Hnf4a (hepatocyte nuclear factor 4, alpha) - Rat Genome Database
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Gene: Hnf4a (hepatocyte nuclear factor 4, alpha) Rattus norvegicus
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Symbol: Hnf4a
Name: hepatocyte nuclear factor 4, alpha
RGD ID: 2810
Description: Exhibits several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; long-chain fatty acid binding activity; and long-chain fatty acyl-CoA binding activity. Involved in several processes, including hepatocyte differentiation; negative regulation of peptidyl-tyrosine phosphorylation; and regulation of cellular biosynthetic process. Localizes to cytoplasm and nucleus. Biomarker of hepatocellular carcinoma and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Fanconi renotubular syndrome 4; familial combined hyperlipidemia; hypoglycemia; maturity-onset diabetes of the young type 1; and type 2 diabetes mellitus. Orthologous to human HNF4A (hepatocyte nuclear factor 4 alpha); PARTICIPATES IN forkhead class A signaling pathway; hypoxia inducible factor pathway; maturity-onset diabetes of the young pathway; INTERACTS WITH 2,2',4,4',5,5'-hexachlorobiphenyl; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha transcription factor 4; hepatic nuclear factor 4; hepatic nuclear factor 4 (alpha transcription factor 4); hepatic nuclear factor 4, alpha; hepatocyte nuclear factor 4 alpha 3; hepatocyte nuclear factor 4 alpha 9; hepatocyte nuclear factor 4-alpha; HNF-4-alpha; Hnf4; Hnf4alpha; HNF4alpha10; HNF4alpha11; HNF4alpha12; nuclear receptor subfamily 2 group A member 1; TCF-14; Tcf4; transcription factor 14; transcription factor HNF-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
mRatBN7.23152,186,787 - 152,248,320 (+)NCBI
Rnor_6.0 Ensembl3159,902,441 - 159,965,003 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03159,902,441 - 159,965,003 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03166,093,091 - 166,155,667 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43154,459,863 - 154,482,825 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13154,365,898 - 154,388,861 (+)NCBI
Celera3150,839,856 - 150,901,426 (+)NCBICelera
RH 3.4 Map31376.5RGD
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3',5'-cyclic AMP  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-azacytidine  (ISO)
6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime  (ISO)
9-cis-retinoic acid  (EXP)
aflatoxin B1  (ISO)
AICA ribonucleotide  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP,ISO)
allyl isothiocyanate  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
androstane  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
Aroclor 1254  (EXP)
atorvastatin calcium  (EXP)
baicalin  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
berberine  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bosentan  (ISO)
bromobenzene  (EXP)
buta-1,3-diene  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
calcitriol  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
cerulenin  (ISO)
cholesterol  (EXP)
cholic acid  (EXP)
choline  (ISO)
chrysin  (ISO)
clofibrate  (ISO)
clothianidin  (ISO)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
D-glucose  (ISO)
deoxynivalenol  (ISO)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
diallyl trisulfide  (ISO)
diclofenac  (EXP)
dicrotophos  (ISO)
DPDPE  (ISO)
emodin  (EXP,ISO)
estriol  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
fructose  (EXP,ISO)
fulvestrant  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (EXP)
glucose  (ISO)
glutathione  (EXP)
GW 4064  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
L-methionine  (ISO)
lead nitrate  (ISO)
lipopolysaccharide  (EXP,ISO)
lithocholic acid  (EXP,ISO)
metformin  (EXP,ISO)
methapyrilene  (EXP,ISO)
methimazole  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
microcystin-LR  (ISO)
mifepristone  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (EXP)
nitrofen  (EXP)
ochratoxin A  (EXP,ISO)
oleic acid  (EXP,ISO)
palmitoyl-CoA  (ISO)
paracetamol  (EXP,ISO)
parathion  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phenobarbital  (EXP)
pirinixic acid  (EXP,ISO)
potassium bromate  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (EXP,ISO)
proanthocyanidin  (EXP)
procymidone  (EXP)
progesterone  (ISO)
propanal  (ISO)
quercitrin  (ISO)
raloxifene  (ISO)
ranitidine  (EXP)
resveratrol  (EXP)
rifampicin  (ISO)
rimonabant  (ISO)
rosuvastatin calcium  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sulindac  (EXP)
tamoxifen  (ISO)
taurocholic acid  (ISO)
terbufos  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP,ISO)
thapsigargin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
Tributyltin oxide  (ISO)
trichlorfon  (ISO)
triclosan  (ISO)
troglitazone  (EXP)
uranium atom  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
zearalenone  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
acyl-CoA metabolic process  (IDA)
aging  (IEP)
anatomical structure development  (IBA)
blood coagulation  (IEA,ISO)
cell differentiation  (IBA,IMP)
cell-cell junction organization  (IDA)
cellular response to hypoxia  (IEP)
cholesterol homeostasis  (IEA,ISO)
establishment of tissue polarity  (IDA)
glucose homeostasis  (IEA,ISO)
hepatocyte differentiation  (IEA,IEP)
intracellular receptor signaling pathway  (IEA)
lipid homeostasis  (IEA,ISO)
lipid metabolic process  (IEA,ISO)
negative regulation of activation of Janus kinase activity  (IDA)
negative regulation of cell growth  (IEA,ISO)
negative regulation of cell migration  (IDA)
negative regulation of cell population proliferation  (IDA,IEA,ISO)
negative regulation of DNA-binding transcription factor activity  (IDA)
negative regulation of mitotic cell cycle  (IDA)
negative regulation of protein import into nucleus  (IDA)
negative regulation of transcription, DNA-templated  (IEA,ISO,ISS)
negative regulation of tyrosine phosphorylation of STAT protein  (IDA)
ornithine metabolic process  (IEA,ISO)
phospholipid homeostasis  (IEA,ISO)
positive regulation of fatty acid biosynthetic process  (IMP)
positive regulation of gluconeogenesis  (IMP)
positive regulation of transcription by RNA polymerase II  (IBA,IDA,IEA,IMP,ISO)
positive regulation of transcription, DNA-templated  (IDA,ISO)
regulation of circadian rhythm  (IEA,ISO,ISS)
regulation of gastrulation  (IEA,ISO)
regulation of insulin secretion  (IEA,ISO)
regulation of lipid metabolic process  (IEA,ISO)
regulation of microvillus assembly  (IMP)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of transcription, DNA-templated  (IEA,ISO)
response to cAMP  (IEP)
response to dexamethasone  (IEP)
response to drug  (IEP)
response to glucose  (IDA,IEA,ISO)
response to lipopolysaccharide  (IEP)
response to nutrient levels  (IEP)
rhythmic process  (IEA)
sex differentiation  (IEA,ISO)
signal transduction involved in regulation of gene expression  (IEA,ISO)
SMAD protein signal transduction  (IEA,ISO)
steroid hormone mediated signaling pathway  (IEA)
triglyceride homeostasis  (IEA,ISO)
type B pancreatic cell development  (IEA)
xenobiotic metabolic process  (IEA,ISO)

Cellular Component
chromatin  (IBA)
cytoplasm  (IDA,IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IDA,IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Adamson AW, etal., Biochem J. 2006 Oct 15;399(2):285-95.
2. Aggelidou E, etal., FEBS J. 2006 May;273(9):1948-58.
3. Barroso I, etal., Diabetes. 2008 Nov;57(11):3161-5. Epub 2008 Aug 26.
4. Bell AW and Michalopoulos GK, Hepatology. 2006 Jul;44(1):186-94.
5. Borlak J and Niehof M, PLoS One. 2009;4(3):e4662. doi: 10.1371/journal.pone.0004662. Epub 2009 Mar 2.
6. Chiba H, etal., Exp Cell Res. 2003 Jun 10;286(2):288-97.
7. Chiba H, etal., Exp Cell Res. 2005 Jan 1;302(1):11-21.
8. Chiba H, etal., J Cell Biol. 2006 Dec 18;175(6):971-80.
9. Dietrich CG, etal., Am J Physiol Gastrointest Liver Physiol. 2007 Sep;293(3):G585-90. Epub 2007 Jul 19.
10. Einstein F, etal., PLoS One. 2010 Jan 26;5(1):e8887. doi: 10.1371/journal.pone.0008887.
11. Flanagan SE, etal., Eur J Endocrinol. 2010 May;162(5):987-92. doi: 10.1530/EJE-09-0861. Epub 2010 Feb 17.
12. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
13. Gautier-Stein A, etal., J Biol Chem. 2006 Oct 20;281(42):31268-78. Epub 2006 Aug 7.
14. GOA data from the GO Consortium
15. Guo H, etal., J Biol Chem 2002 Feb 15;277(7):5054-60.
16. Hata S, etal., Biochim Biophys Acta 1992 Jun 15;1131(2):211-3.
17. Hertz R, etal., J Biol Chem. 2005 Jul 1;280(26):24451-61. Epub 2005 May 3.
18. Holmkvist J, etal., Diabetes. 2008 Jun;57(6):1738-44. Epub 2008 Mar 10.
19. Jin Y, etal., Zhongguo Yi Xue Ke Xue Yuan Xue Bao. 2009 Jun;31(3):330-4.
20. Kapoor RR, etal., Diabetes. 2008 Jun;57(6):1659-63. Epub 2008 Feb 11.
21. Kimata T, etal., Hepatol Res. 2006 May;35(1):3-9. Epub 2006 Mar 24.
22. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
23. Louet JF, etal., J Biol Chem 2002 Oct 11;277(41):37991-8000.
24. Mar-Heyming R, etal., Arterioscler Thromb Vasc Biol. 2008 Jun;28(6):1193-9. doi: 10.1161/ATVBAHA.107.160150. Epub 2008 Mar 13.
25. McIntosh AL, etal., FEBS Lett. 2013 Nov 29;587(23):3787-91. doi: 10.1016/j.febslet.2013.09.043. Epub 2013 Oct 15.
26. Menjivar M, etal., Clin Genet. 2008 Feb;73(2):185-7. Epub 2007 Nov 19.
27. MGD data from the GO Consortium
28. Naiki T, etal., J Biol Chem 2002 Apr 19;277(16):14011-9. Epub 2002 Feb 7.
29. NCBI rat LocusLink and RefSeq merged data July 26, 2002
30. Nedumaran B, etal., J Biol Chem. 2009 Oct 2;284(40):27511-23. doi: 10.1074/jbc.M109.034660. Epub 2009 Aug 3.
31. Ni S, etal., Pharmazie. 2009 Apr;64(4):252-7.
32. Niehof M and Borlak J, Diabetes. 2008 Apr;57(4):1069-77. Epub 2008 Jan 9.
33. Ning BF, etal., Cancer Res. 2010 Oct 1;70(19):7640-51. doi: 10.1158/0008-5472.CAN-10-0824. Epub 2010 Sep 28.
34. Nyirenda MJ, etal., Diabetologia. 2006 Jun;49(6):1412-20. Epub 2006 Mar 29.
35. OMIM Disease Annotation Pipeline
36. Osanai M, etal., Jpn J Cancer Res. 2002 May;93(5):532-41.
37. Park EY, etal., Exp Gerontol. 2013 Dec;48(12):1518-25. doi: 10.1016/j.exger.2013.10.011. Epub 2013 Oct 29.
38. Park SH, etal., Biochem J. 2006 Jul 1;397(1):159-68.
39. Pearson ER, etal., PLoS Med. 2007 Apr;4(4):e118.
40. Petrescu AD, etal., J Biol Chem 2002 Jul 5;277(27):23988-99.
41. Petrescu AD, etal., J Biol Chem. 2003 Dec 19;278(51):51813-24. Epub 2003 Oct 6.
42. Pipeline to import KEGG annotations from KEGG into RGD
43. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
44. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
45. RGD automated import pipeline for gene-chemical interactions
46. Shakib K, etal., Proteomics. 2005 Jul;5(11):2819-38.
47. Sladek FM, etal., Genes Dev 1990 Dec;4(12B):2353-65.
48. Szpirer C, etal., Mamm Genome 2000 Sep;11(9):729-35
49. Wang B, etal., Hepatology. 2001 Nov;34(5):979-89.
50. Wang Z and Burke PA, FEBS J. 2010 Oct;277(19):4066-75. doi: 10.1111/j.1742-4658.2010.07802.x. Epub 2010 Aug 23.
51. Weissglas-Volkov D, etal., Diabetes. 2006 Jul;55(7):1970-7.
52. Xie X, etal., Mol Endocrinol. 2009 Apr;23(4):434-43. doi: 10.1210/me.2007-0531. Epub 2009 Jan 29.
53. Yamagata K, etal., Nature. 1996 Dec 5;384(6608):458-60.
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Additional References at PubMed
PMID:7615825   PMID:7958910   PMID:8306889   PMID:9053305   PMID:9234678   PMID:9408084   PMID:9420335   PMID:9421506   PMID:9795230   PMID:10330009   PMID:10551874   PMID:10859308  
PMID:11158324   PMID:11950391   PMID:12089346   PMID:12193589   PMID:12205093   PMID:12220494   PMID:12650919   PMID:12911579   PMID:12915406   PMID:14563941   PMID:15014077   PMID:15253383  
PMID:15574752   PMID:15581617   PMID:15741159   PMID:15761495   PMID:15767668   PMID:16087161   PMID:16488887   PMID:16498401   PMID:16527247   PMID:16537911   PMID:16639723   PMID:16912278  
PMID:17021047   PMID:17412818   PMID:17603092   PMID:17636037   PMID:17827783   PMID:17932483   PMID:18163890   PMID:18462699   PMID:18561282   PMID:18563319   PMID:18972406   PMID:19353766  
PMID:19387659   PMID:19389810   PMID:19406844   PMID:19575803   PMID:19699314   PMID:19924231   PMID:20938723   PMID:21385945   PMID:22521344   PMID:22589549   PMID:22780989   PMID:23126616  
PMID:24157454   PMID:24234421   PMID:24752868   PMID:28536011   PMID:28807057   PMID:28870599   PMID:29330688   PMID:30530698   PMID:30555544   PMID:30597922   PMID:31637472  


Genomics

Candidate Gene Status
Hnf4a is a candidate Gene for QTL Niddm39
Hnf4a is a candidate Gene for QTL Eau4
Comparative Map Data
Hnf4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23152,186,787 - 152,248,320 (+)NCBI
Rnor_6.0 Ensembl3159,902,441 - 159,965,003 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03159,902,441 - 159,965,003 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03166,093,091 - 166,155,667 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43154,459,863 - 154,482,825 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13154,365,898 - 154,388,861 (+)NCBI
Celera3150,839,856 - 150,901,426 (+)NCBICelera
RH 3.4 Map31376.5RGD
Cytogenetic Map3q42NCBI
HNF4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2044,355,700 - 44,434,596 (+)EnsemblGRCh38hg38GRCh38
GRCh382044,355,699 - 44,434,596 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372042,984,339 - 43,063,236 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh372042,984,441 - 43,061,485 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362042,417,855 - 42,493,444 (+)NCBINCBI36hg18NCBI36
Build 342042,463,337 - 42,486,690NCBI
Celera2039,693,092 - 39,768,681 (+)NCBI
Cytogenetic Map20q13.12NCBI
HuRef2039,720,990 - 39,802,805 (+)NCBIHuRef
CHM1_12042,886,684 - 42,964,390 (+)NCBICHM1_1
Hnf4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392163,348,731 - 163,414,827 (+)NCBIGRCm39mm39
GRCm382163,506,811 - 163,572,907 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2163,506,808 - 163,572,910 (+)EnsemblGRCm38mm10GRCm38
MGSCv372163,372,924 - 163,398,643 (+)NCBIGRCm37mm9NCBIm37
MGSCv362163,238,629 - 163,264,348 (+)NCBImm8
Celera2169,490,574 - 169,516,277 (+)NCBICelera
Cytogenetic Map2H3NCBI
cM Map284.32NCBI
Hnf4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544512,924,662 - 12,984,281 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544512,925,248 - 12,962,501 (-)NCBIChiLan1.0ChiLan1.0
HNF4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12041,823,939 - 41,856,536 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2041,779,034 - 41,856,536 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02040,684,450 - 40,763,824 (+)NCBIMhudiblu_PPA_v0panPan3
HNF4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2431,847,961 - 31,905,916 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12431,847,864 - 31,908,337 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hnf4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365302,401,053 - 2,425,989 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HNF4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1746,783,777 - 46,847,503 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11746,783,772 - 46,847,505 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21752,232,425 - 52,296,703 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HNF4A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1219,390,870 - 19,466,300 (-)NCBI
ChlSab1.1 Ensembl219,388,891 - 19,421,664 (-)Ensembl
Hnf4a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479010,039,344 - 10,065,167 (-)NCBI

Position Markers
D3Rat244  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03159,944,461 - 159,944,681NCBIRnor6.0
Rnor_5.03166,135,125 - 166,135,345UniSTSRnor5.0
RGSC_v3.43154,467,337 - 154,467,558RGDRGSC3.4
RGSC_v3.43154,467,338 - 154,467,558UniSTSRGSC3.4
RGSC_v3.13154,373,373 - 154,373,594RGD
Celera3150,883,112 - 150,883,332UniSTS
SHRSP x BN Map375.4799UniSTS
SHRSP x BN Map375.4799RGD
Cytogenetic Map3q42-q43UniSTS
RH94783  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03159,962,307 - 159,962,502NCBIRnor6.0
Rnor_5.03166,152,971 - 166,153,166UniSTSRnor5.0
RGSC_v3.43154,482,960 - 154,483,155UniSTSRGSC3.4
Celera3150,898,730 - 150,898,925UniSTS
RH 3.4 Map31376.5UniSTS
Cytogenetic Map3q42-q43UniSTS
PMC316400P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03159,956,027 - 159,956,129NCBIRnor6.0
Rnor_5.03166,146,691 - 166,146,793UniSTSRnor5.0
RGSC_v3.43154,476,977 - 154,477,079UniSTSRGSC3.4
Celera3150,892,747 - 150,892,849UniSTS
Cytogenetic Map3q42-q43UniSTS
UniSTS:465392  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03159,941,162 - 159,941,255NCBIRnor6.0
Rnor_5.03166,131,826 - 166,131,919UniSTSRnor5.0
RGSC_v3.43154,464,039 - 154,464,132UniSTSRGSC3.4
Celera3150,879,813 - 150,879,906UniSTS
Cytogenetic Map3q42-q43UniSTS
Hnf4a  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03159,960,944 - 159,962,131NCBIRnor6.0
Rnor_5.03166,151,608 - 166,152,795UniSTSRnor5.0
RGSC_v3.43154,481,597 - 154,482,784UniSTSRGSC3.4
Celera3150,897,367 - 150,898,554UniSTS
Cytogenetic Map3q42-q43UniSTS
Hnf4  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03159,941,143 - 159,942,329NCBIRnor6.0
Rnor_5.03166,131,807 - 166,132,993UniSTSRnor5.0
RGSC_v3.43154,464,020 - 154,465,206UniSTSRGSC3.4
Celera3150,879,794 - 150,880,980UniSTS
Cytogenetic Map3q42-q43UniSTS
Hnf4  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03159,941,143 - 159,942,329NCBIRnor6.0
Rnor_5.03166,131,807 - 166,132,993UniSTSRnor5.0
RGSC_v3.43154,464,020 - 154,465,206UniSTSRGSC3.4
Celera3150,879,794 - 150,880,980UniSTS
Cytogenetic Map3q42-q43UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
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)345406058177699992Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3148348517171467264Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3150368003177699992Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3153918022177699992Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)3153412455170534769Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3146232777177699992Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153381237174632112Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3156381661176418101Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3153412455165355668Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3148348739163640325Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3153412455177699992Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3148034701177699992Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3153381237174632112Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3153381237174632112Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3153381237174632112Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3153381237174632112Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3153381237174632112Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3153381237174632112Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:110
Count of miRNA genes:93
Interacting mature miRNAs:99
Transcripts:ENSRNOT00000011978
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 41 41 41 29 1
Low 4 6 2 2 1 4 18 6 2
Below cutoff 20 12 11 6 6 23 2 22 4 6

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001270931 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001270933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_022180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006235516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF329936 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK483260 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D10554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF193390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EF193392 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ608816 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ608817 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FJ608818 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM042560 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ095211 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ209887 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000120 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000011978   ⟹   ENSRNOP00000011978
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3159,902,524 - 159,958,042 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000078703   ⟹   ENSRNOP00000071432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3159,936,856 - 159,965,003 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089893   ⟹   ENSRNOP00000073501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3159,902,441 - 159,965,003 (+)Ensembl
RefSeq Acc Id: NM_001270931   ⟹   NP_001257860
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23152,186,787 - 152,248,320 (+)NCBI
Rnor_6.03159,902,441 - 159,965,003 (+)NCBI
Rnor_5.03166,093,091 - 166,155,667 (+)NCBI
Celera3150,839,856 - 150,901,426 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001270933   ⟹   NP_001257862
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23152,186,787 - 152,248,320 (+)NCBI
Rnor_6.03159,902,441 - 159,965,003 (+)NCBI
Rnor_5.03166,093,091 - 166,155,667 (+)NCBI
Celera3150,839,856 - 150,901,426 (+)NCBI
Sequence:
RefSeq Acc Id: NM_022180   ⟹   NP_071516
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23152,222,399 - 152,248,320 (+)NCBI
Rnor_6.03159,936,856 - 159,965,003 (+)NCBI
Rnor_5.03166,093,091 - 166,155,667 (+)NCBI
RGSC_v3.43154,459,863 - 154,482,825 (+)RGD
Celera3150,875,385 - 150,901,426 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235515   ⟹   XP_006235577
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23152,222,404 - 152,248,317 (+)NCBI
Rnor_6.03159,936,861 - 159,965,002 (+)NCBI
Rnor_5.03166,093,091 - 166,155,667 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006235516   ⟹   XP_006235578
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23152,222,404 - 152,248,317 (+)NCBI
Rnor_6.03159,936,861 - 159,965,002 (+)NCBI
Rnor_5.03166,093,091 - 166,155,667 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_071516   ⟸   NM_022180
- Peptide Label: isoform 1
- UniProtKB: P22449 (UniProtKB/Swiss-Prot),   A0A0G2K0G1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257860   ⟸   NM_001270931
- Peptide Label: isoform 2
- UniProtKB: A0A0G2K5P1 (UniProtKB/TrEMBL),   A2ICG7 (UniProtKB/TrEMBL),   B9VVT3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001257862   ⟸   NM_001270933
- Peptide Label: isoform 3
- UniProtKB: A2ICG7 (UniProtKB/TrEMBL),   B9VVT2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006235578   ⟸   XM_006235516
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006235577   ⟸   XM_006235515
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000011978   ⟸   ENSRNOT00000011978
RefSeq Acc Id: ENSRNOP00000073501   ⟸   ENSRNOT00000089893
RefSeq Acc Id: ENSRNOP00000071432   ⟸   ENSRNOT00000078703
Protein Domains
NR LBD   Nuclear receptor

Transcriptome

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

Promoters
RGD ID:13692636
Promoter ID:EPDNEW_R3159
Type:multiple initiation site
Name:Hnf4a_2
Description:hepatocyte nuclear factor 4, alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3160  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03159,902,445 - 159,902,505EPDNEW
RGD ID:13692637
Promoter ID:EPDNEW_R3160
Type:multiple initiation site
Name:Hnf4a_1
Description:hepatocyte nuclear factor 4, alpha
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R3159  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03159,936,847 - 159,936,907EPDNEW

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)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 159949364 159949365 C T snv LE/Stm (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2810 AgrOrtholog
Ensembl Genes ENSRNOG00000008895 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011978 UniProtKB/TrEMBL
  ENSRNOP00000071432 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073501 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011978 UniProtKB/TrEMBL
  ENSRNOT00000078703 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089893 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro HNF4A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NHR-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Retinoid-X_rcpt/HNF4 UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25735 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25735 ENTREZGENE
PANTHER PTHR24083:SF41 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Hormone_recep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hnf4a PhenoGen
PRINTS RETINOIDXR UniProtKB/TrEMBL
  STRDHORMONER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOLI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K0G1 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K5P1 ENTREZGENE, UniProtKB/TrEMBL
  A2ICG7 ENTREZGENE, UniProtKB/TrEMBL
  B9VVT2 ENTREZGENE, UniProtKB/TrEMBL
  B9VVT3 ENTREZGENE, UniProtKB/TrEMBL
  G3V750_RAT UniProtKB/TrEMBL
  HNF4A_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q925K8_RAT UniProtKB/TrEMBL
UniProt Secondary A2ICG9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-24 Hnf4a  hepatocyte nuclear factor 4, alpha  Hnf4a  hepatic nuclear factor 4, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Hnf4a  hepatic nuclear factor 4, alpha  Hnf4a  hepatocyte nuclear factor 4, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Hnf4a  hepatocyte nuclear factor 4, alpha      Symbol and Name status set to approved 1299863 APPROVED
2004-07-29 Hnf4a  hepatocyte nuclear factor 4, alpha  Hnf4  hepatic nuclear factor 4  Data Merged 737654 PROVISIONAL
2003-04-09 Hnf4  hepatic nuclear factor 4    Hepatic nuclear factor 4  Name updated 629478 APPROVED
2002-11-06 Hnf4a  hepatocyte nuclear factor 4, alpha    Hepatic nuclear factor 4 (alpha transcription factor 4)  Name updated 625702 APPROVED
2002-06-10 Hnf4a  Hepatic nuclear factor 4 (alpha transcription factor 4)      Symbol and Name status set to approved 70586 APPROVED
2002-06-10 Hnf4  Hepatic nuclear factor 4      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in liver, small intestine, kidney, colon, pancreas, and testis 70641
gene_expression expressed in liver, small intestine, kidney, colon, pancreas, and testis 625581
gene_function homodimers bind to the iNOS promoter DR1 sequence, direct repeats of the hexamer AGGTCA separated by a single nucleotide 70641
gene_function homodimers bind to the iNOS promoter DR1 sequence, direct repeats of the hexamer AGGTCA separated by a single nucleotide 625581
gene_homology 40% amino acid sequence homology to retinoid X receptor 625581
gene_physical_interaction does not form heterodimers with other nuclear receptor and binds to direct repeat-1 DNA sequences as a homodimer 625581
gene_physical_interaction able to bind fatty and xenobiotic acyl-CoAs which results in conformational change 625581
gene_process mediates redox-sensitive iNOS promoter trans-activation by binding to the transcriptional coactivator PC4 in the presence of oxidative stress and interleukin-1 70641
gene_process mediates redox-sensitive iNOS promoter trans-activation by binding to the transcriptional coactivator PC4 in the presence of oxidative stress and interleukin-1 625581
gene_process promotes transcription 70641
gene_process promotes transcription 625581
gene_process important for development and liver-specific gene expression 70641
gene_process important for development and liver-specific gene expression 625581
gene_product member of the steroid hormone receptor superfamily 70641