Atg5 (autophagy related 5) - Rat Genome Database

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Gene: Atg5 (autophagy related 5) Rattus norvegicus
Analyze
Symbol: Atg5
Name: autophagy related 5
RGD ID: 1359580
Description: Involved in several processes, including chaperone-mediated autophagy; response to fluoride; and response to iron(II) ion. Localizes to axon and protein-containing complex. Biomarker of ischemia. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 25. Orthologous to human ATG5 (autophagy related 5); PARTICIPATES IN autophagy pathway; Retinoic acid-inducible gene (RIG) I-like receptor signaling pathway; INTERACTS WITH 3-methyladenine; 4'-epidoxorubicin; 4-nonylphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: APG5 autophagy 5-like; ATG5 autophagy related 5 homolog; ATG5 autophagy related 5 homolog (S. cerevisiae); autophagy protein 5; LOC365601; similar to autophagy 5-like
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
mRatBN7.22047,798,222 - 47,889,216 (+)NCBI
Rnor_6.0 Ensembl2049,318,308 - 49,393,140 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02049,301,783 - 49,393,147 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02050,934,688 - 51,026,125 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42048,273,977 - 48,366,743 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12048,302,673 - 48,395,435 (+)NCBI
Celera2052,117,260 - 52,207,732 (-)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-Tetrandrine  (ISO)
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxyethyl methacrylate  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3-hydroxybutyric acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (EXP,ISO)
4'-epidoxorubicin  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-nonylphenol  (EXP)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
AICA ribonucleotide  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
amiodarone  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (EXP)
arsenous acid  (ISO)
artesunate  (ISO)
atorvastatin calcium  (ISO)
atrazine  (ISO)
bafilomycin A1  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
butyric acid  (ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
camptothecin  (ISO)
capsaicin  (ISO)
carbon disulfide  (ISO)
carbon nanotube  (ISO)
carglumic acid  (ISO)
chloroquine  (EXP,ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cypermethrin  (ISO)
D-glucose  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diphenhydramine  (ISO)
disodium selenite  (ISO)
doxorubicin  (EXP,ISO)
ellagic acid  (ISO)
embelin  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (EXP,ISO)
ferric oxide  (ISO)
fingolimod hydrochloride  (ISO)
flavokawain B  (ISO)
flutamide  (EXP)
folic acid  (ISO)
Fusaric acid  (ISO)
gefitinib  (ISO)
genistein  (ISO)
geraniol  (ISO)
glucose  (EXP)
glutathione  (ISO)
glycochenodeoxycholic acid  (ISO)
glyphosate  (ISO)
gossypetin  (ISO)
hexadecanoic acid  (EXP,ISO)
HU-308  (ISO)
hyaluronic acid  (EXP)
hydroquinone  (ISO)
indometacin  (ISO)
kainic acid  (EXP)
L-leucine  (ISO)
levamisole  (ISO)
lipopolysaccharide  (EXP,ISO)
luteolin  (EXP,ISO)
lycopene  (ISO)
menadione  (EXP,ISO)
methamphetamine  (EXP,ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
NADP zwitterion  (EXP)
NADP(+)  (EXP)
nickel atom  (ISO)
Nonidet P-40  (ISO)
oleanolic acid  (ISO)
oligopeptide  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
Paeonol  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (EXP)
perfluorooctanoic acid  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
promethazine  (ISO)
propiconazole  (ISO)
pyrroloquinoline quinone  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
rotenone  (EXP,ISO)
SB 203580  (ISO)
sirolimus  (EXP,ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP,ISO)
Soman  (EXP)
sorafenib  (ISO)
stilbenoid  (ISO)
streptozocin  (ISO)
T-2 toxin  (EXP)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
thymoquinone  (ISO)
Triptolide  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc oxide  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aggrephagy  (IEA,ISO)
antigen processing and presentation of endogenous antigen  (IEA,ISO)
apoptotic process  (IEA)
autophagosome assembly  (IBA,IMP,ISO)
autophagy  (IEA,IMP,ISO,ISS)
autophagy of mitochondrion  (IBA,IEA,ISO)
autophagy of nucleus  (IBA)
blood vessel remodeling  (IEA,ISO)
C-terminal protein lipidation  (IBA)
cellular response to nitrogen starvation  (IBA)
cellular response to nitrosative stress  (IEA,ISO)
cellular response to starvation  (IEA,ISO)
chaperone-mediated autophagy  (IMP)
heart contraction  (IEA,ISO)
macroautophagy  (ISO)
negative regulation of apoptotic process  (IEA,IMP,ISO)
negative regulation of cell death  (ISO)
negative regulation of histone H4-K16 acetylation  (IEA,ISO)
negative regulation of phagocytosis  (IEA,ISO)
negative regulation of protein ubiquitination  (IEA,ISO)
negative regulation of reactive oxygen species metabolic process  (IEA,ISO)
negative stranded viral RNA replication  (IEA,ISO)
negative thymic T cell selection  (IEA,ISO)
otolith development  (IEA,ISO)
positive regulation by symbiont of host autophagy  (IEA,ISO)
positive regulation of mucus secretion  (IEA,ISO)
post-translational protein modification  (ISO)
protein lipidation involved in autophagosome assembly  (IEA,ISO)
regulation of cilium assembly  (IEA,ISO,ISS)
regulation of cytokine production involved in immune response  (IEA,ISO)
regulation of reactive oxygen species metabolic process  (ISO)
regulation of release of sequestered calcium ion into cytosol  (IEA,ISO)
response to drug  (IEA,ISO)
response to fluoride  (IEP)
response to fungus  (IEA,ISO)
response to iron(II) ion  (IEP)
vasodilation  (IEA,ISO)
ventricular cardiac muscle cell development  (IEA,ISO)

Cellular Component

Molecular Function
protein binding  (IPI,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Castillo K, etal., Autophagy. 2013 Sep;9(9):1308-20. doi: 10.4161/auto.25188. Epub 2013 Jun 6.
2. Chen G, etal., Am J Med Sci. 2013 May;345(5):369-74. doi: 10.1097/MAJ.0b013e318271c031.
3. Chen X, etal., Mol Med Rep. 2015 Apr;11(4):2513-9. doi: 10.3892/mmr.2014.2999. Epub 2014 Nov 26.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Jiang M, etal., Am J Pathol. 2010 Mar;176(3):1181-92. doi: 10.2353/ajpath.2010.090594. Epub 2010 Jan 14.
7. Kochl R, etal., Traffic. 2006 Feb;7(2):129-45.
8. Liu CL, etal., J Cereb Blood Flow Metab. 2008 Apr;28(4):674-83. Epub 2007 Dec 5.
9. Pipeline to import KEGG annotations from KEGG into RGD
10. RGD automated data pipeline
11. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. RGD automated import pipeline for gene-chemical interactions
13. Ribas VT, etal., Brain Pathol. 2015 Mar;25(2):157-70. doi: 10.1111/bpa.12170. Epub 2014 Sep 12.
14. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
15. Suzuki M and Bartlett JD, Biochim Biophys Acta. 2014 Feb;1842(2):245-55. doi: 10.1016/j.bbadis.2013.11.023. Epub 2013 Dec 1.
16. Ulbricht A, etal., Curr Biol. 2013 Mar 4;23(5):430-5. doi: 10.1016/j.cub.2013.01.064. Epub 2013 Feb 21.
17. Weng LQ, etal., Acta Pharmacol Sin. 2014 Aug;35(8):1005-14. doi: 10.1038/aps.2014.45. Epub 2014 Jul 7.
18. Yang Z and Klionsky DJ, Curr Opin Cell Biol. 2010 Apr;22(2):124-31. Epub 2009 Dec 23.
Additional References at PubMed
PMID:11266458   PMID:15292400   PMID:17450150   PMID:18281291   PMID:19273585   PMID:19783847   PMID:20190558   PMID:20453062   PMID:20577052   PMID:22496425   PMID:22710871   PMID:22982048  
PMID:23093945   PMID:23382543   PMID:23446737   PMID:23455425   PMID:23704209   PMID:23863932   PMID:23878245   PMID:23918802   PMID:24035364   PMID:24089205   PMID:24089209   PMID:24185898  
PMID:24550300   PMID:24582693   PMID:26251076   PMID:26812546   PMID:28231469   PMID:28389568   PMID:29241069   PMID:29799519   PMID:30864677  


Genomics

Comparative Map Data
Atg5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22047,798,222 - 47,889,216 (+)NCBI
Rnor_6.0 Ensembl2049,318,308 - 49,393,140 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02049,301,783 - 49,393,147 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02050,934,688 - 51,026,125 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42048,273,977 - 48,366,743 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12048,302,673 - 48,395,435 (+)NCBI
Celera2052,117,260 - 52,207,732 (-)NCBICelera
Cytogenetic Map20q13NCBI
ATG5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6106,045,423 - 106,325,791 (-)EnsemblGRCh38hg38GRCh38
GRCh386106,184,476 - 106,325,789 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376106,632,351 - 106,773,635 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366106,739,045 - 106,880,388 (-)NCBINCBI36hg18NCBI36
Build 346106,739,044 - 106,880,359NCBI
Celera6107,253,905 - 107,395,251 (-)NCBI
Cytogenetic Map6q21NCBI
HuRef6104,079,375 - 104,220,613 (-)NCBIHuRef
CHM1_16106,894,762 - 107,036,172 (-)NCBICHM1_1
Atg5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391044,144,325 - 44,240,295 (+)NCBIGRCm39mm39
GRCm39 Ensembl1044,144,354 - 44,240,287 (+)Ensembl
GRCm381044,268,322 - 44,364,299 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1044,268,358 - 44,364,291 (+)EnsemblGRCm38mm10GRCm38
MGSCv371043,988,164 - 44,084,097 (+)NCBIGRCm37mm9NCBIm37
MGSCv361043,956,773 - 44,052,706 (+)NCBImm8
Celera1045,141,131 - 45,237,099 (+)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1023.24NCBI
Atg5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541131,522,420 - 31,646,827 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541131,501,191 - 31,646,407 (-)NCBIChiLan1.0ChiLan1.0
ATG5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16107,871,201 - 108,027,064 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6107,871,208 - 108,013,807 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06103,997,824 - 104,140,931 (-)NCBIMhudiblu_PPA_v0panPan3
ATG5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11263,565,859 - 63,692,383 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1263,567,568 - 63,683,485 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1263,353,188 - 63,480,151 (-)NCBI
ROS_Cfam_1.01264,411,072 - 64,538,081 (-)NCBI
UMICH_Zoey_3.11263,770,621 - 63,897,766 (-)NCBI
UNSW_CanFamBas_1.01263,612,694 - 63,739,640 (-)NCBI
UU_Cfam_GSD_1.01263,886,649 - 64,013,653 (-)NCBI
Atg5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494698,484,245 - 98,610,566 (-)NCBI
SpeTri2.0NW_0049365642,759,085 - 2,885,394 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATG5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl172,270,799 - 72,520,453 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1172,343,950 - 72,520,402 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ATG5
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11367,482,538 - 67,619,201 (+)NCBI
ChlSab1.1 Ensembl1367,482,595 - 67,617,902 (+)Ensembl
Vero_WHO_p1.0NW_02366604039,817,584 - 39,954,576 (+)NCBI
Atg5
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478015,987,483 - 16,124,158 (+)NCBI

Position Markers
C88337  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22047,888,971 - 47,889,178 (+)MAPPER
Rnor_6.02049,392,903 - 49,393,109NCBIRnor6.0
Rnor_5.02051,025,881 - 51,026,087UniSTSRnor5.0
RGSC_v3.42048,366,499 - 48,366,705UniSTSRGSC3.4
Celera2052,117,298 - 52,117,504UniSTS
Cytogenetic Map20q13UniSTS
AA859872  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22047,888,177 - 47,888,370 (+)MAPPER
Rnor_6.02049,392,109 - 49,392,301NCBIRnor6.0
Rnor_5.02051,025,087 - 51,025,279UniSTSRnor5.0
RGSC_v3.42048,365,705 - 48,365,897UniSTSRGSC3.4
Celera2052,118,106 - 52,118,298UniSTS
RH 3.4 Map20497.9UniSTS
Cytogenetic Map20q13UniSTS
RH127825  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22047,888,177 - 47,888,368 (+)MAPPER
Rnor_6.02049,392,109 - 49,392,299NCBIRnor6.0
Rnor_5.02051,025,087 - 51,025,277UniSTSRnor5.0
RGSC_v3.42048,365,705 - 48,365,895UniSTSRGSC3.4
Celera2052,118,108 - 52,118,298UniSTS
RH 3.4 Map20497.91UniSTS
Cytogenetic Map20q13UniSTS
AW528235  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22047,816,613 - 47,816,767 (+)MAPPER
Rnor_6.02049,319,491 - 49,319,644NCBIRnor6.0
Rnor_5.02050,952,750 - 50,952,903UniSTSRnor5.0
RGSC_v3.42048,292,595 - 48,292,748UniSTSRGSC3.4
Celera2052,189,058 - 52,189,211UniSTS
RH 3.4 Map20497.3UniSTS
Cytogenetic Map20q13UniSTS
AI178683  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22047,889,032 - 47,889,150 (+)MAPPER
Rnor_6.02049,392,964 - 49,393,081NCBIRnor6.0
Rnor_5.02051,025,942 - 51,026,059UniSTSRnor5.0
RGSC_v3.42048,366,560 - 48,366,677UniSTSRGSC3.4
Celera2052,117,326 - 52,117,443UniSTS
RH 3.4 Map20498.4UniSTS
Cytogenetic Map20q13UniSTS
AU049869  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22047,878,216 - 47,878,400 (+)MAPPER
Rnor_6.02049,382,150 - 49,382,329NCBIRnor6.0
Celera2052,127,977 - 52,128,202UniSTS
Cytogenetic Map20q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:467
Count of miRNA genes:245
Interacting mature miRNAs:284
Transcripts:ENSRNOT00000057078
Prediction methods:Microtar, Miranda, Rnahybrid
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 35 57 41 19 41 1 4 74 35 34 11 1
Low 8 7 7 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000057078   ⟹   ENSRNOP00000053910
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2049,319,307 - 49,393,140 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000080283   ⟹   ENSRNOP00000075339
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2049,318,308 - 49,391,940 (+)Ensembl
RefSeq Acc Id: NM_001014250   ⟹   NP_001014272
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,798,290 - 47,889,216 (+)NCBI
Rnor_6.02049,301,783 - 49,393,147 (+)NCBI
Rnor_5.02050,934,688 - 51,026,125 (+)NCBI
RGSC_v3.42048,273,977 - 48,366,743 (+)RGD
Celera2052,117,260 - 52,207,732 (-)RGD
Sequence:
RefSeq Acc Id: XM_039098910   ⟹   XP_038954838
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,798,222 - 47,889,216 (+)NCBI
RefSeq Acc Id: XM_039098911   ⟹   XP_038954839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,798,247 - 47,889,216 (+)NCBI
RefSeq Acc Id: XM_039098912   ⟹   XP_038954840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,798,222 - 47,889,216 (+)NCBI
RefSeq Acc Id: XM_039098913   ⟹   XP_038954841
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,798,254 - 47,888,589 (+)NCBI
RefSeq Acc Id: XM_039098914   ⟹   XP_038954842
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,798,222 - 47,873,587 (+)NCBI
RefSeq Acc Id: XM_039098915   ⟹   XP_038954843
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,798,242 - 47,889,216 (+)NCBI
RefSeq Acc Id: XM_039098916   ⟹   XP_038954844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,798,237 - 47,888,589 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001014272   ⟸   NM_001014250
- UniProtKB: Q5XIS0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075339   ⟸   ENSRNOT00000080283
RefSeq Acc Id: ENSRNOP00000053910   ⟸   ENSRNOT00000057078
RefSeq Acc Id: XP_038954838   ⟸   XM_039098910
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954840   ⟸   XM_039098912
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038954842   ⟸   XM_039098914
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038954844   ⟸   XM_039098916
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038954843   ⟸   XM_039098915
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038954839   ⟸   XM_039098911
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954841   ⟸   XM_039098913
- Peptide Label: isoform X2

Transcriptome

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


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:1359580 AgrOrtholog
Ensembl Genes ENSRNOG00000000322 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000053910 UniProtKB/TrEMBL
  ENSRNOP00000075339 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057078 UniProtKB/TrEMBL
  ENSRNOT00000080283 UniProtKB/TrEMBL
Gene3D-CATH 1.10.246.190 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.10.20.620 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7133143 IMAGE-MGC_LOAD
InterPro Atg5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Atg5_HR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Atg5_UblA_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:365601 UniProtKB/TrEMBL
MGC_CLONE MGC:94348 IMAGE-MGC_LOAD
NCBI Gene 365601 ENTREZGENE
PANTHER PTHR13040 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam APG5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Atg5 PhenoGen
UniProt A0A0G2KAB9_RAT UniProtKB/TrEMBL
  ATG5_RAT UniProtKB/Swiss-Prot
  D3ZJZ1_RAT UniProtKB/TrEMBL
  Q3MQ06 ENTREZGENE
  Q5XIS0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-06-07 Atg5  autophagy related 5  Atg5  ATG5 autophagy related 5 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-30 Atg5  ATG5 autophagy related 5 homolog (S. cerevisiae)  Atg5  autophagy related 5 homolog (S. cerevisiae)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-03 Atg5  autophagy related 5 homolog (S. cerevisiae)   LOC365601  similar to autophagy 5-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED