Foxa1 (forkhead box A1) - Rat Genome Database

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Gene: Foxa1 (forkhead box A1) Rattus norvegicus
Symbol: Foxa1
Name: forkhead box A1
RGD ID: 2807
Description: Enables several functions, including DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and RNA polymerase II-specific DNA-binding transcription factor binding activity. Involved in positive regulation of hydrogen peroxide-mediated programmed cell death and positive regulation of transcription by RNA polymerase II. Acts upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be located in fibrillar center; microvillus; and nucleoplasm. Human ortholog(s) of this gene implicated in breast cancer; gastrointestinal system cancer (multiple); and lung cancer (multiple). Orthologous to human FOXA1 (forkhead box A1); PARTICIPATES IN forkhead class A signaling pathway; INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: forkhead box protein A1; hepatocyte nuclear factor 3 alpha; hepatocyte nuclear factor 3, alpha; hepatocyte nuclear factor 3-alpha; HNF-3-alpha; HNF-3A; Hnf3a
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
mRatBN7.2675,099,907 - 75,136,534 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl675,103,503 - 75,136,188 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx675,551,122 - 75,556,257 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0675,850,458 - 75,855,593 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0675,277,927 - 75,283,064 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0678,516,579 - 78,549,669 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl678,545,804 - 78,549,669 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0688,041,150 - 88,074,240 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4677,976,384 - 78,009,176 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1677,979,509 - 78,012,302 (-)NCBI
Celera673,899,792 - 73,932,602 (-)NCBICelera
RH 3.4 Map6547.4RGD
Cytogenetic Map6q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
9-cis-retinoic acid  (ISO)
aflatoxin B1  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-4-oxoretinol  (ISO)
all-trans-retinoic acid  (ISO)
all-trans-retinol  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
beta-carotene  (ISO)
bexarotene  (EXP)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
buta-1,3-diene  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CHIR 99021  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dichloromethane  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
enzalutamide  (ISO)
epoxiconazole  (ISO)
flusilazole  (ISO)
folic acid  (ISO)
fonofos  (ISO)
fulvestrant  (ISO)
gamma-hexachlorocyclohexane  (EXP)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
irinotecan  (EXP)
L-methionine  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
menadione  (ISO)
methylseleninic acid  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
Monobutylphthalate  (ISO)
N-methyl-N-nitrosourea  (ISO)
naphthalene  (ISO)
oleic acid  (ISO)
paracetamol  (EXP,ISO)
parathion  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenformin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
quercetin  (ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
rotenone  (EXP)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
tunicamycin  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin D  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
alveolar secondary septum development  (IEA,ISO)
anatomical structure formation involved in morphogenesis  (IEA,ISO)
anatomical structure morphogenesis  (IBA)
cell differentiation  (IBA)
chromatin organization  (IEA)
chromatin remodeling  (IEA,ISO)
connective tissue development  (ISO)
dopaminergic neuron differentiation  (IEA,ISO)
dorsal/ventral neural tube patterning  (IEA,ISO)
epithelial cell maturation involved in prostate gland development  (IEA,ISO)
epithelial tube branching involved in lung morphogenesis  (IEA,ISO)
glucose homeostasis  (IEA,ISO)
hormone metabolic process  (IEA,ISO)
lung development  (ISO)
lung epithelial cell differentiation  (IEA,ISO)
lung morphogenesis  (ISO)
mesenchymal-epithelial cell signaling involved in prostate gland development  (IEA,ISO)
negative regulation of epithelial to mesenchymal transition  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,IGI,ISO)
neuron differentiation  (ISO)
neuron fate specification  (IEA,ISO)
Notch signaling pathway  (IEA,ISO)
positive regulation of apoptotic process  (IEA,ISO)
positive regulation of dopaminergic neuron differentiation  (IEA,ISO)
positive regulation of hydrogen peroxide-mediated programmed cell death  (IMP)
positive regulation of intracellular estrogen receptor signaling pathway  (IEA,ISO)
positive regulation of mitotic cell cycle  (IEA,ISO)
positive regulation of smoothened signaling pathway  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IDA,IEA,ISO)
prostate gland epithelium morphogenesis  (IEA,ISO)
prostate gland stromal morphogenesis  (IEA,ISO)
regulation of cell cycle  (ISO)
regulation of DNA-templated transcription  (IEA)
regulation of gene expression  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
respiratory basal cell differentiation  (IEA,ISO)
response to estradiol  (IEA,ISO)
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development  (IEA,ISO)
smoothened signaling pathway  (IEA,ISO)
tube morphogenesis  (ISO)

Cellular Component
fibrillar center  (IEA,ISO)
microvillus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View

References - curated
# Reference Title Reference Citation
1. Opposite roles of FOXA1 and NKX2-1 in lung cancer progression. Deutsch L, etal., Genes Chromosomes Cancer. 2012 Jun;51(6):618-29. doi: 10.1002/gcc.21950. Epub 2012 Mar 2.
2. MicroRNA-212 suppresses tumor growth of human hepatocellular carcinoma by targeting FOXA1. Dou C, etal., Oncotarget. 2015 May 30;6(15):13216-28.
3. PLOD2 regulated by transcription factor FOXA1 promotes metastasis in NSCLC. Du H, etal., Cell Death Dis. 2017 Oct 26;8(10):e3143. doi: 10.1038/cddis.2017.553.
4. 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.
5. FOXA1 inhibits hepatocellular carcinoma progression by suppressing PIK3R1 expression in male patients. He S, etal., J Exp Clin Cancer Res. 2017 Dec 6;36(1):175. doi: 10.1186/s13046-017-0646-6.
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. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
8. HNF-3A, a hepatocyte-enriched transcription factor of novel structure is regulated transcriptionally. Lai E, etal., Genes Dev 1990 Aug;4(8):1427-36.
9. Genome-Wide Analysis of the FOXA1 Transcriptional Network Identifies Novel Protein-Coding and Long Noncoding RNA Targets in Colorectal Cancer Cells. Lazar SB, etal., Mol Cell Biol. 2020 Oct 13;40(21). pii: MCB.00224-20. doi: 10.1128/MCB.00224-20. Print 2020 Oct 13.
10. Role of transcription factor FOXA1 in non‑small cell lung cancer. Li J, etal., Mol Med Rep. 2018 Jan;17(1):509-521. doi: 10.3892/mmr.2017.7885. Epub 2017 Oct 26.
11. Forkhead box A1 (FOXA1) tagging polymorphisms and esophageal cancer risk in a Chinese population: a fine-mapping study. Li M, etal., Biomarkers. 2016 Sep;21(6):523-9. doi: 10.3109/1354750X.2016.1160425. Epub 2016 Apr 6.
12. The hepatocyte nuclear factor 3 alpha gene, HNF3alpha (FOXA1), on chromosome band 14q13 is amplified and overexpressed in esophageal and lung adenocarcinomas. Lin L, etal., Cancer Res. 2002 Sep 15;62(18):5273-9.
13. Overexpression of FOXA1 inhibits cell proliferation and EMT of human gastric cancer AGS cells. Lin M, etal., Gene. 2018 Feb 5;642:145-151. doi: 10.1016/j.gene.2017.11.023. Epub 2017 Nov 10.
14. The clinical significance of forkhead box protein A1 and its role in colorectal cancer. Ma W, etal., Mol Med Rep. 2016 Sep;14(3):2625-31. doi: 10.3892/mmr.2016.5583. Epub 2016 Aug 1.
15. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
16. Physical and functional interactions between homeodomain NKX2.1 and winged helix/forkhead FOXA1 in lung epithelial cells. Minoo P, etal., Mol Cell Biol. 2007 Mar;27(6):2155-65. Epub 2007 Jan 12.
17. 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.
18. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
19. Knockdown of Forkhead box A1 suppresses the tumorigenesis and progression of human colon cancer cells through regulating the phosphatase and tensin homolog/Akt pathway. Pan J, etal., J Int Med Res. 2020 Dec;48(12):300060520971453. doi: 10.1177/0300060520971453.
20. Forkhead‑box A1 regulates tumor cell growth and predicts prognosis in colorectal cancer. Park YL, etal., Int J Oncol. 2019 Jun;54(6):2169-2178. doi: 10.3892/ijo.2019.4771. Epub 2019 Apr 4.
21. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
22. GOA pipeline RGD automated data pipeline
23. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
24. A role for forkhead box A1 in acute lung injury. Song L, etal., Inflammation. 2009 Oct;32(5):322-32. doi: 10.1007/s10753-009-9139-x.
25. The ubiquitinase ZFP91 promotes tumor cell survival and confers chemoresistance through FOXA1 destabilization. Tang DE, etal., Carcinogenesis. 2020 Mar 13;41(1):56-66. doi: 10.1093/carcin/bgz085.
26. Forkhead-box A1 transcription factor is a novel adverse prognosis marker in human glioma. Wang L, etal., J Clin Neurosci. 2013 May;20(5):654-8. doi: 10.1016/j.jocn.2012.03.055. Epub 2013 Mar 16.
27. 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.
28. Trans-acting non-synonymous variant of FOXA1 predisposes to hepatocellular carcinoma through modulating FOXA1-ERα transcriptional program and may have undergone natural selection. Wang S, etal., Carcinogenesis. 2020 Apr 22;41(2):146-158. doi: 10.1093/carcin/bgz136.
29. SOX9 dependent FOXA1 expression promotes tumorigenesis in lung carcinoma. Wang X, etal., Biochem Biophys Res Commun. 2019 Aug 13;516(1):236-244. doi: 10.1016/j.bbrc.2019.05.169. Epub 2019 Jun 17.
30. 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.
31. FOXA1 and CK7 expression in esophageal squamous cell carcinoma and its prognostic significance. Xu Y, etal., Neoplasma. 2018 Mar 14;65(3):469-476. doi: 10.4149/neo_2018_170529N384.
32. Twist1 promotes breast cancer invasion and metastasis by silencing Foxa1 expression. Xu Y, etal., Oncogene. 2017 Feb 23;36(8):1157-1166. doi: 10.1038/onc.2016.286. Epub 2016 Aug 15.
33. miR-194 inhibits the proliferation, invasion, migration, and enhances the chemosensitivity of non-small cell lung cancer cells by targeting forkhead box A1 protein. Zhu X, etal., Oncotarget. 2016 Mar 15;7(11):13139-52. doi: 10.18632/oncotarget.7545.
Additional References at PubMed
PMID:8306889   PMID:9931457   PMID:10049364   PMID:15389796   PMID:15485926   PMID:15539431   PMID:15567715   PMID:15668254   PMID:15748903   PMID:15987773   PMID:16087863   PMID:16214823  
PMID:16331276   PMID:17596284   PMID:19127412   PMID:20160041   PMID:22737085   PMID:22780989   PMID:23266329   PMID:23383217   PMID:25057789   PMID:25446530   PMID:27787633   PMID:28844448  
PMID:31930555   PMID:33629893   PMID:35976271   PMID:37217807  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.2675,099,907 - 75,136,534 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl675,103,503 - 75,136,188 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx675,551,122 - 75,556,257 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0675,850,458 - 75,855,593 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0675,277,927 - 75,283,064 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0678,516,579 - 78,549,669 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl678,545,804 - 78,549,669 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0688,041,150 - 88,074,240 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4677,976,384 - 78,009,176 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1677,979,509 - 78,012,302 (-)NCBI
Celera673,899,792 - 73,932,602 (-)NCBICelera
RH 3.4 Map6547.4RGD
Cytogenetic Map6q23NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh381437,589,552 - 37,595,249 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1437,589,552 - 37,596,059 (-)EnsemblGRCh38hg38GRCh38
GRCh371438,058,757 - 38,064,454 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361437,128,940 - 37,134,240 (-)NCBINCBI36Build 36hg18NCBI36
Celera1417,923,658 - 17,928,958 (-)NCBICelera
Cytogenetic Map14q21.1NCBI
HuRef1418,172,768 - 18,178,319 (-)NCBIHuRef
CHM1_11438,057,377 - 38,062,945 (-)NCBICHM1_1
T2T-CHM13v2.01431,778,686 - 31,784,378 (-)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391257,585,750 - 57,594,815 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1257,587,414 - 57,593,702 (-)EnsemblGRCm39 Ensembl
GRCm381257,540,628 - 57,548,029 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1257,540,628 - 57,546,916 (-)EnsemblGRCm38mm10GRCm38
MGSCv371258,641,618 - 58,647,108 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361258,458,643 - 58,464,133 (-)NCBIMGSCv36mm8
Celera1258,721,436 - 58,726,582 (-)NCBICelera
Cytogenetic Map12C1NCBI
cM Map1224.7NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_00495540923,598,127 - 23,599,461 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540923,598,127 - 23,599,827 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan11438,124,573 - 38,132,255 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01418,347,284 - 18,352,705 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11436,708,885 - 36,711,599 (-)NCBIpanpan1.1PanPan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.1816,072,629 - 16,083,105 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl816,079,140 - 16,083,807 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha815,876,271 - 15,882,016 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0816,196,019 - 16,201,769 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl816,156,721 - 16,201,650 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1815,890,156 - 15,895,900 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0815,954,899 - 15,960,633 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0816,245,465 - 16,251,213 (-)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_02440864048,025,285 - 48,029,333 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649411,529,546 - 11,535,224 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493649411,529,546 - 11,535,224 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl762,471,249 - 62,479,220 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1762,471,233 - 62,479,638 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2767,342,472 - 67,347,857 (+)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.12414,397,759 - 14,403,078 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2414,396,702 - 14,403,094 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660533,433,053 - 3,438,498 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_004624955231,506 - 239,508 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624955234,289 - 239,541 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Foxa1
138 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Prediction methods: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 (
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
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
4889848Pur25Proteinuria QTL 25140.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65672856290198260Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)657730540104085867Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)657730540104085867Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)658632962103632962Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)67222764181132889Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2675,119,401 - 75,119,606 (+)MAPPERmRatBN7.2
Rnor_6.0678,532,586 - 78,532,790NCBIRnor6.0
Rnor_5.0688,057,157 - 88,057,361UniSTSRnor5.0
RGSC_v3.4677,992,391 - 77,992,595UniSTSRGSC3.4
Celera673,915,808 - 73,916,012UniSTS
RH 3.4 Map6546.7UniSTS
Cytogenetic Map6q23-q24UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2675,106,774 - 75,106,883 (+)MAPPERmRatBN7.2
Rnor_6.0678,519,959 - 78,520,067NCBIRnor6.0
Rnor_5.0688,044,530 - 88,044,638UniSTSRnor5.0
RGSC_v3.4677,979,764 - 77,979,872UniSTSRGSC3.4
Celera673,903,172 - 73,903,280UniSTS
RH 3.4 Map6544.9UniSTS
Cytogenetic Map6q23-q24UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2675,103,656 - 75,103,875 (+)MAPPERmRatBN7.2
Rnor_6.0678,516,841 - 78,517,059NCBIRnor6.0
Rnor_5.0688,041,412 - 88,041,630UniSTSRnor5.0
RGSC_v3.4677,976,646 - 77,976,864UniSTSRGSC3.4
Celera673,900,054 - 73,900,272UniSTS
Cytogenetic Map6q23-q24UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2675,103,395 - 75,103,546 (+)MAPPERmRatBN7.2
Rnor_6.0678,516,580 - 78,516,730NCBIRnor6.0
Rnor_5.0688,041,151 - 88,041,301UniSTSRnor5.0
RGSC_v3.4677,976,385 - 77,976,535UniSTSRGSC3.4
Celera673,899,793 - 73,899,943UniSTS
RH 3.4 Map6547.4UniSTS
Cytogenetic Map6q23-q24UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2675,131,533 - 75,131,683 (+)MAPPERmRatBN7.2
Rnor_6.0678,545,015 - 78,545,164NCBIRnor6.0
Rnor_5.0688,069,586 - 88,069,735UniSTSRnor5.0
RGSC_v3.4678,004,522 - 78,004,671UniSTSRGSC3.4
Celera673,927,943 - 73,928,092UniSTS
RH 3.4 Map6543.9UniSTS
Cytogenetic Map6q23-q24UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2675,131,088 - 75,132,010 (+)MAPPERmRatBN7.2
Rnor_6.0678,544,570 - 78,545,491NCBIRnor6.0
Rnor_5.0688,069,141 - 88,070,062UniSTSRnor5.0
RGSC_v3.4678,004,077 - 78,004,998UniSTSRGSC3.4
Celera673,927,498 - 73,928,419UniSTS
Cytogenetic Map6q23-q24UniSTS
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2675,133,531 - 75,133,778 (+)MAPPERmRatBN7.2
Rnor_6.0678,547,013 - 78,547,259NCBIRnor6.0
Rnor_5.0688,071,584 - 88,071,830UniSTSRnor5.0
RGSC_v3.4678,006,520 - 78,006,766UniSTSRGSC3.4
Celera673,929,947 - 73,930,193UniSTS
Cytogenetic Map6q23-q24UniSTS


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 1 11 11 11 2 2
Low 2 2 33 30 3 30 35 20 31 9
Below cutoff 15 13 15 8 9 23 13 8 8


RefSeq Acc Id: ENSRNOT00000009940   ⟹   ENSRNOP00000009940
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl675,103,503 - 75,136,188 (-)Ensembl
Rnor_6.0 Ensembl678,545,804 - 78,549,669 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119772   ⟹   ENSRNOP00000090884
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl675,131,059 - 75,136,188 (-)Ensembl
RefSeq Acc Id: NM_012742   ⟹   NP_036874
RefSeq Status: VALIDATED
Rat AssemblyChrPosition (strand)Source
mRatBN7.2675,131,059 - 75,136,188 (-)NCBI
Rnor_6.0678,516,579 - 78,549,669 (-)NCBI
Rnor_5.0688,041,150 - 88,074,240 (-)NCBI
RGSC_v3.4677,976,384 - 78,009,176 (-)RGD
Celera673,899,792 - 73,932,602 (-)RGD
RefSeq Acc Id: XM_039111792   ⟹   XP_038967720
Rat AssemblyChrPosition (strand)Source
mRatBN7.2675,099,907 - 75,136,534 (-)NCBI
RefSeq Acc Id: XM_039111793   ⟹   XP_038967721
Rat AssemblyChrPosition (strand)Source
mRatBN7.2675,128,275 - 75,136,534 (-)NCBI
Protein Sequences
Protein RefSeqs NP_036874 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967720 (Get FASTA)   NCBI Sequence Viewer  
  XP_038967721 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA39418 (Get FASTA)   NCBI Sequence Viewer  
  EDM03450 (Get FASTA)   NCBI Sequence Viewer  
  P23512 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_036874   ⟸   NM_012742
- UniProtKB: P23512 (UniProtKB/Swiss-Prot),   A0A8I6AF62 (UniProtKB/TrEMBL),   A6HBP6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009940   ⟸   ENSRNOT00000009940
RefSeq Acc Id: XP_038967720   ⟸   XM_039111792
- Peptide Label: isoform X1
- UniProtKB: P23512 (UniProtKB/Swiss-Prot),   F1LR25 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038967721   ⟸   XM_039111793
- Peptide Label: isoform X2
- UniProtKB: P23512 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: ENSRNOP00000090884   ⟸   ENSRNOT00000119772
Protein Domains

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P23512-F1-model_v2 AlphaFold P23512 1-466 view protein structure


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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2807 AgrOrtholog
BioCyc Gene G2FUF-37409 BioCyc
Ensembl Genes ENSRNOG00000009284 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009940 ENTREZGENE
  ENSRNOP00000009940.7 UniProtKB/TrEMBL
  ENSRNOP00000090884.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009940 ENTREZGENE
  ENSRNOT00000009940.7 UniProtKB/TrEMBL
  ENSRNOT00000119772.1 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:25098 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 Foxa1 PhenoGen
  FORK_HEAD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00339 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL

Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Foxa1  forkhead box A1  Hnf3a  hepatocyte nuclear factor 3, alpha  Symbol and Name updated 1299863 APPROVED
2002-11-06 Hnf3a  hepatocyte nuclear factor 3, alpha    Hepatocyte nuclear factor 3 alpha  Name updated 625702 APPROVED
2002-06-10 Hnf3a  Hepatocyte nuclear factor 3 alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization localized to a nuclear fraction 632942