Sqstm1 (sequestosome 1) - Rat Genome Database

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Gene: Sqstm1 (sequestosome 1) Rattus norvegicus
Analyze
Symbol: Sqstm1
Name: sequestosome 1
RGD ID: 69287
Description: Enables identical protein binding activity and protein kinase C binding activity. Involved in positive regulation of protein phosphorylation and response to ischemia. Located in 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: VALIDATED
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
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
mRatBN7.21034,525,517 - 34,536,685 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1034,525,519 - 34,536,673 (-)Ensembl
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,ISO)
(-)-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',4,4',5-Pentachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
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)
20-hydroxyecdysone  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3-chloropropane-1,2-diol  (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)
4-phenylbutyric acid  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (ISO)
7beta-aminocephalosporanic acid  (ISO)
abamectin  (ISO)
ABT-737  (ISO)
acarbose  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
actinomycin D  (ISO)
Ajugasterone C  (ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
aloxistatin  (ISO)
alpha,alpha-trehalose  (ISO)
alpha-D-galactose  (EXP,ISO)
alpha-pinene  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP,ISO)
ammonium hexachloroplatinate  (ISO)
andrographolide  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
antimonite  (ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
arachidonic acid  (ISO)
aristolochic 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)
atrazine  (EXP,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)
chlorpyrifos  (EXP)
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)
coenzyme Q10  (ISO)
colforsin daropate 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)
Curcumol  (EXP)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cyfluthrin  (ISO)
cylindrospermopsin  (ISO)
cypermethrin  (ISO)
D-glucose  (EXP,ISO)
dactolisib  (ISO)
dapagliflozin  (EXP)
DDT  (ISO)
Deguelin  (ISO)
deoxycholic acid  (ISO)
deoxynivalenol  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (EXP,ISO)
diazinon  (EXP,ISO)
dibenzofuran  (ISO)
dibutyl phthalate  (ISO)
dieldrin  (EXP)
diethyl maleate  (ISO)
dimethyl fumarate  (ISO)
dinitrogen  (ISO)
dioxygen  (EXP,ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
disodium selenite  (EXP,ISO)
diuron  (EXP)
dorsomorphin  (EXP,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)
fenvalerate  (EXP)
fingolimod hydrochloride  (ISO)
flavokawain B  (ISO)
flufenoxuron  (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)
ginsenoside Rg2  (ISO)
glucose  (EXP,ISO)
glutathione  (ISO)
glycerol 2-phosphate  (ISO)
glycidol  (EXP)
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)
HU-308  (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)
ivermectin  (ISO)
kainic acid  (EXP)
L-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
L-leucine  (ISO)
lactulose  (EXP,ISO)
lead diacetate  (EXP,ISO)
lead nitrate  (EXP,ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
leflunomide  (EXP,ISO)
lipopolysaccharide  (ISO)
liquiritigenin  (EXP)
liquiritin  (EXP)
lithium chloride  (ISO)
LY294002  (ISO)
lycopene  (ISO)
manganese(II) chloride  (EXP,ISO)
Matrine  (ISO)
melatonin  (EXP,ISO)
melibiose  (ISO)
menadione  (ISO)
mercury dibromide  (ISO)
mesalamine  (EXP)
metformin  (EXP,ISO)
methamphetamine  (EXP,ISO)
methotrexate  (ISO)
methoxyacetic acid  (EXP)
methyl methanesulfonate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (EXP,ISO)
methylmercury(1+)  (EXP)
miconazole  (ISO)
microcystin-LR  (ISO)
mifepristone  (ISO)
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)
notoginsenoside R1  (ISO)
obeticholic acid  (ISO)
ochratoxin A  (ISO)
oligomycin A  (ISO)
organoselenium compound  (ISO)
osimertinib  (ISO)
oxaliplatin  (EXP)
oxidopamine  (EXP,ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
p-cresol  (ISO)
Paeonol  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
patulin  (ISO)
PCB138  (EXP)
pentachlorophenol  (ISO)
pepstatin A  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
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 dichromate  (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)
radon atom  (ISO)
radon(0)  (ISO)
raloxifene  (EXP)
reserpine  (ISO)
resveratrol  (EXP,ISO)
retinyl acetate  (ISO)
Rhein  (ISO)
rifampicin  (ISO)
Riluzole  (ISO)
Ro 31-8220  (ISO)
rotenone  (EXP,ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
salubrinal  (ISO)
SB 203580  (EXP)
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)
SKF-96365 hydrochloride  (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)
Temsirolimus  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
thiamine(1+) chloride  (EXP,ISO)
thiram  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trametinib  (ISO)
trans-piceid  (ISO)
triacsin C  (ISO)
trichloroethene  (EXP,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)

Gene Ontology Annotations     Click to see Annotation Detail View

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
mRatBN7.21034,525,517 - 34,536,685 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1034,525,519 - 34,536,673 (-)Ensembl
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
GRCh375179,233,393 - 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 (-)NCBIGRCm39mm39
GRCm39 Ensembl1150,090,193 - 50,101,654 (-)Ensembl
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 (+)NCBIMhudiblu_PPA_v0panPan3
SQSTM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1111,859,776 - 1,869,289 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl111,859,465 - 1,870,755 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha111,982,949 - 1,993,602 (-)NCBI
ROS_Cfam_1.0111,834,485 - 1,844,494 (-)NCBI
UMICH_Zoey_3.1111,805,423 - 1,816,088 (-)NCBI
UNSW_CanFamBas_1.0111,884,694 - 1,895,335 (-)NCBI
UU_Cfam_GSD_1.0112,124,878 - 2,135,544 (-)NCBI
Sqstm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213119,733,303 - 119,745,506 (-)NCBI
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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12381,536,271 - 81,571,061 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2381,558,082 - 81,574,830 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607512,913,848 - 12,950,392 (+)NCBIVero_WHO_p1.0
Sqstm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473342,689,454 - 42,700,916 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH130114  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21034,525,258 - 34,525,456 (+)MAPPERmRatBN7.2
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
RH 3.4 Map10368.7UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map10q21UniSTS
AI851514  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21034,525,312 - 34,525,424 (+)MAPPERmRatBN7.2
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
mRatBN7.21034,525,674 - 34,525,860 (+)MAPPERmRatBN7.2
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
RH 3.4 Map10349.6UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map10q21UniSTS
RH143664  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21034,525,619 - 34,525,734 (+)MAPPERmRatBN7.2
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
RH 3.4 Map10368.7UniSTS
Cytogenetic Map10q22UniSTS
Cytogenetic Map10q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
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)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
631531Iresp2Immunoglobin response QTL26.3blood immunoglobulin E amount (VT:0002492)serum total immunoglobulin E level (CMO:0001542)102291826836400810Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1600371Mcs21Mammary carcinoma susceptibility QTL 213mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)102887565052200160Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
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)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)103449055945579777Rat

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

Nucleotide Sequences
RefSeq Transcripts NM_001393884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001393885 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001393886 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_175843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_181550 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006246213 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006246214 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006246215 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF053095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF439403 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC061575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225585 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ235251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Y08355 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000004308   ⟹   ENSRNOP00000004308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1034,525,519 - 34,536,670 (-)Ensembl
Rnor_6.0 Ensembl1035,712,615 - 35,716,260 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000059255   ⟹   ENSRNOP00000056021
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1034,525,519 - 34,536,670 (-)Ensembl
Rnor_6.0 Ensembl1035,704,730 - 35,716,294 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098202   ⟹   ENSRNOP00000091620
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1034,525,734 - 34,536,673 (-)Ensembl
RefSeq Acc Id: NM_175843   ⟹   NP_787037
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21034,525,517 - 34,536,670 (-)NCBI
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: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21034,533,478 - 34,536,636 (-)NCBI
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
mRatBN7.21034,525,517 - 34,536,685 (-)NCBI
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
mRatBN7.21034,525,517 - 34,536,685 (-)NCBI
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
mRatBN7.21034,525,517 - 34,536,685 (-)NCBI
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
- 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
RefSeq Acc Id: ENSRNOP00000091620   ⟸   ENSRNOT00000098202
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 (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)
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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: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW