Atf4 (activating transcription factor 4) - Rat Genome Database
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Gene: Atf4 (activating transcription factor 4) Rattus norvegicus
Analyze
Symbol: Atf4
Name: activating transcription factor 4
RGD ID: 621863
Description: Exhibits protein C-terminus binding activity and transcription factor binding activity. Involved in several processes, including cellular response to oxygen-glucose deprivation; gamma-aminobutyric acid signaling pathway; and response to manganese-induced endoplasmic reticulum stress. Localizes to cytoplasm; dendrite membrane; and nucleus. Predicted to colocalize with centrosome. Biomarker of borna disease and pulmonary venoocclusive disease. Human ortholog(s) of this gene implicated in prostate carcinoma. Orthologous to human ATF4 (activating transcription factor 4); PARTICIPATES IN endoplasmic reticulum stress - the unfolded protein response pathway; Endoplasmic Reticulum-associated degradation pathway; gonadotropin-releasing hormone signaling pathway; INTERACTS WITH (+)-schisandrin B; (R)-lipoic acid; (S)-amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: activating transcription factor 4 (tax-responsive enhancer element B67); activating transcription factor ATF-4; cAMP-dependent transcription factor ATF-4; cyclic AMP-dependent transcription factor ATF-4; rATF-4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27111,804,135 - 111,806,457 (+)NCBI
Rnor_6.0 Ensembl7121,480,723 - 121,482,772 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07121,480,723 - 121,482,781 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07121,468,275 - 121,470,587 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47118,537,718 - 118,538,994NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17118,571,947 - 118,573,223NCBI
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(+)-schisandrin B  (EXP)
(-)-citrinin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-lipoic acid  (EXP,ISO)
(S)-amphetamine  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1,4-dithiothreitol  (ISO)
1-naphthyl isothiocyanate  (EXP,ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2-amino-2-deoxy-D-galactopyranose  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-arachidonoylglycerol  (ISO)
2-butoxyethanol  (ISO)
2-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3H-1,2-dithiole-3-thione  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-diisothiocyano-trans-stilbene-2,2'-disulfonic acid  (ISO)
4-hydroxynon-2-enal  (EXP)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (EXP,ISO)
4-tert-Octylphenol  (EXP)
5-fluorouracil  (ISO)
6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide  (EXP)
7,9-dihydro-1H-purine-2,6,8(3H)-trione  (ISO)
acetic acid [2-[[(5-nitro-2-thiazolyl)amino]-oxomethyl]phenyl] ester  (ISO)
acetylsalicylic acid  (ISO)
acrolein  (EXP,ISO)
acrylamide  (ISO)
actinomycin D  (ISO)
aldehydo-D-glucosamine  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinal  (ISO)
all-trans-retinoic acid  (ISO)
alpha-D-galactose  (ISO)
amino acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
atazanavir sulfate  (ISO)
atrazine  (ISO)
bathocuproine disulfonic acid  (ISO)
benzalkonium chloride  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bepridil  (ISO)
beta-D-glucosamine  (ISO)
bis(2-chloroethyl) sulfide  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bongkrekic acid  (ISO)
boric acid  (ISO)
bortezomib  (ISO)
brefeldin A  (ISO)
cadmium dichloride  (ISO)
cadmium sulfate  (ISO)
camptothecin  (ISO)
cannabidiol  (ISO)
cannabigerol  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carboxy-PTIO  (ISO)
chenodeoxycholic acid  (ISO)
chloroacetaldehyde  (ISO)
chloroacetic acid  (ISO)
chloropicrin  (ISO)
chloroquine  (EXP)
chlorpromazine  (EXP,ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
cibenzoline  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (EXP)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cylindrospermopsin  (ISO)
D-glucose  (ISO)
dantrolene  (EXP,ISO)
deoxycholic acid  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
diclofenac  (ISO)
diethylstilbestrol  (EXP)
dihydrocapsaicin  (ISO)
dimethylarsinic acid  (EXP,ISO)
dimethylarsinous acid  (EXP)
dioxygen  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
epoxomicin  (ISO)
erlotinib hydrochloride  (EXP)
ethanol  (EXP,ISO)
etoposide  (ISO)
fangchinoline  (ISO)
fenofibrate  (EXP,ISO)
flavokawain B  (ISO)
fluoranthene  (ISO)
flutamide  (EXP)
fructose  (EXP)
fulvestrant  (ISO)
furan  (ISO)
gadolinium trichloride  (EXP)
galactose  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glafenine  (EXP)
glucose  (ISO)
glutaraldehyde  (ISO)
glutathione  (ISO)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glyphosate  (ISO)
gold atom  (ISO)
gold(0)  (ISO)
GSK2656157  (ISO)
helenalin  (ISO)
hexadecanoic acid  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
hydroquinone  (ISO)
ibuprofen  (ISO)
ifosfamide  (ISO)
ionomycin  (ISO)
ivermectin  (ISO)
KN-93  (EXP)
L-1,4-dithiothreitol  (ISO)
lead diacetate  (EXP,ISO)
lead(II) chloride  (ISO)
leflunomide  (EXP,ISO)
linsidomine  (ISO)
lipoic acid  (EXP,ISO)
lipopolysaccharide  (EXP,ISO)
lithium chloride  (ISO)
LY294002  (ISO)
manganese(II) chloride  (EXP)
melatonin  (EXP)
metformin  (EXP)
methamphetamine  (EXP,ISO)
methapyrilene  (EXP)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
MK-2206  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-hexadecanoylsphingosine  (ISO)
N-methyl-4-phenylpyridinium  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (ISO)
nelfinavir  (ISO)
niclosamide  (ISO)
nimesulide  (EXP)
Nodularin  (ISO)
Nonidet P-40  (ISO)
ochratoxin A  (ISO)
orlistat  (ISO)
oxidopamine  (EXP)
oxycodone  (EXP,ISO)
p-tert-Amylphenol  (EXP)
paracetamol  (EXP,ISO)
paraquat  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (ISO)
PhIP  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
pyrazinecarboxamide  (EXP,ISO)
pyrrolidine dithiocarbamate  (EXP,ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
rifampicin  (EXP,ISO)
rimonabant  (ISO)
rotenone  (EXP,ISO)
salubrinal  (EXP,ISO)
SCH 23390  (EXP)
selenium atom  (ISO)
sertraline  (ISO)
sirolimus  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP,ISO)
sodium fluoride  (EXP)
Soman  (EXP)
sorafenib  (ISO)
SR 144528  (ISO)
streptozocin  (EXP,ISO)
sulforaphane  (ISO)
sulindac  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (EXP,ISO)
tauroursodeoxycholic acid  (ISO)
tetrachloromethane  (EXP,ISO)
thapsigargin  (EXP,ISO)
thymoquinone  (ISO)
Tiron  (ISO)
titanium dioxide  (ISO)
Tributyltin oxide  (EXP,ISO)
triclocarban  (ISO)
trimethylamine N-oxide  (ISO)
triphenyl phosphate  (EXP)
Triptolide  (EXP)
troglitazone  (ISO)
tunicamycin  (EXP,ISO)
urethane  (ISO)
ursodeoxycholic acid  (ISO)
usnic acid  (ISO)
valproic acid  (ISO)
withaferin A  (ISO)
xylitol  (ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
bone mineralization  (ISO,ISS)
cellular calcium ion homeostasis  (ISO)
cellular response to amino acid starvation  (ISO,ISS)
cellular response to dopamine  (ISO)
cellular response to glucose starvation  (ISO)
cellular response to oxidative stress  (ISO,ISS)
cellular response to oxygen-glucose deprivation  (IEP)
cellular response to UV  (ISS)
circadian regulation of gene expression  (ISO,ISS)
circadian rhythm  (ISO)
embryonic hemopoiesis  (ISO,ISS)
endoplasmic reticulum unfolded protein response  (ISO,ISS)
gamma-aminobutyric acid signaling pathway  (IDA)
gluconeogenesis  (ISO)
HRI-mediated signaling  (ISO,ISS)
integrated stress response signaling  (ISO,ISS)
intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress  (ISO,ISS)
L-asparagine metabolic process  (ISO)
lens fiber cell morphogenesis  (ISO,ISS)
mRNA transcription by RNA polymerase II  (ISO,ISS)
negative regulation of cold-induced thermogenesis  (ISO,ISS)
negative regulation of oxidative stress-induced neuron death  (IMP,ISO)
negative regulation of potassium ion transport  (IMP)
negative regulation of transcription by RNA polymerase II  (ISO,ISS)
negative regulation of translational initiation in response to stress  (ISS)
neuron differentiation  (IEP)
PERK-mediated unfolded protein response  (ISO,ISS)
positive regulation of biomineral tissue development  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of neuron apoptotic process  (ISO,ISS)
positive regulation of sodium-dependent phosphate transport  (ISO)
positive regulation of transcription by RNA polymerase I  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO,ISS)
positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress  (ISO)
positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress  (IMP,ISO)
positive regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of vascular associated smooth muscle cell apoptotic process  (ISO)
positive regulation of vascular endothelial growth factor production  (ISO)
regulation of osteoblast differentiation  (ISO,ISS)
regulation of synaptic plasticity  (ISO,ISS)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of transcription, DNA-templated  (ISO,ISS)
response to endoplasmic reticulum stress  (ISO,ISS)
response to manganese-induced endoplasmic reticulum stress  (IEP)
response to nutrient levels  (ISO)
response to toxic substance  (IEP)

References

References - curated
1. Cho YM, etal., Exp Mol Med. 2009 Jun 30;41(6):440-52. doi: 10.3858/emm.2009.41.6.049.
2. Fujinami Y, etal., Neurochem Int. 2010 Feb;56(3):487-94. doi: 10.1016/j.neuint.2009.12.008. Epub 2009 Dec 21.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Jin Y, etal., EMBO Mol Med. 2015 Mar;7(3):315-31. doi: 10.15252/emmm.201404181.
6. Linares JF, etal., Cell Metab. 2017 Dec 5;26(6):817-829.e6. doi: 10.1016/j.cmet.2017.09.001. Epub 2017 Oct 5.
7. Manaud G, etal., Am J Respir Cell Mol Biol. 2020 Jul;63(1):118-131. doi: 10.1165/rcmb.2019-0015OC.
8. MGD data from the GO Consortium
9. NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. Nehring RB, etal., J Biol Chem 2000 Nov 10;275(45):35185-91.
11. Pipeline to import KEGG annotations from KEGG into RGD
12. RGD automated data pipeline
13. RGD automated import pipeline for gene-chemical interactions
14. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
15. Sun X, etal., J Neurosci. 2013 Feb 6;33(6):2398-407. doi: 10.1523/JNEUROSCI.2292-12.2013.
16. Tan Z, etal., J Neuroinflammation. 2018 Sep 21;15(1):275. doi: 10.1186/s12974-018-1311-5.
17. Tanaka T, etal., Genes Cells 1998 Dec;3(12):801-10.
18. Wang C, etal., Metabolism. 2013 Feb;62(2):282-9. doi: 10.1016/j.metabol.2012.07.017. Epub 2012 Sep 11.
19. Wang S and Kaufman RJ, J Cell Biol. 2012 Jun 25;197(7):857-67. doi: 10.1083/jcb.201110131.
20. Williams BL and Lipkin WI, J Virol. 2006 Sep;80(17):8613-26. doi: 10.1128/JVI.00836-06.
21. Xu B, etal., Mol Neurobiol. 2014 Feb;49(1):399-412. doi: 10.1007/s12035-013-8527-2. Epub 2013 Aug 10.
22. Yu S, etal., J Biol Chem. 2008 Feb 29;283(9):5542-53. doi: 10.1074/jbc.M705653200. Epub 2008 Jan 2.
23. Zhang A, etal., Neurosci Lett. 2010 Jun 30;478(1):32-6. doi: 10.1016/j.neulet.2010.04.062. Epub 2010 May 2.
24. Zhang L, etal., Mol Med Rep. 2016 Sep;14(3):2077-84. doi: 10.3892/mmr.2016.5469. Epub 2016 Jul 6.
Additional References at PubMed
PMID:8506317   PMID:10580117   PMID:10602480   PMID:11106749   PMID:11274184   PMID:11478948   PMID:11916968   PMID:11960987   PMID:12749859   PMID:12871976   PMID:14729979   PMID:15013631  
PMID:15277680   PMID:15724149   PMID:15775988   PMID:15788408   PMID:15911876   PMID:16445384   PMID:16682973   PMID:16751105   PMID:18305237   PMID:18617696   PMID:18654882   PMID:18940792  
PMID:19017641   PMID:19061639   PMID:19232401   PMID:19726676   PMID:20873783   PMID:21068199   PMID:21113145   PMID:21159964   PMID:21436843   PMID:21768648   PMID:21821103   PMID:21984568  
PMID:22095285   PMID:22507839   PMID:22915762   PMID:22952236   PMID:22974638   PMID:23663782   PMID:23686245   PMID:24136195   PMID:24939851   PMID:25012492   PMID:26174742   PMID:27233218  
PMID:27484784   PMID:27812542   PMID:27841340   PMID:28188284   PMID:29875265   PMID:31416289   PMID:31787756   PMID:32304741  


Genomics

Comparative Map Data
Atf4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27111,804,135 - 111,806,457 (+)NCBI
Rnor_6.0 Ensembl7121,480,723 - 121,482,772 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07121,480,723 - 121,482,781 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07121,468,275 - 121,470,587 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47118,537,718 - 118,538,994NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17118,571,947 - 118,573,223NCBI
Cytogenetic Map7q34NCBI
ATF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2239,519,672 - 39,522,683 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2239,519,695 - 39,522,683 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2239,519,695 - 39,522,685 (+)EnsemblGRCh38hg38GRCh38
GRCh382239,514,494 - 39,522,686 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372239,916,564 - 39,918,691 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362238,246,515 - 38,248,637 (+)NCBINCBI36hg18NCBI36
Build 342238,241,068 - 38,243,191NCBI
Celera2223,718,625 - 23,720,747 (+)NCBI
Cytogenetic Map22q13.1NCBI
HuRef2222,881,158 - 22,883,280 (+)NCBIHuRef
CHM1_12239,875,303 - 39,877,431 (+)NCBICHM1_1
Atf4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391580,139,385 - 80,141,746 (+)NCBIGRCm39mm39
GRCm39 Ensembl1580,139,385 - 80,141,742 (+)Ensembl
GRCm381580,255,184 - 80,257,545 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1580,255,184 - 80,257,541 (+)EnsemblGRCm38mm10GRCm38
MGSCv371580,085,614 - 80,087,971 (+)NCBIGRCm37mm9NCBIm37
MGSCv361580,082,756 - 80,084,759 (+)NCBImm8
Celera1582,372,526 - 82,374,883 (+)NCBICelera
Cytogenetic Map15E1NCBI
cM Map1537.85NCBI
Atf4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541325,406,589 - 25,412,218 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541325,406,589 - 25,408,727 (+)NCBIChiLan1.0ChiLan1.0
ATF4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12238,246,337 - 38,249,333 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2238,248,094 - 38,249,249 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02220,426,743 - 20,428,892 (+)NCBIMhudiblu_PPA_v0panPan3
ATF4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1025,528,874 - 25,530,993 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11025,528,880 - 25,531,018 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Atf4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364922,114,478 - 2,115,969 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATF4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl58,738,880 - 8,745,225 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.158,742,964 - 8,745,752 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.256,042,584 - 6,044,651 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATF4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11922,092,046 - 22,094,184 (+)NCBI
ChlSab1.1 Ensembl1922,091,667 - 22,095,230 (+)Ensembl
Atf4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247528,822,955 - 8,825,019 (-)NCBI

Position Markers
RH127863  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07121,482,401 - 121,482,609NCBIRnor6.0
Rnor_5.07121,470,216 - 121,470,424UniSTSRnor5.0
RGSC_v3.47118,538,623 - 118,538,831UniSTSRGSC3.4
RH 3.4 Map7861.0UniSTS
Cytogenetic Map7q34UniSTS
PMC19934P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07121,482,102 - 121,482,578NCBIRnor6.0
Rnor_5.07121,469,917 - 121,470,393UniSTSRnor5.0
RGSC_v3.47118,538,324 - 118,538,800UniSTSRGSC3.4
Cytogenetic Map7q34UniSTS
UniSTS:274176  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07121,480,770 - 121,482,000NCBIRnor6.0
Rnor_5.07121,468,585 - 121,469,815UniSTSRnor5.0
RGSC_v3.47118,536,992 - 118,538,222UniSTSRGSC3.4
Cytogenetic Map7q34UniSTS
Atf4  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07121,482,405 - 121,482,653NCBIRnor6.0
Rnor_5.07121,470,220 - 121,470,468UniSTSRnor5.0
Cytogenetic Map7q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)777428105127748511Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)777428234122421148Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)788365265121986709Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)7103815550126525386Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)7103867802126080176Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7112429186126525386Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:153
Count of miRNA genes:124
Interacting mature miRNAs:135
Transcripts:ENSRNOT00000065304
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_024403 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079942 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF252627 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC061546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC158588 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ213021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ214457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ215912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ216398 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ219043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ221881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ232762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000186 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000065304   ⟹   ENSRNOP00000060302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7121,480,723 - 121,482,772 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7121,480,735 - 121,481,478 (+)Ensembl
RefSeq Acc Id: NM_024403   ⟹   NP_077379
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,804,398 - 111,806,457 (+)NCBI
Rnor_6.07121,480,723 - 121,482,781 (+)NCBI
Rnor_5.07121,468,275 - 121,470,587 (+)NCBI
RGSC_v3.47118,537,718 - 118,538,994 (+)RGD
Sequence:
RefSeq Acc Id: XM_039079942   ⟹   XP_038935870
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27111,804,135 - 111,806,448 (+)NCBI
Protein Sequences
Protein RefSeqs NP_077379 (Get FASTA)   NCBI Sequence Viewer  
  XP_038935870 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG31732 (Get FASTA)   NCBI Sequence Viewer  
  AAI58589 (Get FASTA)   NCBI Sequence Viewer  
  Q9ES19 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_077379   ⟸   NM_024403
- UniProtKB: Q9ES19 (UniProtKB/Swiss-Prot),   B0BMW3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000060302   ⟸   ENSRNOT00000065304
RefSeq Acc Id: XP_038935870   ⟸   XM_039079942
- Peptide Label: isoform X1
Protein Domains
bZIP

Transcriptome

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

Promoters
RGD ID:13695496
Promoter ID:EPDNEW_R6021
Type:multiple initiation site
Name:Atf4_1
Description:activating transcription factor 4
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_6.07121,480,721 - 121,480,781EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
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
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
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/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
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 (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
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
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
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
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
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 (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
SBH/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: 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
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 (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 (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/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
WKY/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
WKY/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
WKY/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
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:621863 AgrOrtholog
Ensembl Genes ENSRNOG00000017801 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000060302 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000065304 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:9098368 IMAGE-MGC_LOAD
InterPro ATF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  bZIP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:79255 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:187368 IMAGE-MGC_LOAD
NCBI Gene 79255 ENTREZGENE
PANTHER PTHR13044:SF32 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam bZIP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Atf4 PhenoGen
PROSITE BZIP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BZIP_BASIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART BRLZ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt ATF4_RAT UniProtKB/Swiss-Prot
  B0BMW3 ENTREZGENE, UniProtKB/TrEMBL
  Q9ES19 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-06-05 Atf4  activating transcription factor 4  Atf4  activating transcription factor 4 (tax-responsive enhancer element B67)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Atf4  activating transcription factor 4 (tax-responsive enhancer element B67)  Atf4  activating transcription factor 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Atf4  activating transcription factor 4    activating transcription factor ATF-4  Name updated 1299863 APPROVED
2002-08-07 Atf4  activating transcription factor ATF-4      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_product member of the cAMP response element-binding protein/ATF family 631878