Atf6 (activating transcription factor 6) - Rat Genome Database

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Gene: Atf6 (activating transcription factor 6) Rattus norvegicus
Analyze
Symbol: Atf6
Name: activating transcription factor 6
RGD ID: 1305471
Description: Enables ubiquitin protein ligase binding activity. Predicted to be involved in several processes, including endoplasmic reticulum unfolded protein response; positive regulation of ATF6-mediated unfolded protein response; and positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress. Predicted to act upstream of or within positive regulation of autophagy and positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Biomarker of borna disease. Human ortholog(s) of this gene implicated in achromatopsia 7. Orthologous to human ATF6 (activating transcription factor 6); PARTICIPATES IN endoplasmic reticulum stress - the unfolded protein response pathway; Alzheimer's disease pathway; Endoplasmic Reticulum-associated degradation pathway; INTERACTS WITH (+)-schisandrin B; (S)-nicotine; 1,2-dimethylhydrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: activating transcription factor 6 alpha; ATF6-alpha; cAMP-dependent transcription factor ATF-6 alpha; cyclic AMP-dependent transcription factor ATF-6 alpha; LOC304962
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
mRatBN7.21382,927,579 - 83,106,381 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1382,930,034 - 83,107,177 (-)Ensembl
Rnor_6.01389,053,457 - 89,242,531 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1389,055,983 - 89,242,443 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01393,668,054 - 93,854,918 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41386,543,773 - 86,718,970 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11386,559,136 - 86,734,174 (-)NCBI
Celera1382,588,612 - 82,760,829 (-)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-schisandrin B  (EXP)
(R)-lipoic acid  (ISO)
(S)-nicotine  (EXP)
1,10-phenanthroline  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
15-acetyldeoxynivalenol  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,4-dichlorophenol  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP,ISO)
2-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-acetyldeoxynivalenol  (ISO)
3-chloropropane-1,2-diol  (EXP,ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
4-hydroxynon-2-enal  (EXP)
4-phenylbutyric acid  (EXP,ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucosamine  (EXP,ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
allopurinol  (ISO)
amiodarone  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
atazanavir sulfate  (ISO)
BAPTA  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
beta-D-glucosamine  (EXP,ISO)
bilirubin IXalpha  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
boric acid  (ISO)
brefeldin A  (ISO)
Butylparaben  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (EXP,ISO)
calcitriol  (ISO)
cantharidin  (ISO)
casticin  (ISO)
chenodeoxycholic acid  (ISO)
chloroacetic acid  (ISO)
chlorpyrifos  (EXP)
chromium(6+)  (EXP)
chrysazin  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cyproconazole  (EXP)
D-glucose  (ISO)
D-penicillamine  (ISO)
DDE  (ISO)
decabromodiphenyl ether  (EXP)
demethoxycurcumin  (ISO)
deoxycholic acid  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
dioscin  (EXP,ISO)
dioxygen  (ISO)
diquat  (ISO)
dorsomorphin  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
fisetin  (ISO)
furan  (EXP)
Fusarenone X  (ISO)
gadolinium trichloride  (EXP)
geraniol  (ISO)
ginsenoside Rg1  (ISO)
glucose  (ISO)
glutathione  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
Guanabenz  (ISO)
GW 4064  (ISO)
hexadecanoic acid  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
L-serine  (ISO)
lead diacetate  (EXP,ISO)
letrozole  (EXP)
lipoic acid  (ISO)
lipopolysaccharide  (ISO)
luteolin  (ISO)
LY294002  (EXP,ISO)
lycopene  (EXP)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP,ISO)
melatonin  (EXP)
menadione  (ISO)
metformin  (ISO)
methamphetamine  (EXP,ISO)
methapyrilene  (EXP)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
metyrapone  (ISO)
minocycline  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-hexadecanoylsphingosine  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
naltrexone  (ISO)
nefazodone  (ISO)
nelfinavir  (ISO)
nickel atom  (EXP)
nickel sulfate  (EXP)
nicotine  (EXP)
nilotinib  (ISO)
Nivalenol  (ISO)
Nonidet P-40  (ISO)
Norbinaltorphimine  (ISO)
ochratoxin A  (ISO)
oleic acid  (ISO)
oxaliplatin  (EXP)
paracetamol  (ISO)
paraquat  (EXP,ISO)
phenethyl caffeate  (ISO)
poly(guanylic acid)  (EXP)
potassium dichromate  (EXP,ISO)
propiconazole  (ISO)
pyocyanine  (EXP)
pyrazinecarboxamide  (ISO)
quercetin  (EXP,ISO)
quercetin 3-O-beta-D-glucofuranoside  (EXP)
quercetin 3-O-beta-D-glucopyranoside  (EXP)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (ISO)
Riluzole  (ISO)
rimonabant  (ISO)
rotenone  (ISO)
salubrinal  (ISO)
saquinavir  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (EXP)
simvastatin  (EXP)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP)
sodium fluoride  (EXP,ISO)
SR 144528  (ISO)
streptozocin  (EXP)
sulindac  (ISO)
tacrolimus hydrate  (ISO)
tauroursodeoxycholic acid  (EXP,ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (EXP,ISO)
thioacetamide  (ISO)
thymoquinone  (ISO)
Tiron  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP)
triclocarban  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
Triptolide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
tunicamycin  (EXP,ISO)
valproic acid  (ISO)
vincristine  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:9837962   PMID:10564271   PMID:11163209   PMID:11256944   PMID:11779464   PMID:12477932   PMID:12805554   PMID:14752510   PMID:14973138   PMID:16236796   PMID:16469704   PMID:18319259  
PMID:18450959   PMID:18927462   PMID:19615339   PMID:20102225   PMID:21821716   PMID:23869584   PMID:24180212   PMID:24269637   PMID:24976582   PMID:25312904   PMID:25331812   PMID:25447309  
PMID:25609649   PMID:26029869   PMID:26261584   PMID:27035093   PMID:27581066   PMID:27785700   PMID:28473536   PMID:29414031   PMID:33238217   PMID:33537827   PMID:33666503  


Genomics

Comparative Map Data
Atf6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21382,927,579 - 83,106,381 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1382,930,034 - 83,107,177 (-)Ensembl
Rnor_6.01389,053,457 - 89,242,531 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1389,055,983 - 89,242,443 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01393,668,054 - 93,854,918 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41386,543,773 - 86,718,970 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11386,559,136 - 86,734,174 (-)NCBI
Celera1382,588,612 - 82,760,829 (-)NCBICelera
Cytogenetic Map13q24NCBI
ATF6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1161,766,298 - 161,977,574 (+)EnsemblGRCh38hg38GRCh38
GRCh381161,766,320 - 161,964,070 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371161,736,110 - 161,933,860 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361160,002,708 - 160,195,476 (+)NCBINCBI36hg18NCBI36
Build 341158,467,741 - 158,660,510NCBI
Celera1134,839,502 - 135,032,269 (+)NCBI
Cytogenetic Map1q23.3NCBI
HuRef1132,980,970 - 133,178,653 (+)NCBIHuRef
CHM1_11163,157,827 - 163,355,630 (+)NCBICHM1_1
Atf6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391170,532,026 - 170,696,414 (-)NCBIGRCm39mm39
GRCm39 Ensembl1170,532,243 - 170,695,340 (-)Ensembl
GRCm381170,704,457 - 170,868,585 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1170,704,674 - 170,867,771 (-)EnsemblGRCm38mm10GRCm38
MGSCv371172,634,588 - 172,797,902 (-)NCBIGRCm37mm9NCBIm37
MGSCv361172,541,132 - 172,710,564 (-)NCBImm8
Celera1173,146,825 - 173,324,073 (-)NCBICelera
Cytogenetic Map1H3NCBI
cM Map176.96NCBI
Atf6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546214,357,945 - 14,548,543 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495546214,352,956 - 14,553,299 (-)NCBIChiLan1.0ChiLan1.0
ATF6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11140,977,750 - 141,181,837 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1140,977,750 - 141,176,725 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01137,178,629 - 137,382,256 (+)NCBIMhudiblu_PPA_v0panPan3
ATF6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13820,705,167 - 20,903,852 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3820,709,038 - 20,903,814 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3820,758,598 - 20,956,710 (-)NCBI
ROS_Cfam_1.03820,788,925 - 20,987,730 (-)NCBI
UMICH_Zoey_3.13820,761,253 - 20,959,710 (-)NCBI
UNSW_CanFamBas_1.03821,114,892 - 21,313,427 (-)NCBI
UU_Cfam_GSD_1.03821,406,602 - 21,593,774 (-)NCBI
Atf6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050587,651,241 - 7,833,831 (+)NCBI
SpeTri2.0NW_004937131170,649 - 183,942 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATF6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl488,591,280 - 88,818,372 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1488,591,279 - 88,806,156 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2496,614,364 - 96,821,004 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATF6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1202,112,819 - 2,304,063 (-)NCBI
ChlSab1.1 Ensembl202,117,982 - 2,304,027 (-)Ensembl
Vero_WHO_p1.0NW_0236660381,151,751 - 1,344,350 (-)NCBI
Atf6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624826189,899 - 412,540 (+)NCBI

Position Markers
D13Rat133  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21383,005,889 - 83,006,034 (+)MAPPERmRatBN7.2
Rnor_6.01389,141,946 - 89,142,088NCBIRnor6.0
Rnor_5.01393,755,047 - 93,755,189UniSTSRnor5.0
RGSC_v3.41386,617,943 - 86,618,086RGDRGSC3.4
RGSC_v3.41386,617,944 - 86,618,086UniSTSRGSC3.4
RGSC_v3.11386,632,132 - 86,632,274RGD
Celera1382,659,564 - 82,659,706UniSTS
RH 3.4 Map13551.0RGD
RH 3.4 Map13551.0UniSTS
RH 2.0 Map13605.7RGD
SHRSP x BN Map1338.4998RGD
Cytogenetic Map13q24UniSTS
RH134430  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21382,930,487 - 82,930,706 (+)MAPPERmRatBN7.2
Rnor_6.01389,056,365 - 89,056,583NCBIRnor6.0
Rnor_5.01393,670,962 - 93,671,180UniSTSRnor5.0
RGSC_v3.41386,542,671 - 86,542,889UniSTSRGSC3.4
Celera1382,587,510 - 82,587,728UniSTS
RH 3.4 Map13547.5UniSTS
Cytogenetic Map13q24UniSTS
AU046924  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21383,005,821 - 83,006,015 (+)MAPPERmRatBN7.2
Rnor_6.01389,141,878 - 89,142,069NCBIRnor6.0
Rnor_5.01393,754,979 - 93,755,170UniSTSRnor5.0
RGSC_v3.41386,617,876 - 86,618,067UniSTSRGSC3.4
Celera1382,659,496 - 82,659,687UniSTS
Cytogenetic Map13q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133124133193395974Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133124133193395974Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
12879444Bp397Blood pressure QTL 397arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134504940490049404Rat
12879471Bp398Blood pressure QTL 398arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134551471990514719Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
738026Lnnr5Liver neoplastic nodule remodeling QTL 53.29liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)135987440885581182Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
8655945Rf61Renal function QTL 613.6blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)136906051986800898Rat
1331783Bp221Blood pressure QTL 2213.72886arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)136906051986800898Rat
1300166Kidm6Kidney mass QTL 63.93kidney mass (VT:0002707)single kidney wet weight to body weight ratio (CMO:0000622)136906051986800898Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
738027Lnnr6Liver neoplastic nodule remodeling QTL 63.3liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)137486211785581182Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:275
Count of miRNA genes:189
Interacting mature miRNAs:215
Transcripts:ENSRNOT00000029202
Prediction methods:Miranda
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 40 57 41 19 41 8 9 74 35 38 11 8
Low 3 2 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029202   ⟹   ENSRNOP00000032766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1382,930,034 - 83,107,177 (-)Ensembl
Rnor_6.0 Ensembl1389,055,983 - 89,242,443 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097534   ⟹   ENSRNOP00000081916
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1382,930,034 - 83,090,328 (-)Ensembl
RefSeq Acc Id: NM_001107196   ⟹   NP_001100666
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21382,931,590 - 83,106,345 (-)NCBI
Rnor_6.01389,057,467 - 89,242,460 (-)NCBI
Rnor_5.01393,668,054 - 93,854,918 (-)NCBI
RGSC_v3.41386,543,773 - 86,718,970 (-)RGD
Celera1382,588,612 - 82,760,829 (-)RGD
Sequence:
RefSeq Acc Id: XM_008769738   ⟹   XP_008767960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21382,927,579 - 83,106,381 (-)NCBI
Rnor_6.01389,053,457 - 89,242,531 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100666 (Get FASTA)   NCBI Sequence Viewer  
  XP_008767960 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68890 (Get FASTA)   NCBI Sequence Viewer  
  EDM09246 (Get FASTA)   NCBI Sequence Viewer  
  G3V909 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100666   ⟸   NM_001107196
- UniProtKB: G3V909 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008767960   ⟸   XM_008769738
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000032766   ⟸   ENSRNOT00000029202
RefSeq Acc Id: ENSRNOP00000081916   ⟸   ENSRNOT00000097534
Protein Domains
bZIP

Transcriptome

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

Promoters
RGD ID:13698987
Promoter ID:EPDNEW_R9512
Type:multiple initiation site
Name:Atf6_1
Description:activating transcription factor 6
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_6.01389,242,457 - 89,242,517EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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)
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
LN/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
M520/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
M520/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
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)
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
MNS/Gib (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
MR/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
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/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)
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
SHRSP/Gcrc (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
SR/JrHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305471 AgrOrtholog
Ensembl Genes ENSRNOG00000024632 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000032766 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000029202 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro ATF6A UniProtKB/Swiss-Prot
  bZIP UniProtKB/Swiss-Prot
KEGG Report rno:304962 UniProtKB/Swiss-Prot
NCBI Gene 304962 ENTREZGENE
PANTHER PTHR46164:SF1 UniProtKB/Swiss-Prot
Pfam bZIP_1 UniProtKB/Swiss-Prot
PhenoGen Atf6 PhenoGen
PROSITE BZIP UniProtKB/Swiss-Prot
  BZIP_BASIC UniProtKB/Swiss-Prot
SMART BRLZ UniProtKB/Swiss-Prot
UniProt ATF6A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B5DF18 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Atf6  activating transcription factor 6   Atf6_predicted  activating transcription factor 6 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Atf6_predicted  activating transcription factor 6 (predicted)      Symbol and Name status set to approved 70820 APPROVED