Foxa1 (forkhead box A1) - Rat Genome Database

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Gene: Foxa1 (forkhead box A1) Mus musculus
Analyze
Symbol: Foxa1
Name: forkhead box A1
RGD ID: 10718
MGI Page MGI
Description: Enables DNA-binding transcription factor activity; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in chromatin remodeling. Acts upstream of or within several processes, including lung development; prostate gland development; and regulation of transcription by RNA polymerase II. Located in microvillus and nucleus. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; respiratory system; and sensory organ. 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).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: fork head domain; forkhead box protein A1; hepatocyte nuclear factor 3 alpha (winged helix transcription factor); hepatocyte nuclear factor 3-alpha; Hnf; Hnf-; HNF-3-alpha; Hnf-3a; Hnf3a; Tcf-3; Tcf-3a; Tcf3; Tcf3a
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
4,4'-sulfonyldiphenol  (EXP)
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  (EXP,ISO)
all-trans-retinol  (ISO)
amiodarone  (ISO)
ammonium chloride  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (EXP)
beta-carotene  (ISO)
bexarotene  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
bortezomib  (ISO)
buta-1,3-diene  (EXP)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
capsaicin  (ISO)
carbamazepine  (EXP,ISO)
carbon nanotube  (EXP,ISO)
CHIR 99021  (ISO)
chlorpyrifos  (EXP)
choline  (EXP,ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
crocidolite asbestos  (EXP)
curcumin  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dichloromethane  (EXP)
diclofenac  (ISO)
dicrotophos  (ISO)
dioxygen  (EXP)
enzalutamide  (ISO)
epoxiconazole  (EXP)
flusilazole  (EXP)
folic acid  (EXP)
fonofos  (ISO)
FR900359  (ISO)
fulvestrant  (EXP,ISO)
gamma-hexachlorocyclohexane  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
irinotecan  (ISO)
L-methionine  (EXP,ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
LY294002  (ISO)
menadione  (ISO)
methylseleninic acid  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
Monobutylphthalate  (EXP)
N-methyl-N-nitrosourea  (ISO)
naphthalene  (EXP)
oleic acid  (ISO)
paracetamol  (ISO)
parathion  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (ISO)
phenformin  (ISO)
phenobarbital  (EXP)
pinostrobin  (ISO)
pirinixic acid  (EXP)
potassium dichromate  (EXP)
quercetin  (EXP,ISO)
reactive oxygen species  (ISO)
resveratrol  (ISO)
rifampicin  (ISO)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
tetracycline  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
tunicamycin  (ISO)
valdecoxib  (ISO)
valproic acid  (ISO)
vinclozolin  (ISO)
vitamin D  (EXP)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

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

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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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.
10. 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.
11. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
12. MGDs mouse GO annotations MGD data from the GO Consortium
13. MGD IEA MGD IEA
14. 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.
15. 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.
16. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
17. Mouse MP Annotation Import Pipeline RGD automated import pipeline
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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:1612587   PMID:1672118   PMID:7671812   PMID:7689224   PMID:7768172   PMID:7862129   PMID:7894157   PMID:7958446   PMID:8029022   PMID:8034310   PMID:8069909   PMID:8069910  
PMID:8187630   PMID:8248124   PMID:8287471   PMID:8306889   PMID:8375339   PMID:8652662   PMID:9032290   PMID:9119385   PMID:9136932   PMID:9152011   PMID:9260895   PMID:9415428  
PMID:9441679   PMID:9486531   PMID:9651517   PMID:9712518   PMID:9739106   PMID:9851841   PMID:10049364   PMID:10208738   PMID:10364163   PMID:10421635   PMID:10468578   PMID:10479450  
PMID:10600708   PMID:10725233   PMID:10818213   PMID:10866673   PMID:10887078   PMID:10899756   PMID:11002334   PMID:11297512   PMID:11518730   PMID:11748835   PMID:11846474   PMID:11864602  
PMID:11934848   PMID:11973269   PMID:12395314   PMID:12477932   PMID:12645927   PMID:14521963   PMID:14660441   PMID:14681479   PMID:15005571   PMID:15013800   PMID:15033168   PMID:15057272  
PMID:15252040   PMID:15282310   PMID:15389796   PMID:15485926   PMID:15539431   PMID:15562441   PMID:15567715   PMID:15584907   PMID:15618518   PMID:15668254   PMID:15748903   PMID:15959514  
PMID:15987773   PMID:16214823   PMID:16376864   PMID:16467259   PMID:16602821   PMID:16884697   PMID:16945627   PMID:17003337   PMID:17070019   PMID:17151600   PMID:17198697   PMID:17220277  
PMID:17383628   PMID:17452023   PMID:17596284   PMID:17626057   PMID:18287559   PMID:18332127   PMID:18336786   PMID:18358466   PMID:18381283   PMID:18400219   PMID:18554416   PMID:18635606  
PMID:18973680   PMID:19060336   PMID:19141476   PMID:19213785   PMID:19270025   PMID:19339686   PMID:19415718   PMID:19436110   PMID:19562671   PMID:19607821   PMID:19633360   PMID:19687299  
PMID:19720144   PMID:19737349   PMID:19737569   PMID:19805295   PMID:19865483   PMID:19897491   PMID:19916800   PMID:20018680   PMID:20211142   PMID:20347503   PMID:20348100   PMID:20501593  
PMID:20534694   PMID:20572855   PMID:20878115   PMID:21093585   PMID:21122108   PMID:21150899   PMID:21167261   PMID:21224212   PMID:21267068   PMID:21331042   PMID:21677750   PMID:21731673  
PMID:21803035   PMID:21873635   PMID:21935353   PMID:22001115   PMID:22203039   PMID:22223659   PMID:22232429   PMID:22265403   PMID:22510988   PMID:22696295   PMID:22711520   PMID:22737085  
PMID:22780989   PMID:22783724   PMID:22988430   PMID:23006325   PMID:23266329   PMID:23383217   PMID:23471965   PMID:23637192   PMID:23884445   PMID:24373287   PMID:24451200   PMID:24486549  
PMID:24531377   PMID:24802759   PMID:24803390   PMID:24840332   PMID:24853420   PMID:24952961   PMID:25152336   PMID:25249463   PMID:25249938   PMID:25446530   PMID:25701738   PMID:25804738  
PMID:25907831   PMID:26283356   PMID:26321050   PMID:26395490   PMID:26416771   PMID:26551672   PMID:26677878   PMID:26919034   PMID:26929406   PMID:26980469   PMID:27045898   PMID:27173853  
PMID:27721237   PMID:27934886   PMID:28049658   PMID:28069742   PMID:28154153   PMID:28235042   PMID:28400434   PMID:29023691   PMID:30061015   PMID:30061411   PMID:30063881   PMID:30380057  
PMID:30475207   PMID:30670749   PMID:30959515   PMID:31644911   PMID:31850343   PMID:32001436   PMID:32453714   PMID:32467237   PMID:32561546   PMID:32645357   PMID:32868762   PMID:33636105  
PMID:33658226   PMID:34009125   PMID:34074765   PMID:34095148   PMID:34101624   PMID:34215813   PMID:34321664   PMID:34323272   PMID:34599818   PMID:35364055   PMID:35398294   PMID:35831953  
PMID:35835117   PMID:36064451   PMID:36476860   PMID:37459395   PMID:37491794   PMID:37752418   PMID:38143008   PMID:38324694  


Genomics

Comparative Map Data
Foxa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
FOXA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
Foxa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8680,838,380 - 80,871,195 (-)NCBIGRCr8
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
Foxa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540923,598,127 - 23,599,461 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540923,598,127 - 23,599,827 (+)NCBIChiLan1.0ChiLan1.0
FOXA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21538,908,063 - 38,918,029 (-)NCBINHGRI_mPanPan1-v2
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
FOXA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
Foxa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864048,025,285 - 48,029,333 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649411,529,546 - 11,535,224 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649411,529,546 - 11,535,224 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
FOXA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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
Foxa1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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

.
Variants in Foxa1
275 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:453
Count of miRNA genes:324
Interacting mature miRNAs:362
Transcripts:ENSMUST00000044380
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 (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12541844077031203Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12955000084146774Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121166000197176774Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121534102679040364Mouse
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121759644780956883Mouse
1301989Hdlq18_mHDL QTL 18 (mouse)Not determined122916068563160884Mouse
1300636Gct2_mgranulosa cell tumorigenesis 2 (mouse)Not determined122916068563160884Mouse
4141843Moen3_mmodifier of engrailed QTL 3 (mouse)Not determined122980158463801733Mouse
14747008Mancz10_mmandible centroid size 10 (mouse)122986352263863522Mouse
10402492Dipa8_mdrug induced psychomotor activation 8 (mouse)Not determined123493387268934019Mouse
1300818Bbaa10_mB.burgdorferi-associated arthritis 10 (mouse)Not determined123509100465511019Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
1357479Splwt1_mspleen weight 1 (mouse)Not determined124169317590887526Mouse
1357757Lnopy2_mlens opacity 2 (mouse)Not determined125284662686846796Mouse
1357749Vtbt13_mvertebral trabecular bone trait 13 (mouse)Not determined125313200287132145Mouse
12832727Ahrq1_mairway hyperresponsiveness QTL 1 (mouse)125469591082665939Mouse
12903999Opfaq8_mopen field activity QTL 8 (mouse)125490765357870585Mouse
13504832Bacszq2_mbaculum size QTL 2 (mouse)125694579875345787Mouse

Markers in Region
Foxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,541,235 - 57,541,722UniSTSGRCm38
MGSCv371258,643,013 - 58,643,315UniSTSGRCm37
MGSCv371258,641,648 - 58,642,579UniSTSGRCm37
MGSCv371258,643,026 - 58,643,262UniSTSGRCm37
Celera1258,722,040 - 58,722,528UniSTS
Cytogenetic Map12C1UniSTS
cM Map1226.0UniSTS
cM Map1226.0UniSTS
UniSTS:236853  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,541,435 - 57,541,723UniSTSGRCm38
MGSCv371258,642,422 - 58,642,710UniSTSGRCm37
Celera1258,722,240 - 58,722,529UniSTS
Cytogenetic Map12C1UniSTS
cM Map1226.0UniSTS
UniSTS:224681  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,541,777 - 57,541,970UniSTSGRCm38
MGSCv371258,642,764 - 58,642,957UniSTSGRCm37
Celera1258,722,584 - 58,722,781UniSTS
Cytogenetic Map12C1UniSTS
cM Map1226.0UniSTS
PMC316377P6  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,543,179 - 57,543,361UniSTSGRCm38
MGSCv371258,644,166 - 58,644,348UniSTSGRCm37
Celera1258,723,990 - 58,724,172UniSTS
Cytogenetic Map12C1UniSTS
cM Map1226.0UniSTS
PMC316473P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,543,082 - 57,543,328UniSTSGRCm38
MGSCv371258,644,069 - 58,644,315UniSTSGRCm37
Celera1258,723,893 - 58,724,139UniSTS
Cytogenetic Map12C1UniSTS
cM Map1226.0UniSTS
Foxa2  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,541,406 - 57,541,504UniSTSGRCm38
MGSCv371258,642,393 - 58,642,491UniSTSGRCm37
Celera1258,722,211 - 58,722,309UniSTS
Cytogenetic Map2G3UniSTS
Cytogenetic Map12C1UniSTS
cM Map284.0UniSTS
cM Map1226.0UniSTS
Foxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,540,661 - 57,541,592UniSTSGRCm38
MGSCv371258,641,648 - 58,642,579UniSTSGRCm37
Celera1258,721,466 - 58,722,397UniSTS
Cytogenetic Map12C1UniSTS
Foxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12C1UniSTS
Foxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12C1UniSTS
Foxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12C1UniSTS
Foxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,542,039 - 57,542,275UniSTSGRCm38
MGSCv371258,643,026 - 58,643,262UniSTSGRCm37
Celera1258,722,850 - 58,723,086UniSTS
Cytogenetic Map12C1UniSTS
Foxa1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381257,542,026 - 57,542,328UniSTSGRCm38
MGSCv371258,643,013 - 58,643,315UniSTSGRCm37
Celera1258,722,837 - 58,723,139UniSTS
Cytogenetic Map12C1UniSTS
cM Map1226.0UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000044380   ⟹   ENSMUSP00000041118
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1257,587,414 - 57,592,907 (-)Ensembl
GRCm38.p6 Ensembl1257,540,628 - 57,546,121 (-)Ensembl
RefSeq Acc Id: ENSMUST00000218398
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1257,592,620 - 57,593,702 (-)Ensembl
GRCm38.p6 Ensembl1257,545,834 - 57,546,916 (-)Ensembl
RefSeq Acc Id: NM_008259   ⟹   NP_032285
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391257,587,414 - 57,592,897 (-)NCBI
GRCm381257,540,628 - 57,546,111 (-)NCBI
MGSCv371258,641,618 - 58,647,108 (-)RGD
Celera1258,721,436 - 58,726,582 (-)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006515479   ⟹   XP_006515542
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391257,585,750 - 57,593,613 (-)NCBI
GRCm381257,540,628 - 57,546,827 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006515481   ⟹   XP_006515544
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391257,587,414 - 57,593,413 (-)NCBI
GRCm381257,540,628 - 57,546,627 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006515483   ⟹   XP_006515546
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391257,585,750 - 57,593,697 (-)NCBI
GRCm381257,540,628 - 57,546,911 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017314962   ⟹   XP_017170451
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391257,585,750 - 57,594,815 (-)NCBI
GRCm381257,540,628 - 57,548,029 (-)NCBI
Sequence:
RefSeq Acc Id: XM_030246562   ⟹   XP_030102422
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391257,585,750 - 57,593,250 (-)NCBI
GRCm381257,540,628 - 57,546,464 (-)NCBI
Sequence:
RefSeq Acc Id: NP_032285   ⟸   NM_008259
- UniProtKB: Q4VA63 (UniProtKB/Swiss-Prot),   Q61108 (UniProtKB/Swiss-Prot),   P35582 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006515546   ⟸   XM_006515483
- Peptide Label: isoform X1
- UniProtKB: Q4VA63 (UniProtKB/Swiss-Prot),   Q61108 (UniProtKB/Swiss-Prot),   P35582 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006515542   ⟸   XM_006515479
- Peptide Label: isoform X1
- UniProtKB: Q4VA63 (UniProtKB/Swiss-Prot),   Q61108 (UniProtKB/Swiss-Prot),   P35582 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006515544   ⟸   XM_006515481
- Peptide Label: isoform X1
- UniProtKB: Q4VA63 (UniProtKB/Swiss-Prot),   Q61108 (UniProtKB/Swiss-Prot),   P35582 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017170451   ⟸   XM_017314962
- Peptide Label: isoform X1
- UniProtKB: Q4VA63 (UniProtKB/Swiss-Prot),   Q61108 (UniProtKB/Swiss-Prot),   P35582 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_030102422   ⟸   XM_030246562
- Peptide Label: isoform X1
- UniProtKB: Q4VA63 (UniProtKB/Swiss-Prot),   P35582 (UniProtKB/Swiss-Prot),   Q61108 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: ENSMUSP00000041118   ⟸   ENSMUST00000044380
Protein Domains
Fork-head

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P35582-F1-model_v2 AlphaFold P35582 1-468 view protein structure

Promoters
RGD ID:8678326
Promoter ID:EPDNEW_M17194
Type:multiple initiation site
Name:Foxa1_1
Description:Mus musculus forkhead box A1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381257,546,001 - 57,546,061EPDNEW
RGD ID:6822958
Promoter ID:MM_KWN:11723
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Liver,   Lung
Transcripts:ENSMUST00000044380
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361258,647,156 - 58,647,907 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1347472 AgrOrtholog
Ensembl Genes ENSMUSG00000035451 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000044380 ENTREZGENE
  ENSMUST00000044380.8 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Fork-head_N UniProtKB/Swiss-Prot
  Fork_head_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Forkhead_box_C UniProtKB/Swiss-Prot
  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 mmu:15375 UniProtKB/Swiss-Prot
MGD MGI:1347472 ENTREZGENE
NCBI Gene 15375 ENTREZGENE
PANTHER FORKHEAD BOX PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HEPATOCYTE NUCLEAR FACTOR 3-ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Forkhead UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Forkhead_N UniProtKB/Swiss-Prot
  HNF_C UniProtKB/Swiss-Prot
PhenoGen Foxa1 PhenoGen
PRINTS FORKHEAD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE FORK_HEAD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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
UniProt FOXA1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q4VA63 ENTREZGENE
  Q61108 ENTREZGENE
  Q61583_MOUSE UniProtKB/TrEMBL
UniProt Secondary Q4VA63 UniProtKB/Swiss-Prot
  Q61108 UniProtKB/Swiss-Prot