Becn1 (beclin 1) - Rat Genome Database

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Gene: Becn1 (beclin 1) Rattus norvegicus
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Symbol: Becn1
Name: beclin 1
RGD ID: 620190
Description: Enables ubiquitin protein ligase binding activity. Involved in several processes, including cellular response to metal ion; regulation of apoptotic process; and regulation of vacuole organization. Located in cytoplasm; dendrite; and nucleus. Colocalizes with trans-Golgi network. Used to study brain ischemia and middle cerebral artery infarction. Biomarker of several diseases, including Barrett's esophagus; acute necrotizing pancreatitis; artery disease (multiple); brain disease (multiple); and neuropathy (multiple). Human ortholog(s) of this gene implicated in Machado-Joseph disease. Orthologous to human BECN1 (beclin 1); PARTICIPATES IN autophagy pathway; inositol metabolic pathway; mitochondrial autophagy pathway; INTERACTS WITH (+)-pilocarpine; (-)-anisomycin; 2,2',5,5'-tetrachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: beclin 1 (coiled-coil, myosin-like BCL2-interacting protein); beclin 1, autophagy related; beclin-1; Beclin1; coiled-coil myosin-like BCL2-interacting protein
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
mRatBN7.21086,231,387 - 86,246,742 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1086,231,388 - 86,246,742 (-)Ensembl
Rnor_6.01089,209,944 - 89,225,297 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1089,209,940 - 89,225,297 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01089,008,975 - 89,024,328 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41090,317,957 - 90,333,329 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11090,332,322 - 90,347,231 (-)NCBI
Celera1084,949,343 - 84,964,691 (-)NCBICelera
Cytogenetic Map10q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Experimental Pancreatitis  (ISO)
acute necrotizing pancreatitis  (IEP)
Alzheimer's disease  (ISO)
amyotrophic lateral sclerosis  (ISO)
anterior ischemic optic neuropathy  (IEP)
Barrett's esophagus  (IEP,ISO)
brain infarction  (IEP)
Brain Injuries  (IEP,ISO)
brain ischemia  (IEP,IMP)
Burns  (IEP)
Cardiomegaly  (IEP)
Cerebral Hemorrhage  (IEP)
Chronic Intermittent Hypoxia  (IEP)
Colonic Neoplasms  (ISO)
congestive heart failure  (IEP)
degenerative disc disease  (IEP)
Diabetic Nephropathies  (IEP)
diabetic neuropathy  (IEP)
end stage renal disease  (IEP)
epilepsy  (IEP)
esophagus adenocarcinoma  (IEP)
Experimental Diabetes Mellitus  (IEP)
Experimental Seizures  (IEP)
glaucoma  (IEP)
glioblastoma  (ISO)
Head Injuries, Closed  (ISO)
Heat Stroke  (IEP)
Hyperalgesia  (IEP)
hypertension  (IEP)
hypertrophic cardiomyopathy  (ISO)
Hypoxia-Ischemia, Brain  (IEP)
intrahepatic cholangiocarcinoma  (ISO)
ischemia  (IEP)
Kidney Reperfusion Injury  (IEP)
Lewy body dementia  (ISO)
liver cirrhosis  (ISO)
Lung Neoplasms  (ISO)
Machado-Joseph disease  (ISO)
mental depression  (ISO)
middle cerebral artery infarction  (IMP)
myocardial infarction  (IEP,ISO)
Myocardial Reperfusion Injury  (IDA,ISO)
Neointima  (IMP)
Nerve Degeneration  (IEP)
osteoarthritis  (ISO)
Osteoarthritis, Experimental  (IEP)
paraplegia  (IEP)
Parkinsonism  (IEP,ISO)
perinatal necrotizing enterocolitis  (ISO)
peritonitis  (IEP)
polycystic kidney disease  (IEP,ISO)
Reperfusion Injury  (IEP)
schizophrenia  (IEP)
Spinal Cord Injuries  (IEP,ISO)
Spinal Cord Reperfusion Injury  (IEP)
status epilepticus  (IEP,ISO)
Subarachnoid Hemorrhage  (IEP)
systemic lupus erythematosus  (ISS)
Temporomandibular Joint Disorders  (IEP)
Temporomandibular Joint Osteoarthritis  (IEP)
transient cerebral ischemia  (IEP)
type 2 diabetes mellitus  (IEP)
ureteral obstruction  (IEP)
viral encephalitis  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(+)-Tetrandrine  (ISO)
(-)-anisomycin  (EXP)
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-benzoquinone  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (EXP,ISO)
2,2-(2-Chlorophenyl-4'-chlorophenyl)-1,1-dichloroethene  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (EXP)
2,6-dinitrotoluene  (EXP)
2-deoxy-D-glucose  (ISO)
2-hydroxyethyl methacrylate  (ISO)
2-hydroxypropanoic acid  (ISO)
3-hydroxybutyric acid  (ISO)
3-methyladenine  (EXP,ISO)
3H-1,2-dithiole-3-thione  (EXP)
4'-epidoxorubicin  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-nonylphenol  (EXP)
4-phenylbutyric acid  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (EXP)
ABT-737  (ISO)
acadesine  (ISO)
actinomycin D  (ISO)
AICA ribonucleotide  (EXP)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (ISO)
alpha,alpha-trehalose  (ISO)
alpha-D-galactose  (EXP)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
apocynin  (EXP)
aristolochic acid  (EXP,ISO)
arsane  (EXP,ISO)
arsenic atom  (EXP,ISO)
arsenous acid  (ISO)
atorvastatin calcium  (ISO)
atrazine  (EXP,ISO)
azinphos-methyl  (ISO)
bafilomycin A1  (EXP,ISO)
benzo[a]pyrene  (EXP,ISO)
beta-lapachone  (ISO)
beta-thujaplicin  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
brazilin  (ISO)
butyric acid  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
calciol  (ISO)
calcipotriol  (ISO)
calcitriol  (ISO)
camptothecin  (ISO)
cannabidiol  (ISO)
Cannabidivarin  (ISO)
capsaicin  (EXP)
captan  (ISO)
carbon disulfide  (ISO)
carbon nanotube  (EXP,ISO)
carboplatin  (ISO)
carglumic acid  (ISO)
carmustine  (ISO)
carvedilol  (EXP)
CCCP  (EXP,ISO)
celastrol  (EXP)
CGS-21680  (ISO)
chloroquine  (EXP,ISO)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
colistin  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
Corynoxine B  (ISO)
cucurbitacin E  (ISO)
Curcumol  (EXP)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
D-glucose  (EXP,ISO)
dapagliflozin  (EXP)
DDE  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
diquat  (ISO)
disodium selenite  (ISO)
divinyl sulfone  (ISO)
dorsomorphin  (EXP,ISO)
doxorubicin  (EXP,ISO)
elemental selenium  (EXP)
embelin  (ISO)
endosulfan  (EXP)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (ISO)
ferric oxide  (ISO)
fingolimod hydrochloride  (ISO)
fisetin  (ISO)
fluoxetine  (ISO)
flutamide  (EXP)
folic acid  (ISO)
folpet  (ISO)
galactose  (EXP)
galangin  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gingerol  (ISO)
glucose  (EXP,ISO)
glycerol 2-phosphate  (ISO)
glycochenodeoxycholic acid  (ISO)
glyphosate  (EXP)
gossypetin  (ISO)
graphene oxide  (ISO)
graphite  (ISO)
hesperidin  (EXP)
hexadecanoic acid  (ISO)
HU-308  (ISO)
hydrogen peroxide  (EXP,ISO)
hydroquinone  (ISO)
hydroxamic acid  (EXP)
kainic acid  (EXP)
L-ascorbic acid 2-phosphate  (ISO)
L-leucine  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
levamisole  (ISO)
linuron  (EXP)
lipopolysaccharide  (EXP,ISO)
luteolin  (EXP,ISO)
LY294002  (EXP,ISO)
lycopene  (ISO)
maneb  (ISO)
manganese(II) chloride  (EXP,ISO)
Maprotiline  (ISO)
Matrine  (ISO)
melatonin  (ISO)
menadione  (ISO)
methamidophos  (ISO)
methamphetamine  (EXP,ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
microcystin-LR  (ISO)
morphine  (ISO)
morpholines  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methylnicotinate  (ISO)
NADP zwitterion  (EXP)
NADP(+)  (EXP)
nicotine  (ISO)
Nonidet P-40  (ISO)
oleanolic acid  (ISO)
oligopeptide  (ISO)
omethoate  (ISO)
ozone  (EXP)
p-cresol  (EXP,ISO)
p-menthan-3-ol  (ISO)
paclitaxel  (ISO)
Paeonol  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
phosphoramide mustard  (EXP)
platycodin D  (ISO)
potassium iodide  (ISO)
procyanidin B2  (ISO)
promethazine  (ISO)
pyrovalerone  (ISO)
pyruvic acid  (EXP)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
Rhein  (ISO)
rotenone  (EXP,ISO)
rottlerin  (ISO)
salubrinal  (ISO)
SB 203580  (EXP,ISO)
selenium atom  (EXP)
silicon dioxide  (EXP,ISO)
sirolimus  (EXP,ISO)
SKF-96365 hydrochloride  (EXP)
sodium arsenite  (EXP,ISO)
sodium dichromate  (ISO)
sodium fluoride  (EXP,ISO)
spironolactone  (EXP)
staurosporine  (ISO)
streptozocin  (ISO)
sulfur dioxide  (EXP)
sunitinib  (EXP,ISO)
swainsonine  (EXP)
syringic acid  (ISO)
T-2 toxin  (EXP)
temozolomide  (ISO)
tetrachloromethane  (ISO)
tetramethylpyrazine  (ISO)
thalidomide  (ISO)
Tiron  (ISO)
titanium dioxide  (ISO)
tributylstannane  (EXP)
trifloxystrobin  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
ursolic acid  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin D  (ISO)
vitamin E  (EXP)
vorinostat  (ISO)
WIN 55212-2  (ISO)
wortmannin  (EXP,ISO)
zearalenone  (EXP,ISO)
zinc oxide  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
amyloid-beta metabolic process  (ISO)
apoptotic process  (IEA)
autophagosome assembly  (IBA,IMP,ISO,ISS)
autophagosome maturation  (IEA,ISO)
autophagy  (IMP,ISO,ISS)
autophagy of mitochondrion  (ISO)
cell division  (IEA)
cellular response to aluminum ion  (IEP)
cellular response to amino acid starvation  (IEP)
cellular response to copper ion  (IEP)
cellular response to epidermal growth factor stimulus  (IEP)
cellular response to glucose starvation  (ISO,ISS)
cellular response to hydrogen peroxide  (IEP)
cellular response to nitrogen starvation  (IBA)
defense response to virus  (IEA)
early endosome to late endosome transport  (ISO,ISS)
engulfment of apoptotic cell  (ISO)
late endosome to vacuole transport  (IBA)
lysosome organization  (ISO)
macroautophagy  (ISO,ISS)
mitophagy  (ISO)
mitotic metaphase plate congression  (ISO)
negative regulation of apoptotic process  (IMP,ISO)
negative regulation of autophagosome assembly  (ISO)
negative regulation of autophagy  (ISO)
negative regulation of cell death  (IMP,ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of lysosome organization  (IMP)
negative regulation of reactive oxygen species metabolic process  (ISO)
neuron development  (ISO)
phosphatidylinositol-3-phosphate biosynthetic process  (IEA,ISO)
positive regulation of attachment of mitotic spindle microtubules to kinetochore  (ISO)
positive regulation of autophagosome assembly  (IMP)
positive regulation of autophagy  (IMP,ISO,ISS)
positive regulation of cardiac muscle hypertrophy  (ISO)
positive regulation of intrinsic apoptotic signaling pathway  (IMP,ISO,ISS)
protein phosphorylation  (IEA,ISO)
receptor catabolic process  (ISO)
regulation of autophagy  (ISO)
regulation of catalytic activity  (ISO)
regulation of cytokinesis  (ISO,ISS)
regulation of macroautophagy  (ISO)
response to hypoxia  (IEP)
response to iron(II) ion  (IEP)
response to lead ion  (IEP)
response to mitochondrial depolarisation  (ISO)
response to nutrient levels  (IEP)
response to other organism  (ISO)
response to vitamin E  (IEP)
response to xenobiotic stimulus  (IEP)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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81. Yan J, etal., J Nutr Biochem. 2012 Jul;23(7):716-24. doi: 10.1016/j.jnutbio.2011.03.014. Epub 2011 Aug 4.
82. Yang H, etal., Autophagy. 2020 Feb;16(2):271-288. doi: 10.1080/15548627.2019.1606647. Epub 2019 Apr 21.
83. Yang S, etal., Pancreas. 2012 Apr;41(3):367-73.
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Additional References at PubMed
PMID:9765397   PMID:12372286   PMID:14657337   PMID:17330750   PMID:17468177   PMID:17589504   PMID:17891140   PMID:18281291   PMID:19273585   PMID:19335206   PMID:19520853   PMID:19901551  
PMID:20190558   PMID:20208530   PMID:20643123   PMID:21646862   PMID:22328594   PMID:22393062   PMID:22493499   PMID:22543707   PMID:22917477   PMID:23184933   PMID:23332761   PMID:23364696  
PMID:23392707   PMID:23478334   PMID:23590156   PMID:23629966   PMID:23798385   PMID:23868341   PMID:23878393   PMID:24056303   PMID:24324270   PMID:24579466   PMID:24872334   PMID:25046113  
PMID:25127057   PMID:25215947   PMID:25816157   PMID:25891078   PMID:26386349   PMID:26647915   PMID:26783301   PMID:26822891   PMID:27472881   PMID:27853422   PMID:27994061   PMID:28340591  
PMID:28383560   PMID:28428545   PMID:28578340   PMID:28893091   PMID:28964771   PMID:29196028   PMID:29797121   PMID:30951836   PMID:31140414   PMID:31168983   PMID:31583941   PMID:31707369  
PMID:32016995   PMID:33167086   PMID:34217716  


Genomics

Comparative Map Data
Becn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21086,231,387 - 86,246,742 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1086,231,388 - 86,246,742 (-)Ensembl
Rnor_6.01089,209,944 - 89,225,297 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1089,209,940 - 89,225,297 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01089,008,975 - 89,024,328 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41090,317,957 - 90,333,329 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11090,332,322 - 90,347,231 (-)NCBI
Celera1084,949,343 - 84,964,691 (-)NCBICelera
Cytogenetic Map10q31NCBI
BECN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1742,810,134 - 42,833,350 (-)EnsemblGRCh38hg38GRCh38
GRCh381742,810,132 - 42,824,282 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371740,962,150 - 40,976,300 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361738,215,678 - 38,229,807 (-)NCBINCBI36hg18NCBI36
Build 341738,215,677 - 38,229,807NCBI
Celera1737,618,135 - 37,632,364 (-)NCBI
Cytogenetic Map17q21.31NCBI
HuRef1736,726,539 - 36,740,774 (-)NCBIHuRef
CHM1_11741,197,767 - 41,211,922 (-)NCBICHM1_1
Becn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911101,179,084 - 101,193,112 (-)NCBIGRCm39mm39
GRCm39 Ensembl11101,176,778 - 101,193,112 (-)Ensembl
GRCm3811101,288,258 - 101,302,286 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11101,285,952 - 101,302,286 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711101,149,581 - 101,163,581 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611102,067,439 - 102,081,397 (-)NCBImm8
MGSCv3611101,104,357 - 101,118,357 (-)NCBImm8
Cytogenetic Map11DNCBI
Becn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545116,616,595 - 16,625,730 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545116,616,595 - 16,625,731 (-)NCBIChiLan1.0ChiLan1.0
BECN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11714,719,781 - 14,733,286 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1714,719,781 - 14,733,286 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01714,493,619 - 14,507,809 (+)NCBIMhudiblu_PPA_v0panPan3
BECN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1920,204,203 - 20,215,081 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl920,204,220 - 20,214,236 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha919,665,517 - 19,676,150 (+)NCBI
ROS_Cfam_1.0920,922,592 - 20,933,221 (+)NCBI
UMICH_Zoey_3.1919,707,479 - 19,718,113 (+)NCBI
UNSW_CanFamBas_1.0919,973,720 - 19,984,352 (+)NCBI
UU_Cfam_GSD_1.0920,076,426 - 20,087,053 (+)NCBI
Becn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560219,544,014 - 19,557,039 (+)NCBI
SpeTri2.0NW_00493649017,518,100 - 17,531,126 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BECN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1220,041,956 - 20,054,373 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11220,041,914 - 20,054,249 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21220,256,871 - 20,268,928 (+)NCBISscrofa10.2Sscrofa10.2susScr3
BECN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11663,469,187 - 63,482,627 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1663,469,192 - 63,485,322 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607734,260,316 - 34,273,836 (+)NCBIVero_WHO_p1.0
Becn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247951,386,154 - 1,406,314 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH127824  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21086,231,563 - 86,231,767 (+)MAPPERmRatBN7.2
Rnor_6.01089,210,121 - 89,210,324NCBIRnor6.0
Rnor_5.01089,009,152 - 89,009,355UniSTSRnor5.0
RGSC_v3.41090,318,134 - 90,318,337UniSTSRGSC3.4
Celera1084,949,520 - 84,949,723UniSTS
RH 3.4 Map10877.09UniSTS
Cytogenetic Map10q32.1UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
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
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
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
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
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107563188787055282Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)107889965587307728Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108256485692369470Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108400727295933025Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108400727295933025Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108402232193995963Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:322
Count of miRNA genes:210
Interacting mature miRNAs:246
Transcripts:ENSRNOT00000027868
Prediction methods:Microtar, 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: ENSRNOT00000027868   ⟹   ENSRNOP00000027868
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1086,231,399 - 86,246,681 (-)Ensembl
Rnor_6.0 Ensembl1089,209,944 - 89,225,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075886
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1086,239,364 - 86,246,742 (-)Ensembl
Rnor_6.0 Ensembl1089,217,566 - 89,225,222 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076146
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1089,212,680 - 89,215,849 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076489
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1089,209,940 - 89,212,536 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077048
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1089,215,499 - 89,217,147 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082010   ⟹   ENSRNOP00000071966
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1086,231,388 - 86,246,742 (-)Ensembl
Rnor_6.0 Ensembl1089,209,945 - 89,225,297 (-)Ensembl
RefSeq Acc Id: NM_001034117   ⟹   NP_001029289
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21086,231,387 - 86,246,742 (-)NCBI
Rnor_6.01089,209,944 - 89,225,297 (-)NCBI
Rnor_5.01089,008,975 - 89,024,328 (-)NCBI
RGSC_v3.41090,317,957 - 90,333,329 (-)RGD
Celera1084,949,343 - 84,964,691 (-)RGD
Sequence:
RefSeq Acc Id: NM_053739   ⟹   NP_446191
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21086,231,387 - 86,246,742 (-)NCBI
Rnor_6.01089,209,944 - 89,225,297 (-)NCBI
Rnor_5.01089,008,975 - 89,024,328 (-)NCBI
RGSC_v3.41090,317,957 - 90,333,329 (-)RGD
Celera1084,949,343 - 84,964,691 (-)RGD
Sequence:
RefSeq Acc Id: XM_017596950   ⟹   XP_017452439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21086,231,387 - 86,246,688 (-)NCBI
Rnor_6.01089,209,947 - 89,225,228 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039085038   ⟹   XP_038940966
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21086,231,387 - 86,246,693 (-)NCBI
RefSeq Acc Id: XM_039085039   ⟹   XP_038940967
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21086,231,387 - 86,246,647 (-)NCBI
RefSeq Acc Id: XM_039085040   ⟹   XP_038940968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21086,231,387 - 86,238,249 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001029289   ⟸   NM_001034117
- UniProtKB: Q91XJ1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_446191   ⟸   NM_053739
- UniProtKB: Q91XJ1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017452439   ⟸   XM_017596950
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000071966   ⟸   ENSRNOT00000082010
RefSeq Acc Id: ENSRNOP00000027868   ⟸   ENSRNOT00000027868
RefSeq Acc Id: XP_038940966   ⟸   XM_039085038
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038940967   ⟸   XM_039085039
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038940968   ⟸   XM_039085040
- Peptide Label: isoform X3

Transcriptome

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

Promoters
RGD ID:13697758
Promoter ID:EPDNEW_R8277
Type:initiation region
Name:Becn1_1
Description:beclin 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_6.01089,225,222 - 89,225,282EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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
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)
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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: 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
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620190 AgrOrtholog
Ensembl Genes ENSRNOG00000020513 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027868 UniProtKB/Swiss-Prot
  ENSRNOP00000071966 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027868 UniProtKB/Swiss-Prot
  ENSRNOT00000082010 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.418.40 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7100185 IMAGE-MGC_LOAD
InterPro Atg6/Beclin UniProtKB/Swiss-Prot
  Atg6/Beclin_C_sf UniProtKB/Swiss-Prot
  Atg6/beclin_CC UniProtKB/Swiss-Prot
  Atg6_BARA UniProtKB/Swiss-Prot
  BECN1 UniProtKB/Swiss-Prot
  BH3_dom UniProtKB/Swiss-Prot
KEGG Report rno:114558 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91559 IMAGE-MGC_LOAD
NCBI Gene 114558 ENTREZGENE
PANTHER PTHR12768 UniProtKB/Swiss-Prot
  PTHR12768:SF6 UniProtKB/Swiss-Prot
Pfam APG6 UniProtKB/Swiss-Prot
  APG6_N UniProtKB/Swiss-Prot
  BH3 UniProtKB/Swiss-Prot
PhenoGen Becn1 PhenoGen
UniProt BECN1_RAT UniProtKB/Swiss-Prot, ENTREZGENE