Foxa2 (forkhead box A2) - Rat Genome Database

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Gene: Foxa2 (forkhead box A2) Rattus norvegicus
Symbol: Foxa2
Name: forkhead box A2
RGD ID: 2808
Description: Enables several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and SMAD binding activity. Involved in positive regulation of transcription by RNA polymerase II and response to insulin. Located in nucleus. Human ortholog(s) of this gene implicated in type 2 diabetes mellitus. Orthologous to human FOXA2 (forkhead box A2); PARTICIPATES IN forkhead class A signaling pathway; Hedgehog signaling pathway; maturity-onset diabetes of the young pathway; INTERACTS WITH 1,2-dimethylhydrazine; 1-naphthyl isothiocyanate; 17beta-estradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: forkhead box protein A2; hepatocyte nuclear factor 3 beta; hepatocyte nuclear factor 3, beta; hepatocyte nuclear factor 3-beta; HNF-3-beta; HNF-3B; Hnf3b
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr83155,923,305 - 155,927,508 (-)NCBIGRCr8
mRatBN7.23135,470,123 - 135,474,326 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3135,470,131 - 135,474,326 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3139,406,140 - 139,410,336 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03147,990,259 - 147,994,455 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03145,698,089 - 145,702,294 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03142,383,084 - 142,387,493 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3142,383,278 - 142,387,481 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03148,793,310 - 148,797,690 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43136,739,009 - 136,743,204 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13136,644,581 - 136,648,777 (-)NCBI
Celera3134,324,023 - 134,328,218 (-)NCBICelera
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (EXP)
acetaldehyde  (ISO)
acetic acid  (ISO)
aflatoxin B1  (ISO)
alachlor  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (EXP)
amitrole  (EXP)
ammonium chloride  (EXP)
arsenite(3-)  (ISO)
baicalin  (ISO)
Benoxacor  (ISO)
benzo[a]pyrene  (EXP,ISO)
bexarotene  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (ISO)
butan-1-ol  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
caffeine  (ISO)
carbamazepine  (ISO)
carbendazim  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
CHIR 99021  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
cypermethrin  (ISO)
cyproconazole  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibenz[a,h]anthracene  (ISO)
dimethyl sulfoxide  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
epoxiconazole  (ISO)
estriol  (ISO)
fentin chloride  (EXP)
flusilazole  (ISO)
folic acid  (ISO)
fumonisin B1  (ISO)
gamma-aminobutyric acid  (ISO)
genistein  (ISO)
geraniol  (ISO)
glafenine  (EXP)
glucose  (ISO)
hexaconazole  (ISO)
ketoconazole  (EXP)
L-ascorbic acid  (EXP)
L-methionine  (ISO)
lead nitrate  (ISO)
lead(0)  (ISO)
lipopolysaccharide  (ISO)
Mesaconitine  (EXP)
metformin  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
N-methyl-N-nitrosourea  (ISO)
N-nitrosodimethylamine  (EXP)
naphthalene  (ISO)
nefazodone  (EXP)
nitrofen  (EXP,ISO)
ozone  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenformin  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
Ptaquiloside  (ISO)
raloxifene  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
streptozocin  (EXP)
sulfadimethoxine  (EXP)
testosterone  (EXP)
tetraphene  (ISO)
titanium dioxide  (ISO)
trichloroethene  (ISO)
triphenyl phosphate  (EXP)
urethane  (ISO)
valproic acid  (ISO)
vitamin D  (ISO)
vitamin E  (EXP,ISO)
zinc atom  (ISO)
zinc dichloride  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult locomotory behavior  (ISO,ISS)
anatomical structure formation involved in morphogenesis  (ISO)
anatomical structure morphogenesis  (IBA,IEA,ISO)
anterior/posterior pattern specification  (ISO)
cell development  (ISO)
cell differentiation  (IBA)
cell differentiation in hindbrain  (ISO)
cell fate specification  (ISO,ISS)
cellular response to cadmium ion  (ISO)
chromatin organization  (IEA)
connective tissue development  (ISO)
dopaminergic neuron differentiation  (IEA,ISO,ISS)
dorsal/ventral neural tube patterning  (ISO)
dorsal/ventral pattern formation  (ISO)
ectoderm formation  (ISO)
endocrine pancreas development  (IEA,ISO)
epithelial tube branching involved in lung morphogenesis  (ISO)
gene expression  (ISO)
glucose mediated signaling pathway  (ISO)
in utero embryonic development  (ISO)
lung development  (ISO)
lung epithelial cell differentiation  (ISO)
mesendoderm development  (ISO)
negative regulation of epithelial to mesenchymal transition  (IEA,ISO)
negative regulation of neuron differentiation  (ISO)
negative regulation of transcription from RNA polymerase II promoter by glucose  (ISO)
neuron differentiation  (ISO)
neuron fate specification  (ISO)
Notch signaling pathway  (ISO)
pattern specification process  (ISO)
positive regulation of DNA-templated transcription  (ISO,ISS)
positive regulation of dopaminergic neuron differentiation  (ISO)
positive regulation of embryonic development  (ISO,ISS)
positive regulation of gastrulation  (ISO,ISS)
positive regulation of neuron differentiation  (ISO)
positive regulation of smoothened signaling pathway  (ISO)
positive regulation of transcription by RNA polymerase II  (IDA,IEA,IMP,ISO)
positive regulation of transcription by RNA polymerase III  (ISO)
positive regulation of transcription from RNA polymerase II promoter by glucose  (ISO)
primitive streak formation  (ISO,ISS)
regulation of blood coagulation  (IEA,ISO)
regulation of DNA-templated transcription  (IDA,ISO)
regulation of gene expression  (ISO)
regulation of insulin secretion involved in cellular response to glucose stimulus  (ISO)
regulation of lipid metabolic process  (ISO)
regulation of steroid metabolic process  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
response to insulin  (IEP)
signal transduction involved in regulation of gene expression  (ISO)
smoothened signaling pathway  (ISO)
somite rostral/caudal axis specification  (ISO)
transcription by RNA polymerase II  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View

References - curated
# Reference Title Reference Citation
1. Genetic variation in the hepatocyte nuclear factor-3beta gene (HNF3B) does not contribute to maturity-onset diabetes of the young in French Caucasians. Abderrahmani A, etal., Diabetes. 2000 Feb;49(2):306-8.
2. Hepatocyte nuclear factor 3beta inhibits hepatitis B virus replication in vivo. Banks KE, etal., J Virol 2002 Dec;76(24):12974-80.
3. Transcriptional regulation of the distal promoter of the rat pyruvate carboxylase gene by hepatocyte nuclear factor 3beta/Foxa2 and upstream stimulatory factors in insulinoma cells. Boonsaen T, etal., Biochem J. 2007 Jul 15;405(2):359-67.
4. SLC2A2 gene expression in kidney of diabetic rats is regulated by HNF-1alpha and HNF-3beta. Freitas HS, etal., Mol Cell Endocrinol. 2009 Jun 16;305(1-2):63-70. Epub 2009 Mar 4.
5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Upstream region of rat serum albumin gene promoter contributes to promoter activity: presence of functional binding site for hepatocyte nuclear factor-3. Hsiang CH, etal., Biochem J. 1999 Mar 1;338 ( Pt 2):241-9.
7. Hepatocyte nuclear factor 3 alpha belongs to a gene family in mammals that is homologous to the Drosophila homeotic gene fork head. Lai E, etal., Genes Dev 1991 Mar;5(3):416-27.
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. SMAD3 prevents binding of NKX2.1 and FOXA1 to the SpB promoter through its MH1 and MH2 domains. Minoo P, etal., Nucleic Acids Res. 2008 Jan;36(1):179-88. Epub 2007 Nov 14.
10. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Identification of DNA-dependent protein kinase as a cofactor for the forkhead transcription factor FoxA2. Nock A, etal., J Biol Chem. 2009 Jul 24;284(30):19915-26. Epub 2009 May 28.
12. Inhibitory cross-talk between STAT5b and liver nuclear factor HNF3beta: impact on the regulation of growth hormone pulse-stimulated, male-specific liver cytochrome P-450 gene expression. Park SH and Waxman DJ, J Biol Chem 2001 Nov 16;276(46):43031-9.
13. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
14. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
15. GOA pipeline RGD automated data pipeline
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Tissue-specific deletion of Foxa2 in pancreatic beta cells results in hyperinsulinemic hypoglycemia. Sund NJ, etal., Genes Dev. 2001 Jul 1;15(13):1706-15.
18. Genetic variants of FOXA2: risk of type 2 diabetes and effect on metabolic traits in North Indians. Tabassum R, etal., J Hum Genet. 2008;53(11-12):957-65. Epub 2008 Sep 17.
19. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
20. Low levels of eosinophil cationic proteins in patients with asthma. Venge P, etal., Lancet 1977 Aug 20;2(8034):373-5.
21. Foxa2 (HNF3beta ) controls multiple genes implicated in metabolism-secretion coupling of glucose-induced insulin release. Wang H, etal., J Biol Chem. 2002 May 17;277(20):17564-70. Epub 2002 Mar 1.
22. Transducin-like enhancer of split proteins, the human homologs of Drosophila groucho, interact with hepatic nuclear factor 3beta. Wang JC, etal., J Biol Chem. 2000 Jun 16;275(24):18418-23.
23. The ratio of FoxA1 to FoxA2 in lung adenocarcinoma is regulated by LncRNA HOTAIR and chromatin remodeling factor LSH. Wang R, etal., Sci Rep. 2015 Dec 11;5:17826. doi: 10.1038/srep17826.
24. Hepatocyte nuclear factor-4alpha interacts with other hepatocyte nuclear factors in regulating transthyretin gene expression. 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.
25. Role of Foxa-2 in adipocyte metabolism and differentiation. Wolfrum C, etal., J Clin Invest. 2003 Aug;112(3):345-56. Epub 2003 Jul 15.
26. Identification of missense mutations in the hepatocyte nuclear factor-3beta gene in Japanese subjects with late-onset Type II diabetes mellitus. Zhu Q, etal., Diabetologia. 2000 Sep;43(9):1197-200.
Additional References at PubMed
PMID:8813084   PMID:9152011   PMID:9226455   PMID:9931457   PMID:10498685   PMID:10859308   PMID:11291865   PMID:11914369   PMID:12124776   PMID:12488434   PMID:12642491   PMID:12911579  
PMID:14701942   PMID:15485926   PMID:15539431   PMID:15567715   PMID:15668254   PMID:15680365   PMID:15737987   PMID:15987774   PMID:16364283   PMID:16522789   PMID:16912278   PMID:17596284  
PMID:17922007   PMID:18076286   PMID:18462699   PMID:18590716   PMID:19951692   PMID:20160041   PMID:21269961   PMID:21385937   PMID:22696295   PMID:22737085   PMID:22780989   PMID:22921202  
PMID:23117660   PMID:23118920   PMID:23383217   PMID:24157454   PMID:24399192   PMID:25057789   PMID:25446530   PMID:26494787   PMID:29200841   PMID:30082727   PMID:30341519   PMID:31843527  
PMID:32495363   PMID:38135007  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
GRCr83155,923,305 - 155,927,508 (-)NCBIGRCr8
mRatBN7.23135,470,123 - 135,474,326 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3135,470,131 - 135,474,326 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3139,406,140 - 139,410,336 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03147,990,259 - 147,994,455 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03145,698,089 - 145,702,294 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03142,383,084 - 142,387,493 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3142,383,278 - 142,387,481 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03148,793,310 - 148,797,690 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43136,739,009 - 136,743,204 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13136,644,581 - 136,648,777 (-)NCBI
Celera3134,324,023 - 134,328,218 (-)NCBICelera
Cytogenetic Map3q41NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh382022,580,998 - 22,585,490 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2022,580,998 - 22,585,455 (-)EnsemblGRCh38hg38GRCh38
GRCh372022,561,636 - 22,566,128 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362022,509,823 - 22,514,102 (-)NCBINCBI36Build 36hg18NCBI36
Celera2022,635,086 - 22,639,544 (-)NCBICelera
Cytogenetic Map20p11.21NCBI
HuRef2022,523,682 - 22,527,950 (-)NCBIHuRef
CHM1_12022,562,253 - 22,566,723 (-)NCBICHM1_1
T2T-CHM13v2.02022,640,367 - 22,644,859 (-)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm392147,884,797 - 147,888,889 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2147,884,797 - 147,888,889 (-)EnsemblGRCm39 Ensembl
GRCm382148,042,877 - 148,046,969 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2148,042,877 - 148,046,969 (-)EnsemblGRCm38mm10GRCm38
MGSCv372147,868,614 - 147,872,705 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362147,734,364 - 147,738,410 (-)NCBIMGSCv36mm8
Celera2149,306,403 - 149,310,523 (-)NCBICelera
Cytogenetic Map2G3NCBI
cM Map273.38NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495541529,982,940 - 29,986,255 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541529,982,940 - 29,987,093 (-)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan1-v22123,451,059 - 23,454,654 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12023,447,894 - 23,451,489 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02022,519,942 - 22,524,262 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12022,872,251 - 22,874,997 (-)NCBIpanpan1.1PanPan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.1241,010,370 - 1,013,791 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl241,010,651 - 1,013,072 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha241,034,459 - 1,038,788 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0241,413,104 - 1,417,432 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl241,414,234 - 1,417,447 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1241,010,961 - 1,015,301 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0241,114,770 - 1,118,263 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0241,388,439 - 1,392,767 (+)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_024408640149,544,748 - 149,549,068 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366202,966,341 - 2,969,349 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366202,966,341 - 2,969,349 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl1729,997,401 - 30,001,707 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11729,997,397 - 30,001,704 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21734,053,453 - 34,057,746 (-)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.1251,577,127 - 51,585,168 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl251,577,833 - 51,580,297 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660786,377,377 - 6,381,582 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_00462474122,645,519 - 22,649,854 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474122,645,580 - 22,649,722 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Foxa2
8 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:72
Count of miRNA genes:65
Interacting mature miRNAs:70
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

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

miRNA Target Status data imported from miRGate (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
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)331172320163586636Rat
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
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
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
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)359242096157323038Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
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)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23135,471,448 - 135,471,736 (-)MAPPERmRatBN7.2
Rnor_6.03142,385,880 - 142,386,167NCBIRnor6.0
Rnor_5.03148,796,077 - 148,796,364UniSTSRnor5.0
RGSC_v3.43136,740,327 - 136,740,614UniSTSRGSC3.4
Celera3134,325,341 - 134,325,628UniSTS
Cytogenetic Map3q41UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23135,471,443 - 135,471,646 (-)MAPPERmRatBN7.2
Rnor_6.03142,385,970 - 142,386,172NCBIRnor6.0
Rnor_5.03148,796,167 - 148,796,369UniSTSRnor5.0
RGSC_v3.43136,740,322 - 136,740,524UniSTSRGSC3.4
Celera3134,325,336 - 134,325,538UniSTS
Cytogenetic Map3q41UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23135,471,091 - 135,471,539 (-)MAPPERmRatBN7.2
Rnor_6.03142,386,077 - 142,386,524NCBIRnor6.0
Rnor_5.03148,796,274 - 148,796,721UniSTSRnor5.0
RGSC_v3.43136,739,970 - 136,740,417UniSTSRGSC3.4
Celera3134,324,984 - 134,325,431UniSTS
Cytogenetic Map3q41UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23135,471,502 - 135,471,639 (-)MAPPERmRatBN7.2
Rnor_6.03142,385,977 - 142,386,113NCBIRnor6.0
Rnor_5.03148,796,174 - 148,796,310UniSTSRnor5.0
Celera3134,325,395 - 134,325,531UniSTS
Cytogenetic Map3q41UniSTS


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
Medium 24 24 24 4 11
Low 3 2 18 17 1 17 25 22
Below cutoff 6 6 10 2 2 19 11 17 2


RefSeq Acc Id: ENSRNOT00000017742   ⟹   ENSRNOP00000017742
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3135,470,131 - 135,474,326 (-)Ensembl
Rnor_6.0 Ensembl3142,383,278 - 142,387,481 (+)Ensembl
RefSeq Acc Id: NM_001399085   ⟹   NP_001386014
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
GRCr83155,923,305 - 155,926,488 (-)NCBI
mRatBN7.23135,470,123 - 135,473,306 (-)NCBI
RefSeq Acc Id: NM_012743   ⟹   NP_036875
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
GRCr83155,923,307 - 155,927,508 (-)NCBI
mRatBN7.23135,470,125 - 135,474,326 (-)NCBI
Rnor_6.03142,383,290 - 142,387,485 (+)NCBI
Rnor_5.03148,793,310 - 148,797,690 (+)NCBI
RGSC_v3.43136,739,009 - 136,743,204 (-)RGD
Celera3134,324,023 - 134,328,218 (-)RGD
Protein Sequences
Protein RefSeqs NP_001386014 (Get FASTA)   NCBI Sequence Viewer  
  NP_036875 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41338 (Get FASTA)   NCBI Sequence Viewer  
  EDL95107 (Get FASTA)   NCBI Sequence Viewer  
  EDL95108 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017742
GenBank Protein P32182 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_036875   ⟸   NM_012743
- Peptide Label: isoform 2
- UniProtKB: P32182 (UniProtKB/Swiss-Prot),   G3V7Q2 (UniProtKB/TrEMBL),   A6K7B1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017742   ⟸   ENSRNOT00000017742
RefSeq Acc Id: NP_001386014   ⟸   NM_001399085
- Peptide Label: isoform 1
- UniProtKB: P32182 (UniProtKB/Swiss-Prot)
Protein Domains

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P32182-F1-model_v2 AlphaFold P32182 1-458 view protein structure


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

RGD ID:13692494
Promoter ID:EPDNEW_R3019
Type:multiple initiation site
Description:forkhead box A2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
Rat AssemblyChrPosition (strand)Source
Rnor_6.03142,383,261 - 142,383,321EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2808 AgrOrtholog
BioCyc Gene G2FUF-47523 BioCyc
Ensembl Genes ENSRNOG00000013133 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017742 ENTREZGENE
  ENSRNOT00000017742.4 UniProtKB/TrEMBL
Gene3D-CATH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Fork-head_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fork_head_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Forkhead_box_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_fork_head_CS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_fork_head_CS_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25099 UniProtKB/Swiss-Prot
Pfam Forkhead UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Forkhead_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Foxa2 PhenoGen
  FORK_HEAD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013133 RatGTEx
SMART SM00339 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC209148
  FOXA2_RAT UniProtKB/Swiss-Prot

Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Foxa2  forkhead box A2  Hnf3b  hepatocyte nuclear factor 3, beta  Symbol and Name updated 1299863 APPROVED
2002-11-06 Hnf3b  hepatocyte nuclear factor 3, beta    Hepatocyte nuclear factor 3 beta  Name updated 625702 APPROVED
2002-06-10 Hnf3b  Hepatocyte nuclear factor 3 beta      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process modulates stimulation of male-specific liver Cyp2c11 expression by Stat5b 70587
gene_process in combination with with other liver transcription factors, including Hnf1, Cebpa (C/EBP)and Hnf6, mediates liver-specific expression of hepatic Cyp genes. 70587