Atf2 (activating transcription factor 2) - Rat Genome Database

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Gene: Atf2 (activating transcription factor 2) Rattus norvegicus
Analyze
Symbol: Atf2
Name: activating transcription factor 2
RGD ID: 621862
Description: Enables cAMP response element binding activity. Involved in several processes, including amelogenesis; positive regulation of neuron apoptotic process; and regulation of transcription by RNA polymerase II. Located in nucleus. Used to study hypertension and transient cerebral ischemia. Biomarker of glaucoma and transient cerebral ischemia. Orthologous to human ATF2 (activating transcription factor 2); PARTICIPATES IN adenosine signaling pathway; interleukin-12 signaling pathway; influenza A pathway; INTERACTS WITH (+)-pilocarpine; (S)-amphetamine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: cAMP response element-binding protein CRE-BP1; cAMP-dependent transcription factor ATF-2; cyclic AMP-dependent transcription factor ATF-2; RATF2
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
mRatBN7.2358,718,323 - 58,795,280 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl358,718,332 - 58,795,236 (-)Ensembl
Rnor_6.0360,721,137 - 60,795,951 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl360,721,135 - 60,795,951 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0367,199,880 - 67,274,694 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4356,403,676 - 56,496,473 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1356,323,607 - 56,392,845 (-)NCBI
Celera358,247,269 - 58,321,865 (-)NCBICelera
RH 3.4 Map5689.89RGD
Cytogenetic Map3q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(+)-Pimaric acid  (ISO)
(-)-anisomycin  (ISO)
(R,R,R)-alpha-tocopherol  (ISO)
(S)-amphetamine  (EXP)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-ethoxyethanol  (EXP)
2-hydroxypropanoic acid  (ISO)
2-methoxyethanol  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
5-Nitro-2-(3-phenylpropylamino)benzoic acid  (ISO)
acetamide  (EXP)
acrolein  (EXP,ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
andrographolide  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
apocynin  (ISO)
arachidonic acid  (ISO)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
baicalin  (EXP)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP)
bortezomib  (ISO)
bucladesine  (ISO)
cadmium dichloride  (ISO)
cadmium sulfate  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
choline  (ISO)
chromium trioxide  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclophosphamide  (EXP)
cyclosporin A  (EXP,ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
dibenziodolium  (ISO)
dibromoacetic acid  (ISO)
dichlorine  (EXP)
diclofenac  (ISO)
dicrotophos  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
doxycycline  (ISO)
enalapril  (EXP)
ethanol  (ISO)
etoposide  (ISO)
folic acid  (ISO)
genistein  (EXP)
gingerol  (ISO)
Goe 6976  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
indometacin  (EXP)
isoprenaline  (ISO)
isotretinoin  (ISO)
KT 5720  (ISO)
L-methionine  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
linalool  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
manganese(II) chloride  (ISO)
melatonin  (ISO)
methotrexate  (ISO)
methyl beta-cyclodextrin  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
mevinphos  (EXP)
microcystin-LR  (ISO)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (ISO)
nickel dichloride  (ISO)
oxaliplatin  (EXP)
ozone  (EXP,ISO)
perfluorodecanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylarsine oxide  (ISO)
piperine  (ISO)
piperonyl butoxide  (ISO)
pterostilbene  (ISO)
quercetin  (ISO)
rac-lactic acid  (ISO)
resveratrol  (EXP,ISO)
SB 203580  (EXP,ISO)
SB 431542  (ISO)
selenomethionine  (ISO)
sertraline  (ISO)
sevoflurane  (ISO)
simvastatin  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
streptozocin  (EXP)
succimer  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
triptonide  (ISO)
trovafloxacin  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
wortmannin  (EXP)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc sulfate  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
abducens nucleus development  (IEA,ISO)
adipose tissue development  (ISO)
amelogenesis  (IDA)
apoptotic process  (ISO)
apoptotic process involved in development  (IEA,ISO)
BMP signaling pathway  (ISO)
brainstem development  (IEA,ISO)
cellular lipid metabolic process  (IEA,ISO)
cellular response to anisomycin  (ISO)
cellular response to DNA damage stimulus  (ISO,ISS)
cellular response to leucine starvation  (IEA,ISO)
cellular response to oxidative stress  (IEA,ISO)
cellular response to virus  (IEA,ISO)
detection of cell density  (ISO)
facial nucleus development  (IEA,ISO)
fat cell differentiation  (ISO)
gene expression  (IEA,ISO)
growth plate cartilage chondrocyte differentiation  (ISO)
growth plate cartilage chondrocyte proliferation  (ISO)
heart development  (ISO)
hematopoietic progenitor cell differentiation  (IEA,ISO)
hepatocyte apoptotic process  (IEA,ISO)
histone H2B acetylation  (ISO)
histone H4 acetylation  (ISO)
hypoglossal nucleus development  (IEA,ISO)
in utero embryonic development  (IEA,ISO)
intrinsic apoptotic signaling pathway in response to hypoxia  (ISO)
JNK cascade  (IEA,ISO)
liver development  (IEA,ISO)
MAPK cascade  (ISO)
mitotic intra-S DNA damage checkpoint signaling  (ISO,ISS)
motor neuron apoptotic process  (IEA,ISO)
mRNA transcription by RNA polymerase II  (ISO)
negative regulation of angiogenesis  (ISO)
negative regulation of epithelial cell proliferation  (IMP)
negative regulation of transcription by RNA polymerase II  (IMP)
neurofilament cytoskeleton organization  (IEA,ISO)
NK T cell differentiation  (IEA,ISO)
outflow tract morphogenesis  (ISO)
p38MAPK cascade  (IEA,ISO)
peptidyl-threonine phosphorylation  (IEA,ISO)
positive regulation of cardiac muscle myoblast proliferation  (ISO)
positive regulation of DNA-binding transcription factor activity  (ISO,ISS)
positive regulation of gene expression  (ISO)
positive regulation of mitochondrial membrane permeability involved in apoptotic process  (ISO,ISS)
positive regulation of neuron apoptotic process  (IMP)
positive regulation of protein phosphorylation  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IDA,ISO)
positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of transforming growth factor beta2 production  (ISO)
protein import into nucleus  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of transcription, DNA-templated  (ISO,ISS)
response to organic cyclic compound  (ISO)
response to osmotic stress  (ISO,ISS)
response to water deprivation  (IEP)
vacuole organization  (IEA,ISO)
white fat cell differentiation  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Feng A, etal., PLoS One. 2013 Dec 2;8(12):e80997. doi: 10.1371/journal.pone.0080997. eCollection 2013.
2. Feng AW, etal., Fitoterapia. 2011 May 27.
3. Fischer TA, etal., Hypertension. 2001 May;37(5):1222-8.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Hu BR, etal., Neuroscience. 1999 Mar;89(2):437-52.
7. Kageyama R, etal., J Biol Chem 1991 Aug 15;266(23):15525-31.
8. Kreutz MR, etal., Brain Res Mol Brain Res. 1999 Jun 8;69(2):232-41.
9. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
10. Kyosseva SV, etal., Arch Gen Psychiatry. 2000 Jul;57(7):685-91.
11. Lee MY, etal., Diabetes. 2002 Dec;51(12):3400-7.
12. Levkovitch-Verbin H, etal., Exp Eye Res. 2007 Aug;85(2):250-8. Epub 2007 May 13.
13. Ma C, etal., J Biol Chem. 2007 Oct 19;282(42):30901-9. Epub 2007 Apr 11.
14. Martin-Villalba A, etal., Brain Res Mol Brain Res. 1998 Nov 20;62(2):158-66.
15. Meeker RB and Fernandes A, Neuroendocrinology. 2002 Aug;76(2):111-20.
16. MGD data from the GO Consortium
17. Mouse Genome Database (MGD)
18. NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Nieto-Bodelon M, etal., Acta Neuropathol. 2006 Apr;111(4):341-50. Epub 2006 Feb 23.
20. Nishikawa S Anat Sci Int. 2004 Jun;79(2):87-94.
21. Pearson AG, etal., Neuroscience. 2005;133(2):437-51.
22. Pipeline to import KEGG annotations from KEGG into RGD
23. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
24. Pipeline to import SMPDB annotations from SMPDB into RGD
25. Pruitt KD and Maglott DR, Nucleic Acids Res. 2001 Jan 1;29(1):137-40.
26. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
27. RGD automated import pipeline for gene-chemical interactions
28. Suzuki T, etal., J Biol Chem 2002 Oct 25;277(43):40768-74.
29. Xiao L, etal., Am J Physiol Cell Physiol. 2010 May;298(5):C1226-34. doi: 10.1152/ajpcell.00021.2010. Epub 2010 Feb 24.
30. Yamada T, etal., Brain Res. 1997 Feb 28;749(2):329-34.
31. Yuan Z, etal., Mol Cell Biol. 2009 May;29(9):2431-42. doi: 10.1128/MCB.01344-08. Epub 2009 Mar 2.
Additional References at PubMed
PMID:2196176   PMID:2516827   PMID:8798441   PMID:9139739   PMID:10821277   PMID:12220541   PMID:15030387   PMID:15916964   PMID:16125722   PMID:16300731   PMID:16407200   PMID:16452470  
PMID:17767158   PMID:17804813   PMID:18305237   PMID:18320311   PMID:18386196   PMID:18387947   PMID:18397884   PMID:18671972   PMID:19861239   PMID:19923798   PMID:19948881   PMID:21098032  
PMID:21300140   PMID:21996423   PMID:22304920   PMID:22982025   PMID:23729669   PMID:24368669   PMID:26601778   PMID:26781764   PMID:28977001   PMID:29921170  


Genomics

Comparative Map Data
Atf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2358,718,323 - 58,795,280 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl358,718,332 - 58,795,236 (-)Ensembl
Rnor_6.0360,721,137 - 60,795,951 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl360,721,135 - 60,795,951 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0367,199,880 - 67,274,694 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4356,403,676 - 56,496,473 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1356,323,607 - 56,392,845 (-)NCBI
Celera358,247,269 - 58,321,865 (-)NCBICelera
RH 3.4 Map5689.89RGD
Cytogenetic Map3q23NCBI
ATF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2175,072,250 - 175,168,382 (-)EnsemblGRCh38hg38GRCh38
GRCh382175,072,259 - 175,168,203 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372175,936,987 - 176,032,931 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362175,647,252 - 175,741,143 (-)NCBINCBI36hg18NCBI36
Build 342175,764,514 - 175,858,404NCBI
Celera2169,552,560 - 169,646,448 (-)NCBI
Cytogenetic Map2q31.1NCBI
HuRef2167,817,672 - 167,913,976 (-)NCBIHuRef
CHM1_12175,942,954 - 176,038,909 (-)NCBICHM1_1
Atf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39273,646,853 - 73,723,094 (-)NCBIGRCm39mm39
GRCm39 Ensembl273,646,853 - 73,722,983 (-)Ensembl
GRCm38273,816,509 - 73,892,677 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl273,816,509 - 73,892,639 (-)EnsemblGRCm38mm10GRCm38
MGSCv37273,654,578 - 73,730,685 (-)NCBIGRCm37mm9NCBIm37
MGSCv36273,617,360 - 73,693,467 (-)NCBImm8
Celera275,503,543 - 75,579,494 (-)NCBICelera
Cytogenetic Map2C3NCBI
Atf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955449338,193 - 411,218 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955449332,563 - 411,218 (+)NCBIChiLan1.0ChiLan1.0
ATF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B179,799,362 - 179,895,007 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B179,799,365 - 179,895,007 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B62,348,245 - 62,444,428 (-)NCBIMhudiblu_PPA_v0panPan3
ATF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13619,032,376 - 19,103,382 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3619,010,717 - 19,103,292 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3619,041,505 - 19,126,647 (-)NCBI
ROS_Cfam_1.03619,170,174 - 19,255,411 (-)NCBI
UMICH_Zoey_3.13619,246,271 - 19,331,371 (-)NCBI
UNSW_CanFamBas_1.03619,244,588 - 19,329,566 (-)NCBI
UU_Cfam_GSD_1.03619,355,712 - 19,440,684 (-)NCBI
Atf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303136,176,081 - 136,272,458 (-)NCBI
SpeTri2.0NW_0049365094,729,984 - 4,826,367 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ATF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1580,984,977 - 81,091,532 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11580,984,969 - 81,076,573 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21590,260,285 - 90,303,424 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ATF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11060,644,623 - 60,734,465 (-)NCBIChlSab1.1chlSab2
ChlSab1.11060,644,623 - 60,734,465 (-)NCBIChlSab1.1chlSab2
ChlSab1.11060,644,623 - 60,734,465 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1060,644,635 - 60,734,475 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040138,879,027 - 138,969,502 (+)NCBIVero_WHO_p1.0
Atf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478712,241,838 - 12,338,089 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Got255  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2358,760,594 - 58,760,754 (+)MAPPERmRatBN7.2
Rnor_6.0360,761,289 - 60,761,448NCBIRnor6.0
Rnor_5.0367,240,032 - 67,240,191UniSTSRnor5.0
RGSC_v3.4356,461,809 - 56,461,968UniSTSRGSC3.4
Celera358,287,192 - 58,287,365UniSTS
Cytogenetic Map3q23UniSTS
RH142313  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2358,731,515 - 58,732,666 (+)MAPPERmRatBN7.2
Rnor_6.0360,732,211 - 60,733,361NCBIRnor6.0
Rnor_5.0367,210,954 - 67,212,104UniSTSRnor5.0
RGSC_v3.4356,432,731 - 56,433,881UniSTSRGSC3.4
Celera358,258,115 - 58,259,265UniSTS
RH 3.4 Map5689.89UniSTS
Cytogenetic Map3q23UniSTS
BE107846  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2358,713,791 - 58,713,943 (+)MAPPERmRatBN7.2
Rnor_6.0360,714,319 - 60,714,470NCBIRnor6.0
Rnor_5.0367,193,062 - 67,193,213UniSTSRnor5.0
RGSC_v3.4356,412,450 - 56,412,601UniSTSRGSC3.4
Celera358,240,451 - 58,240,602UniSTS
Cytogenetic Map3q23UniSTS
Atf2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2358,719,387 - 58,719,451 (+)MAPPERmRatBN7.2
Rnor_6.0360,719,915 - 60,719,978NCBIRnor6.0
Rnor_5.0367,198,658 - 67,198,721UniSTSRnor5.0
RGSC_v3.4356,406,942 - 56,407,005UniSTSRGSC3.4
Celera358,246,047 - 58,246,110UniSTS
Cytogenetic Map3q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32824968773249687Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)33945463762951183Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582249Bw77Body weight QTL 773.20.0025epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)35318459364655484Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:88
Count of miRNA genes:55
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000002174, ENSRNOT00000050513
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 40 56 40 19 40 5 5 74 35 41 11 5
Low 3 1 1 1 3 6 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002174   ⟹   ENSRNOP00000002174
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl358,718,335 - 58,795,166 (-)Ensembl
Rnor_6.0 Ensembl360,721,135 - 60,795,951 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000050513   ⟹   ENSRNOP00000046001
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl358,718,332 - 58,795,236 (-)Ensembl
Rnor_6.0 Ensembl360,721,171 - 60,765,645 (-)Ensembl
RefSeq Acc Id: NM_031018   ⟹   NP_112280
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2358,720,610 - 58,795,266 (-)NCBI
Rnor_6.0360,721,137 - 60,795,951 (-)NCBI
Rnor_5.0367,199,880 - 67,274,694 (-)NCBI
RGSC_v3.4356,403,676 - 56,496,473 (-)RGD
Celera358,247,269 - 58,321,865 (-)RGD
Sequence:
RefSeq Acc Id: XM_039105916   ⟹   XP_038961844
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2358,718,323 - 58,795,280 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_112280   ⟸   NM_031018
- UniProtKB: Q00969 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002174   ⟸   ENSRNOT00000002174
RefSeq Acc Id: ENSRNOP00000046001   ⟸   ENSRNOT00000050513
RefSeq Acc Id: XP_038961844   ⟸   XM_039105916
- 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:13692146
Promoter ID:EPDNEW_R2671
Type:initiation region
Name:Atf2_1
Description:activating transcription factor 2
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_6.0360,795,965 - 60,796,025EPDNEW

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)
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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
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)
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)
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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)
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)
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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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 60721256 60721257 G A snv ACI/N (MCW), Buf/N (MCW), WKY/N (MCW), M520/N (MCW), MR/N (MCW), F344/NRrrc (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621862 AgrOrtholog
Ensembl Genes ENSRNOG00000001597 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000002174 UniProtKB/Swiss-Prot
  ENSRNOP00000046001 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002174 UniProtKB/Swiss-Prot
  ENSRNOT00000050513 UniProtKB/Swiss-Prot
InterPro ATF2 UniProtKB/Swiss-Prot
  bZIP UniProtKB/Swiss-Prot
  TF_CRE-BP1-typ UniProtKB/Swiss-Prot
  Znf_C2H2_sf UniProtKB/Swiss-Prot
  Znf_C2H2_type UniProtKB/Swiss-Prot
KEGG Report rno:81647 UniProtKB/Swiss-Prot
NCBI Gene 81647 ENTREZGENE
PANTHER PTHR19304:SF9 UniProtKB/Swiss-Prot
Pfam bZIP_1 UniProtKB/Swiss-Prot
PhenoGen Atf2 PhenoGen
PIRSF ATF2_CRE-BP1 UniProtKB/Swiss-Prot
PROSITE BZIP UniProtKB/Swiss-Prot
  BZIP_BASIC UniProtKB/Swiss-Prot
  ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot
  ZINC_FINGER_C2H2_2 UniProtKB/Swiss-Prot
SMART BRLZ UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot
UniProt ATF2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62870 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Atf2  activating transcription factor 2    RATF2  Name updated 1299863 APPROVED
2002-08-07 Atf2  RATF2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction binds the cAMP responsive element of the tyrosine hydroxylase gene 727574