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: Exhibits ubiquitin protein ligase binding activity. Involved in several processes, including cellular response to metal ion; regulation of apoptotic process; and regulation of vacuole organization. Localizes to 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; artery disease (multiple); brain disease (multiple); ischemia (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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21086,231,387 - 86,246,742 (-)NCBI
Rnor_6.0 Ensembl1089,209,940 - 89,225,297 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01089,209,944 - 89,225,297 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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 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 Pancreatitis, Acute  (ISO)
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)
acadesine  (ISO)
actinomycin D  (ISO)
AICA ribonucleotide  (EXP)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (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)
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  (ISO)
caffeine  (ISO)
calciol  (ISO)
calcipotriol  (ISO)
calcitriol  (ISO)
camptothecin  (ISO)
cannabidiol  (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)
cycloheximide  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
D-glucose  (EXP,ISO)
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)
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)
morphine  (ISO)
morpholines  (ISO)
N-acetyl-L-cysteine  (EXP,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)
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)
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)
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)
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)
positive regulation of attachment of mitotic spindle microtubules to kinetochore  (ISO)
positive regulation of autophagosome assembly  (IMP)
positive regulation of autophagy  (IMP)
positive regulation of cardiac muscle hypertrophy  (ISO)
positive regulation of intrinsic apoptotic signaling pathway  (IMP,ISO,ISS)
receptor catabolic process  (ISO)
regulation of catalytic activity  (ISO)
regulation of cytokinesis  (ISO,ISS)
response to drug  (IEP)
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)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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86. Ye W, etal., Connect Tissue Res. 2013;54(1):22-8. doi: 10.3109/03008207.2012.715702. Epub 2012 Aug 23.
87. Ye WF, etal., Zhejiang Da Xue Xue Bao Yi Xue Ban. 2012 Jul;41(4):402-9.
88. Yin F, etal., Neural Regen Res. 2014 Sep 15;9(18):1665-71. doi: 10.4103/1673-5374.141801.
89. Yu YF, etal., Zhonghua Yi Xue Za Zhi. 2013 Dec 3;93(45):3632-5.
90. Zeng KW, etal., Toxicol In Vitro. 2012 Mar;26(2):215-20. Epub 2011 Nov 26.
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93. Zhang M, etal., Apoptosis. 2013 Apr;18(4):423-34. doi: 10.1007/s10495-013-0811-0.
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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  


Genomics

Comparative Map Data
Becn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21086,231,387 - 86,246,742 (-)NCBI
Rnor_6.0 Ensembl1089,209,940 - 89,225,297 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01089,209,944 - 89,225,297 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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 - 41,211,946 (-)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11663,469,187 - 63,482,627 (+)NCBI
ChlSab1.1 Ensembl1663,469,192 - 63,485,322 (+)Ensembl
Becn1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247951,386,154 - 1,406,314 (+)NCBI

Position Markers
RH127824  
Rat AssemblyChrPosition (strand)SourceJBrowse
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 (Rnor_6.0)
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)10642907599492409Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109841807108540162Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101482789492423564Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014827894107857673Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014827894110992275Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)1020170031102897474Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12152390690312401Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)12152390690312401Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102152390690312401Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102290149793886300Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1023861015112626471Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1024483076107857673Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)1027237530101482600Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1027237530102427718Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)103618592995845311Rat
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)1041260363106105607Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1041260363107857673Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1043289657108540162Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104659302198939209Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104684834691848346Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104684834691848346Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104684834691848346Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)105063833795638337Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105310471898104718Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1053621375112626471Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1053621375112626471Rat
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)105362581598939209Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105363748594807701Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)1055224855100224855Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1055678976112626471Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)1055679084102427604Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1056698730101698730Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1060450007105450007Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1060875260105875260Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1060875260105875260Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1060875260105875260Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1062096293107096293Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)1064648175101691360Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1064648175102149713Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1064648175102149713Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1065590122110590122Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1065992275110992275Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1065992275110992275Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1067880046112626471Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1067988218110992091Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1069123603101482600Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1069385595112626471Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1069385595112626471Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1070166960112626471Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1070800069112626471Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1071692298112626471Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1073008136112626471Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1073008136112626471Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1073008136112626471Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1073467158112626471Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107504539197308358Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1075544754112626471Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1075544754112626471Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107598380599492217Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107705574198282519Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)107834302790042115Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107897027998282519Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1078970279112626471Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1079927661112626471Rat
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)1080239190112626471Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1081515116101758478Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)108164977590297007Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108338982894488181Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1083389828104994768Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1085079943112626471Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108551382295638337Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1086566908112626471Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108696256399303173Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108696256399303173Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108697786197308569Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1088544136107545372Rat

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
Rnor_6.0 Ensembl1089,209,944 - 89,225,297 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075886
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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 (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (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/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 (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)
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
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
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/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
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (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
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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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
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
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 (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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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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/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
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 (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 (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620190 AgrOrtholog
Ensembl Genes ENSRNOG00000020513 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027868 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000071966 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027868 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000082010 ENTREZGENE, 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


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-04 Becn1  beclin 1  Becn1  beclin 1, autophagy related  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Becn1  beclin 1, autophagy related  Becn1  beclin 1 (coiled-coil, myosin-like BCL2-interacting protein)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Becn1  beclin 1 (coiled-coil, myosin-like BCL2-interacting protein)      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Becn1  beclin 1 (coiled-coil, myosin-like BCL2-interacting protein)      Symbol and Name status set to provisional 70820 PROVISIONAL