (ISO)
wortmannin  (ISO)
zearalenone  (EXP,ISO)
zidovudine  (EXP)
zinc atom  (ISO)
zinc oxide  (ISO)
zinc pyrithione  (ISO)
zinc(0)  (ISO)


Cellular Component

References

References - curated
1. Castillo K, etal., Autophagy. 2013 Sep;9(9):1308-20. doi: 10.4161/auto.25188. Epub 2013 Jun 6.
2. Croci C, etal., J Biol Chem 2003 Feb 21;278(8):6128-35.
3. Durcan TM and Fon EA, Genes Dev. 2015 May 15;29(10):989-99. doi: 10.1101/gad.262758.115.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Gong J, etal., Science. 1999 Sep 3;285(5433):1565-9.
6. Hayes JD and Dinkova-Kostova AT, Trends Biochem Sci. 2014 Apr;39(4):199-218. doi: 10.1016/j.tibs.2014.02.002. Epub 2014 Mar 16.
7. Jiang T, etal., Pharmacol Res. 2013 May;71:61-8. doi: 10.1016/j.phrs.2013.03.001. Epub 2013 Mar 15.
8. Kitaoka Y, etal., Cell Death Dis. 2013 Oct 17;4:e860. doi: 10.1038/cddis.2013.391.
9. Kubli DA and Gustafsson AB, Circ Res. 2012 Oct 12;111(9):1208-21. doi: 10.1161/CIRCRESAHA.112.265819.
10. Laurin N, etal., Am J Hum Genet. 2002 Jun;70(6):1582-8. Epub 2002 Apr 30.
11. Liu RY, etal., Neurosci Bull. 2014 Feb;30(1):90-8. doi: 10.1007/s12264-013-1371-6. Epub 2013 Jul 25.
12. MGD data from the GO Consortium
13. Nakaso K, etal., Brain Res. 2004 Jun 25;1012(1-2):42-51.
14. NCBI rat LocusLink and RefSeq merged data July 26, 2002
15. OMIM Disease Annotation Pipeline
16. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
17. Puls A, etal., Proc Natl Acad Sci U S A 1997 Jun 10;94(12):6191-6.
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. RGD comprehensive gene curation
21. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
22. Syed V and Hecht NB, Endocrinology 1998 Aug;139(8):3503-11.
23. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
24. Wang W, etal., Brain Inj. 2013;27(7-8):924-33. doi: 10.3109/02699052.2013.793397. Epub 2013 Jun 19.
Additional References at PubMed
PMID:8650207   PMID:10366737   PMID:11162503   PMID:11244088   PMID:11500922   PMID:11981755   PMID:12857745   PMID:14676191   PMID:15143057   PMID:15489334   PMID:15802564   PMID:16079148  
PMID:16169070   PMID:16246731   PMID:16252010   PMID:17580304   PMID:17699685   PMID:18174161   PMID:18374665   PMID:19004011   PMID:19056867   PMID:19182904   PMID:19640926   PMID:20168092  
PMID:20173742   PMID:20357094   PMID:20421418   PMID:20452972   PMID:20457763   PMID:20562859   PMID:20814419   PMID:20979579   PMID:21173155   PMID:21220506   PMID:21455601   PMID:21536669  
PMID:21707618   PMID:21900206   PMID:22033522   PMID:22622177   PMID:22761437   PMID:22792322   PMID:22948227   PMID:23148214   PMID:24035364   PMID:24713655   PMID:24954904   PMID:24959866  
PMID:25127057   PMID:25150927   PMID:25416956   PMID:25686248   PMID:25708205   PMID:25761618   PMID:26199377   PMID:26284655   PMID:26364802   PMID:27368102   PMID:27564518   PMID:27631370  
PMID:28076378   PMID:28404643   PMID:28655770   PMID:29057768   PMID:29554128   PMID:30273743   PMID:30744518  


Genomics

Comparative Map Data
Sqstm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01035,704,728 - 35,716,316 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1035,704,730 - 35,716,294 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01035,463,172 - 35,474,754 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41035,751,300 - 35,762,630 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11035,752,706 - 35,763,676 (-)NCBI
Celera1033,874,680 - 33,885,832 (-)NCBICelera
Cytogenetic Map10q22NCBI
SQSTM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl5179,806,398 - 179,838,078 (+)EnsemblGRCh38hg38GRCh38
GRCh385179,806,393 - 179,838,078 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh375179,233,388 - 179,265,078 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365179,180,503 - 179,197,684 (+)NCBINCBI36hg18NCBI36
Build 345179,180,502 - 179,197,681NCBI
Celera5174,858,545 - 174,890,234 (+)NCBI
Cytogenetic Map5q35.3NCBI
HuRef5173,959,564 - 173,990,246 (+)NCBIHuRef
CHM1_15178,665,789 - 178,697,494 (+)NCBICHM1_1
Sqstm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391150,090,979 - 50,105,303 (-)NCBI
GRCm381150,200,152 - 50,210,820 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1150,199,366 - 50,210,827 (-)EnsemblGRCm38mm10GRCm38
MGSCv371150,013,654 - 50,024,292 (-)NCBIGRCm37mm9NCBIm37
MGSCv361150,043,575 - 50,054,213 (-)NCBImm8
Celera1154,760,561 - 54,771,199 (-)NCBICelera
Cytogenetic Map11B1.3NCBI
Sqstm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955408757,426 - 771,615 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955408757,426 - 764,989 (-)NCBIChiLan1.0ChiLan1.0
SQSTM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15182,271,070 - 182,299,093 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5182,284,436 - 182,299,093 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05174,960,727 - 174,989,946 (+)NCBI
SQSTM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl111,859,465 - 1,870,755 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1111,859,776 - 1,869,289 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sqstm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936739943,080 - 955,296 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SQSTM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl278,752,768 - 78,784,256 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1278,752,768 - 78,763,998 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2280,318,820 - 80,330,048 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SQSTM1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2381,558,082 - 81,574,830 (+)Ensembl
ChlSab1.12381,536,271 - 81,571,061 (+)NCBI
Sqstm1
(Heterocephalus glaber - naked mole-rat)
No map positions available.

Position Markers
RH130114  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01035,704,470 - 35,704,667NCBIRnor6.0
Rnor_5.01035,462,914 - 35,463,111UniSTSRnor5.0
RGSC_v3.41035,751,042 - 35,751,239UniSTSRGSC3.4
Celera1033,874,422 - 33,874,619UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map10q21UniSTS
RH 3.4 Map10368.7UniSTS
AI851514  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01035,704,524 - 35,704,635NCBIRnor6.0
Rnor_5.01035,462,968 - 35,463,079UniSTSRnor5.0
RGSC_v3.41035,751,096 - 35,751,207UniSTSRGSC3.4
Celera1033,874,476 - 33,874,587UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map10q21UniSTS
RH128379  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01035,704,886 - 35,705,071NCBIRnor6.0
Rnor_5.01035,463,330 - 35,463,515UniSTSRnor5.0
RGSC_v3.41035,751,458 - 35,751,643UniSTSRGSC3.4
Celera1033,874,838 - 33,875,023UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map10q21UniSTS
RH 3.4 Map10349.6UniSTS
RH143664  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01035,704,831 - 35,704,945NCBIRnor6.0
Rnor_5.01035,463,275 - 35,463,389UniSTSRnor5.0
RGSC_v3.41035,751,403 - 35,751,517UniSTSRGSC3.4
Celera1033,874,783 - 33,874,897UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map10q21UniSTS
RH 3.4 Map10368.7UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138594330Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142669970Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)10144902893Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1076442166221621Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10587753664401490Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10622909575983805Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10622928936185929Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10642907599492409Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10752145052521450Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101263951357639513Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101263951357639513Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101537547462469074Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101646873661468736Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11712154262121542Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101824639453637634Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101940281464402814Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102152390683549467Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102170776664648311Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum total immunoglobulin E level (CMO:0001542)102240281738204229Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102386101566539843Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)102488408447487910Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102723753064648311Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102878928073789280Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)103002135454057745Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103009990975099909Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103009990975099909Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)103098380575983805Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103191939778343192Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103317903078179030Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103334319278343192Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103513942480139424Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103566946546851407Rat
2298480Eau7Experimental allergic uveoretinitis QTL 70.0049uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103566957336185929Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:230
Count of miRNA genes:92
Interacting mature miRNAs:110
Transcripts:ENSRNOT00000004308, ENSRNOT00000059255
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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004308   ⟹   ENSRNOP00000004308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1035,712,615 - 35,716,260 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000059255   ⟹   ENSRNOP00000056021
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1035,704,730 - 35,716,294 (-)Ensembl
RefSeq Acc Id: NM_175843   ⟹   NP_787037
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01035,704,728 - 35,716,294 (-)NCBI
Rnor_5.01035,463,172 - 35,474,754 (-)NCBI
RGSC_v3.41035,751,300 - 35,762,630 (-)RGD
Celera1033,874,680 - 33,885,832 (-)RGD
Sequence:
RefSeq Acc Id: NM_181550   ⟹   NP_853528
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01035,713,103 - 35,716,260 (-)NCBI
Rnor_5.01035,463,172 - 35,474,754 (-)NCBI
RGSC_v3.41035,751,300 - 35,762,630 (-)RGD
Celera1033,882,640 - 33,885,798 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006246213   ⟹   XP_006246275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01035,704,728 - 35,716,316 (-)NCBI
Rnor_5.01035,463,172 - 35,474,754 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006246214   ⟹   XP_006246276
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01035,704,728 - 35,716,316 (-)NCBI
Rnor_5.01035,463,172 - 35,474,754 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006246215   ⟹   XP_006246277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01035,704,728 - 35,716,316 (-)NCBI
Rnor_5.01035,463,172 - 35,474,754 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_787037   ⟸   NM_175843
- Peptide Label: isoform 1
- UniProtKB: O08623 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_853528   ⟸   NM_181550
- Peptide Label: isoform 2
- UniProtKB: O08623 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006246277   ⟸   XM_006246215
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006246276   ⟸   XM_006246214
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006246275   ⟸   XM_006246213
- Peptide Label: isoform X1
- UniProtKB: O08623 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004308   ⟸   ENSRNOT00000004308
RefSeq Acc Id: ENSRNOP00000056021   ⟸   ENSRNOT00000059255
Protein Domains
PB1   UBA   ZZ-type

Transcriptome

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

Promoters
RGD ID:13697149
Promoter ID:EPDNEW_R7674
Type:single initiation site
Name:Sqstm1_1
Description:sequestosome 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_6.01035,716,294 - 35,716,354EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
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
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
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/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
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/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/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/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (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 (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (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:69287 AgrOrtholog
Ensembl Genes ENSRNOG00000003147 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000004308 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000056021 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004308 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000059255 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.60.90 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6887571 IMAGE-MGC_LOAD
InterPro PB1_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PB1_p62 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SQSTM_UBA UniProtKB/Swiss-Prot
  UBA UniProtKB/Swiss-Prot
  UBA-like_sf UniProtKB/Swiss-Prot
  Znf_ZZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_ZZ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:113894 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72976 IMAGE-MGC_LOAD
NCBI Gene 113894 ENTREZGENE
Pfam PB1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00569 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UBA_5 UniProtKB/Swiss-Prot
PhenoGen Sqstm1 PhenoGen
PROSITE PB1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UBA UniProtKB/Swiss-Prot
  ZF_ZZ_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZF_ZZ_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PB1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UBA UniProtKB/Swiss-Prot
  ZnF_ZZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46934 UniProtKB/Swiss-Prot
TIGR TC204232
UniGene Rn.107103 ENTREZGENE
UniProt A0A0H2UHB5_RAT UniProtKB/TrEMBL
  O08623 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q8CH59 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-05-02 Sqstm1  sequestosome 1  Osi  oxidative stress induced  Data Merged 737654 APPROVED
2002-08-07 Osi  oxidative stress induced      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Sqstm1  sequestosome 1      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains ZZ-zinc finger domain which interacts with 10 amino acids of rho 1-3 634214
gene_expression expressed in the non-neuronal, neuronal tissues and the retina 634214
gene_transcript splice variant of PKC-zeta interacting protein family 634214
 



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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.