Atg7 (autophagy related 7) - Rat Genome Database

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Gene: Atg7 (autophagy related 7) Rattus norvegicus
Analyze
Symbol: Atg7
Name: autophagy related 7
RGD ID: 1304817
Description: Predicted to enable Atg12 activating enzyme activity; Atg8 activating enzyme activity; and protein homodimerization activity. Involved in several processes, including cellular response to morphine; negative regulation of mitochondrial DNA replication; and negative regulation of oxidative stress-induced neuron death. Located in axon. Used to study high grade glioma. Biomarker of hypertension; myocardial infarction; neurodegenerative disease; and paraplegia. Orthologous to human ATG7 (autophagy related 7); PARTICIPATES IN autophagy pathway; mitochondrial autophagy pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: APG7-like; Apg7l; ATG12-activating enzyme E1 ATG7; ATG7 autophagy related 7 homolog; ATG7 autophagy related 7 homolog (S. cerevisiae); autophagy 7-like; autophagy 7-like (S. cerevisiae); autophagy related 7 homolog; autophagy related 7 homolog (S. cerevisiae); autophagy-related 7; autophagy-related 7 (yeast); autophagy-related protein 7; LOC312647; ubiquitin-activating enzyme E1-like protein; ubiquitin-like modifier-activating enzyme ATG7
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
mRatBN7.24147,718,663 - 147,925,656 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl4147,718,752 - 147,925,593 (+)Ensembl
Rnor_6.04146,570,113 - 146,777,093 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4146,598,413 - 146,777,124 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04209,861,459 - 210,067,618 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44150,814,706 - 150,992,704 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14151,059,546 - 151,153,422 (+)NCBI
Celera4136,643,475 - 136,821,326 (+)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-Tetrandrine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2-(2-Chlorophenyl-4'-chlorophenyl)-1,1-dichloroethene  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-deoxy-D-glucose  (ISO)
2-methoxyethanol  (EXP)
3,3',5-triiodo-L-thyronine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methyladenine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxyphenyl retinamide  (ISO)
4-nonylphenol  (EXP)
acrolein  (ISO)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-D-galactose  (EXP,ISO)
amiodarone  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atazanavir sulfate  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfide  (ISO)
caffeine  (ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
chenodeoxycholic acid  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
Curcumol  (EXP)
cyclophosphamide  (ISO)
cyclosporin A  (ISO)
cypermethrin  (ISO)
DDE  (ISO)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dinitrogen  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (ISO)
fenofibrate  (ISO)
fingolimod hydrochloride  (ISO)
flavokawain B  (ISO)
folic acid  (ISO)
Fusaric acid  (ISO)
galactose  (EXP,ISO)
gefitinib  (ISO)
geraniol  (ISO)
glutathione  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
L-leucine  (ISO)
levamisole  (ISO)
lipopolysaccharide  (ISO)
lycopene  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methylnicotinate  (ISO)
nefazodone  (ISO)
nickel atom  (ISO)
Nonidet P-40  (ISO)
oligopeptide  (ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
platycodin D  (ISO)
promethazine  (ISO)
pyrroloquinoline quinone  (ISO)
quercetin  (ISO)
quercitrin  (ISO)
rotenone  (ISO)
rottlerin  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium fluoride  (EXP,ISO)
staurosporine  (ISO)
tamoxifen  (ISO)
taurine  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thymoquinone  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult walking behavior  (ISO)
aging  (IEP)
amino acid homeostasis  (ISO)
autophagosome assembly  (IBA,ISO)
autophagy  (ISO,ISS)
autophagy of mitochondrion  (IBA,ISO)
C-terminal protein lipidation  (IBA)
cardiac muscle cell development  (ISO)
cellular response to hyperoxia  (ISO,ISS)
cellular response to morphine  (IEP)
cellular response to nitrogen starvation  (IBA)
cellular response to reactive oxygen species  (ISO)
cellular response to starvation  (ISO,ISS)
cellular sphingolipid homeostasis  (ISO)
central nervous system neuron axonogenesis  (ISO)
cerebellar Purkinje cell layer development  (ISO)
cerebral cortex development  (ISO)
chaperone-mediated autophagy  (IMP)
defense response to virus  (ISO)
late nucleophagy  (IBA)
liver development  (ISO)
macroautophagy  (ISO)
membrane organization  (ISO)
mitochondrion organization  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cell death  (IMP,ISO)
negative regulation of histone H4-K16 acetylation  (ISO)
negative regulation of mitochondrial DNA replication  (IMP)
negative regulation of oxidative stress-induced neuron death  (IMP)
negative regulation of phagocytosis  (ISO)
negative regulation of sphingolipid biosynthetic process  (ISO)
negative stranded viral RNA replication  (ISO)
nervous system process  (ISO)
neuron projection development  (ISO)
organelle organization  (ISO)
piecemeal microautophagy of the nucleus  (IBA)
positive regulation by symbiont of host autophagy  (ISO)
positive regulation of apoptotic process  (ISO,ISS)
positive regulation of autophagy  (IDA,IMP)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (ISO)
positive regulation of mucus secretion  (ISO)
positive regulation of proteasomal ubiquitin-dependent protein catabolic process  (ISO)
positive regulation of protein catabolic process  (ISO,ISS)
positive regulation of protein modification process  (ISO)
post-embryonic development  (ISO)
protein catabolic process  (ISO)
protein lipidation  (ISO)
protein modification by small protein conjugation  (IBA,ISO)
protein transport  (IEA)
pyramidal neuron development  (ISO)
regulation of cell development  (ISO)
regulation of circadian rhythm  (ISO,ISS)
regulation of hemopoiesis  (ISO)
regulation of neuron death  (IMP)
regulation of protein ubiquitination  (ISO)
response to fluoride  (IEP)
response to glucose  (IEP)
response to nutrient levels  (IEP)
response to starvation  (ISO)
rhythmic process  (IEA)
suppression by virus of host autophagy  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bloemberg D, etal., Acta Physiol (Oxf). 2014 Feb;210(2):381-91. doi: 10.1111/apha.12178. Epub 2013 Nov 5.
2. Feng YM, etal., Autophagy. 2013 Sep;9(9):1395-406. doi: 10.4161/auto.25468. Epub 2013 Jun 20.
3. Fry CS, etal., Muscle Nerve. 2012 Nov;46(5):793-8. doi: 10.1002/mus.23423.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Ginet V, etal., Autophagy. 2014 May;10(5):846-60. doi: 10.4161/auto.28264. Epub 2014 Mar 11.
6. GOA data from the GO Consortium
7. Guo Y, etal., Biochim Biophys Acta. 2015 Feb;1852(2):319-31. doi: 10.1016/j.bbadis.2014.05.017. Epub 2014 May 27.
8. Hagiwara S, etal., Inflammation. 2012 Feb;35(1):249-58. doi: 10.1007/s10753-011-9311-y.
9. He B, etal., Obes Surg. 2015 Jan;25(1):109-18. doi: 10.1007/s11695-014-1342-7.
10. Jannig PR, etal., PLoS One. 2014 Jan 10;9(1):e85820. doi: 10.1371/journal.pone.0085820. eCollection 2014.
11. McMullen CA, etal., Exp Gerontol. 2009 Jun-Jul;44(6-7):420-5. doi: 10.1016/j.exger.2009.03.006. Epub 2009 Mar 31.
12. Pipeline to import KEGG annotations from KEGG into RGD
13. Radoshevich L, etal., Cell. 2010 Aug 20;142(4):590-600. doi: 10.1016/j.cell.2010.07.018.
14. RGD automated data pipeline
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. RGD comprehensive gene curation
18. Ribas VT, etal., Brain Pathol. 2015 Mar;25(2):157-70. doi: 10.1111/bpa.12170. Epub 2014 Sep 12.
19. 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.
20. Tanida I, etal., Int J Biochem Cell Biol. 2004 Dec;36(12):2503-18.
21. Teng YC, etal., Toxicol Lett. 2015 Mar 18;233(3):239-45. doi: 10.1016/j.toxlet.2015.01.018. Epub 2015 Jan 29.
22. Ulbricht A, etal., Curr Biol. 2013 Mar 4;23(5):430-5. doi: 10.1016/j.cub.2013.01.064. Epub 2013 Feb 21.
23. Wei H, etal., Biochim Biophys Acta. 2015 Oct;1853(10 Pt B):2784-90. doi: 10.1016/j.bbamcr.2015.03.013. Epub 2015 Apr 1.
24. Wohlgemuth SE, etal., Rejuvenation Res. 2007 Sep;10(3):281-92.
25. Yamamoto E, etal., Biochem Biophys Res Commun. 2014 Oct 10;453(1):19-24. doi: 10.1016/j.bbrc.2014.09.040. Epub 2014 Sep 19.
26. Yang Z and Klionsky DJ, Curr Opin Cell Biol. 2010 Apr;22(2):124-31. Epub 2009 Dec 23.
27. Zanotto-Filho A, etal., Cancer Lett. 2015 Mar 28;358(2):220-31. doi: 10.1016/j.canlet.2014.12.044. Epub 2014 Dec 24.
28. Zare N, etal., J Mol Neurosci. 2015 Nov;57(3):317-24. doi: 10.1007/s12031-015-0619-1. Epub 2015 Jul 25.
29. Zhang X, etal., Autophagy. 2013 Sep;9(9):1321-33. doi: 10.4161/auto.25132. Epub 2013 Jun 12.
Additional References at PubMed
PMID:11096062   PMID:11890701   PMID:12477932   PMID:12482611   PMID:12890687   PMID:14627652   PMID:15489334   PMID:15866887   PMID:16625205   PMID:16885219   PMID:17450150   PMID:17726112  
PMID:19279012   PMID:20080761   PMID:20543840   PMID:20577052   PMID:21402742   PMID:21617129   PMID:22354037   PMID:22496425   PMID:23152632   PMID:23290079   PMID:23704209   PMID:23863932  
PMID:23918799   PMID:23981124   PMID:23986436   PMID:24035364   PMID:24089209   PMID:24105478   PMID:24185898   PMID:24550300   PMID:24681637   PMID:25327288   PMID:25332431   PMID:28389568  
PMID:28860495   PMID:29311554   PMID:29937374   PMID:32043463   PMID:33372336   PMID:33491285  


Genomics

Comparative Map Data
Atg7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24147,718,663 - 147,925,656 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl4147,718,752 - 147,925,593 (+)Ensembl
Rnor_6.04146,570,113 - 146,777,093 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4146,598,413 - 146,777,124 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04209,861,459 - 210,067,618 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44150,814,706 - 150,992,704 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14151,059,546 - 151,153,422 (+)NCBI
Celera4136,643,475 - 136,821,326 (+)NCBICelera
Cytogenetic Map4q42NCBI
ATG7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl311,272,309 - 11,557,665 (+)EnsemblGRCh38hg38GRCh38
GRCh38311,272,348 - 11,564,652 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37311,314,083 - 11,606,126 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36311,315,160 - 11,571,557 (+)NCBINCBI36hg18NCBI36
Build 34311,289,101 - 11,571,556NCBI
Celera311,249,448 - 11,534,544 (+)NCBI
Cytogenetic Map3p25.3NCBI
HuRef311,248,262 - 11,532,686 (+)NCBIHuRef
CHM1_1311,264,079 - 11,549,266 (+)NCBICHM1_1
Atg7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396114,620,075 - 114,837,565 (+)NCBIGRCm39mm39
GRCm39 Ensembl6114,620,058 - 114,837,575 (+)Ensembl
GRCm386114,643,127 - 114,860,604 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6114,643,097 - 114,860,614 (+)EnsemblGRCm38mm10GRCm38
MGSCv376114,593,143 - 114,809,954 (+)NCBIGRCm37mm9NCBIm37
MGSCv366114,608,744 - 114,825,555 (+)NCBImm8
Celera6116,482,450 - 116,697,418 (+)NCBICelera
Cytogenetic Map6E3NCBI
Atg7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542914,076,960 - 14,304,236 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542914,076,976 - 14,301,034 (+)NCBIChiLan1.0ChiLan1.0
ATG7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1311,554,100 - 11,833,638 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl311,554,100 - 11,833,398 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0311,208,600 - 11,488,757 (+)NCBIMhudiblu_PPA_v0panPan3
ATG7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1206,916,354 - 7,154,849 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl206,916,515 - 7,154,800 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha206,951,793 - 7,189,666 (-)NCBI
ROS_Cfam_1.0206,945,628 - 7,184,158 (-)NCBI
UMICH_Zoey_3.1206,661,904 - 6,900,228 (-)NCBI
UNSW_CanFamBas_1.0207,018,478 - 7,256,616 (-)NCBI
UU_Cfam_GSD_1.0206,989,268 - 7,228,243 (-)NCBI
Atg7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494216,730,443 - 16,981,101 (+)NCBI
SpeTri2.0NW_0049366021,938,720 - 2,179,239 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATG7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1367,417,938 - 67,707,660 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11367,301,756 - 67,699,141 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21374,636,936 - 74,915,764 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ATG7
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12247,187,305 - 47,571,309 (+)NCBI
ChlSab1.1 Ensembl2247,325,614 - 47,571,070 (+)Ensembl
Vero_WHO_p1.0NW_023666041118,943,702 - 119,213,969 (-)NCBI
Atg7
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624943231,978 - 480,933 (-)NCBI


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4120926564148090731Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4103194656148194656Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4126395976167139601Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4132422778177422778Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4138503169179293946Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4124303370169303370Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)485253748148090731Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131730738167139601Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4146565735175236377Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4132396220177396220Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4138503169173369699Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132642577167139601Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4124778595169778595Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4125590636170590636Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4147278504167139601Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:84
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000067532
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 17 2 18 2 58 31 39 11
Low 43 40 39 1 39 8 11 16 4 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000067532   ⟹   ENSRNOP00000063617
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4147,747,009 - 147,925,551 (+)Ensembl
Rnor_6.0 Ensembl4146,598,413 - 146,777,124 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095118   ⟹   ENSRNOP00000091366
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4147,718,752 - 147,842,012 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096019   ⟹   ENSRNOP00000090070
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4147,718,752 - 147,924,709 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099380   ⟹   ENSRNOP00000088044
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4147,718,752 - 147,924,887 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000104390   ⟹   ENSRNOP00000079344
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4147,718,752 - 147,841,307 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109260   ⟹   ENSRNOP00000091777
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4147,747,009 - 147,925,593 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118521   ⟹   ENSRNOP00000091824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4147,718,754 - 147,846,524 (+)Ensembl
RefSeq Acc Id: NM_001012097   ⟹   NP_001012097
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24147,747,014 - 147,924,905 (+)NCBI
Rnor_6.04146,598,416 - 146,776,407 (+)NCBI
Rnor_5.04209,861,459 - 210,067,618 (+)NCBI
RGSC_v3.44150,814,706 - 150,992,704 (+)RGD
Celera4136,643,475 - 136,821,326 (+)RGD
Sequence:
RefSeq Acc Id: XM_008763239   ⟹   XP_008761461
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24147,718,663 - 147,859,190 (+)NCBI
Rnor_6.04146,570,113 - 146,698,968 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005503229
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24147,747,010 - 147,925,656 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001012097   ⟸   NM_001012097
- UniProtKB: Q641Y5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008761461   ⟸   XM_008763239
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000063617   ⟸   ENSRNOT00000067532
RefSeq Acc Id: ENSRNOP00000088044   ⟸   ENSRNOT00000099380
RefSeq Acc Id: ENSRNOP00000091366   ⟸   ENSRNOT00000095118
RefSeq Acc Id: ENSRNOP00000090070   ⟸   ENSRNOT00000096019
RefSeq Acc Id: ENSRNOP00000091777   ⟸   ENSRNOT00000109260
RefSeq Acc Id: ENSRNOP00000079344   ⟸   ENSRNOT00000104390
RefSeq Acc Id: ENSRNOP00000091824   ⟸   ENSRNOT00000118521

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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: 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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: 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)
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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
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)
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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
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:1304817 AgrOrtholog
Ensembl Genes ENSRNOG00000007486 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000063617 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000067532 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.140.100 UniProtKB/Swiss-Prot
  3.40.140.70 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7132421 IMAGE-MGC_LOAD
InterPro Atg7 UniProtKB/Swiss-Prot
  Atg7_N UniProtKB/Swiss-Prot
  Atg7_N_1 UniProtKB/Swiss-Prot
  Atg7_N_2 UniProtKB/Swiss-Prot
  ThiF_NAD_FAD-bd UniProtKB/Swiss-Prot
  Ubiquitin-activating_enz UniProtKB/Swiss-Prot
KEGG Report rno:312647 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95213 IMAGE-MGC_LOAD
NCBI Gene 312647 ENTREZGENE
Pfam ATG7_N UniProtKB/Swiss-Prot
  ThiF UniProtKB/Swiss-Prot
PhenoGen Atg7 PhenoGen
Superfamily-SCOP SSF69572 UniProtKB/Swiss-Prot
TIGRFAMs E1_like_apg7 UniProtKB/Swiss-Prot
UniProt ATG7_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-06-07 Atg7  autophagy related 7  Atg7  autophagy related 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-06-07 Atg7  autophagy related 7  Atg7  ATG7 autophagy related 7 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-06-07 Atg7  autophagy related 7  Atg7  autophagy related 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-06-27 Atg7  ATG7 autophagy related 7 homolog (S. cerevisiae)  Atg7  autophagy related 7 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-12 Atg7  autophagy related 7 homolog (S. cerevisiae)  Atg7  autophagy-related 7 (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Atg7  autophagy-related 7 (yeast)  Apg7l  autophagy 7-like (S. cerevisiae)  Symbol and Name updated 1299863 APPROVED
2005-12-06 Apg7l  autophagy 7-like (S. cerevisiae)  Apg7l_predicted  autophagy 7-like (S. cerevisiae) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Apg7l_predicted  autophagy 7-like (S. cerevisiae) (predicted)      Symbol and Name status set to approved 70820 APPROVED