Foxa1 (forkhead box A1) - Rat Genome Database
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Gene: Foxa1 (forkhead box A1) Rattus norvegicus
Analyze
Symbol: Foxa1
Name: forkhead box A1
RGD ID: 2807
Description: Exhibits several functions, including DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and transcription factor binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Localizes to nucleus. 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
Also 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
Orthologs:
Homo sapiens (human) : FOXA1 (forkhead box A1)  HGNC  Alliance
Mus musculus (house mouse) : Foxa1 (forkhead box A1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Foxa1 (forkhead box A1)
Pan paniscus (bonobo/pygmy chimpanzee) : FOXA1 (forkhead box A1)
Canis lupus familiaris (dog) : FOXA1 (forkhead box A1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Foxa1 (forkhead box A1)
Sus scrofa (pig) : FOXA1 (forkhead box A1)
Chlorocebus sabaeus (African green monkey) : FOXA1 (forkhead box A1)
Heterocephalus glaber (naked mole-rat) : Foxa1 (forkhead box A1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1677,979,509 - 78,012,302 (-)NCBI
Celera673,899,792 - 73,932,602 (-)NCBICelera
Cytogenetic Map6q23NCBI
RH 3.4 Map6547.4RGD
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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)
arsenous acid  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (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)
capsaicin  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CHIR 99021  (ISO)
choline  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dichloromethane  (ISO)
diclofenac  (ISO)
dicrotophos  (ISO)
dioxygen  (ISO)
flusilazole  (ISO)
folic acid  (ISO)
fonofos  (ISO)
gamma-hexachlorocyclohexane  (EXP)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
irinotecan  (EXP)
L-methionine  (ISO)
leflunomide  (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  (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)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
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 remodeling  (IEA,ISO)
connective tissue development  (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)
epithelial-mesenchymal signaling involved in prostate gland development  (IEA,ISO)
glucose homeostasis  (IEA,ISO)
hormone metabolic process  (IEA,ISO)
lung development  (ISO)
lung epithelial cell differentiation  (IEA,ISO)
lung morphogenesis  (ISO)
negative regulation of epithelial to mesenchymal transition  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,IGI,ISO)
neuron fate specification  (IEA,ISO)
Notch signaling pathway  (IEA,ISO)
positive regulation of apoptotic process  (IEA,ISO)
positive regulation of DNA-binding transcription factor activity  (IEA,ISO)
positive regulation of intracellular estrogen receptor signaling pathway  (IEA,ISO)
positive regulation of mitotic cell cycle  (IEA,ISO)
positive regulation of neuron differentiation  (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 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)
tube morphogenesis  (ISO)

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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

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:19649697   PMID:20160041   PMID:22737085   PMID:22780989   PMID:23266329   PMID:23383217   PMID:25057789   PMID:25446530   PMID:27787633  
PMID:28844448  


Genomics

Comparative Map Data
Foxa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1677,979,509 - 78,012,302 (-)NCBI
Celera673,899,792 - 73,932,602 (-)NCBICelera
Cytogenetic Map6q23NCBI
RH 3.4 Map6547.4RGD
FOXA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1437,589,552 - 37,596,059 (-)EnsemblGRCh38hg38GRCh38
GRCh381437,589,552 - 37,595,249 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371438,058,757 - 38,064,325 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361437,128,940 - 37,134,240 (-)NCBINCBI36hg18NCBI36
Celera1417,923,658 - 17,928,958 (-)NCBI
Cytogenetic Map14q21.1NCBI
HuRef1418,172,768 - 18,178,319 (-)NCBIHuRef
CHM1_11438,057,377 - 38,062,945 (-)NCBICHM1_1
Foxa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391257,585,750 - 57,594,815 (-)NCBI
GRCm381257,540,628 - 57,548,029 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1257,540,628 - 57,546,916 (-)EnsemblGRCm38mm10GRCm38
MGSCv371258,641,618 - 58,647,108 (-)NCBIGRCm37mm9NCBIm37
MGSCv361258,458,643 - 58,464,133 (-)NCBImm8
Celera1258,721,436 - 58,726,582 (-)NCBICelera
Cytogenetic Map12C1NCBI
cM Map1224.7NCBI
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
PanPan1.11436,708,885 - 36,711,599 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01418,347,284 - 18,352,705 (-)NCBIMhudiblu_PPA_v0panPan3
FOXA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl816,079,140 - 16,083,807 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1816,072,629 - 16,083,105 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Foxa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493649411,529,546 - 11,535,224 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl762,471,228 - 62,479,223 (+)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl2414,396,702 - 14,403,094 (-)Ensembl
ChlSab1.12414,397,759 - 14,403,078 (-)NCBI
Foxa1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624955234,289 - 239,541 (-)NCBI

Position Markers
BI301884  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map6q23-q24UniSTS
RH 3.4 Map6546.7UniSTS
AI105057  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map6q23-q24UniSTS
RH 3.4 Map6544.9UniSTS
RH94853  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
RH94854  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map6q23-q24UniSTS
RH 3.4 Map6547.4UniSTS
BM386117  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic Map6q23-q24UniSTS
RH 3.4 Map6543.9UniSTS
Foxa1  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
PMC316473P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)percentage of deaths in a study population during a period of time (CMO:0001024)67009971115379601Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63810630883106308Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64167904686679046Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
4889848Pur25Proteinuria QTL 25140.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65980306594001333Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)67562339384763275Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:16
Count of miRNA genes:16
Interacting mature miRNAs:16
Transcripts:ENSRNOT00000009940
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.


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 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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009940   ⟹   ENSRNOP00000009940
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl678,545,804 - 78,549,669 (-)Ensembl
RefSeq Acc Id: NM_012742   ⟹   NP_036874
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
Sequence:
Protein Sequences
Protein RefSeqs NP_036874 (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  
Reference Sequences
RefSeq Acc Id: NP_036874   ⟸   NM_012742
- Sequence:
RefSeq Acc Id: ENSRNOP00000009940   ⟸   ENSRNOT00000009940
Protein Domains
Fork-head

Transcriptome

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


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)
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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
BN/SsN (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
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)
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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
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)
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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
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2807 AgrOrtholog
Ensembl Genes ENSRNOG00000009284 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009940 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009940 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 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
NCBI Gene 25098 ENTREZGENE
Pfam Forkhead UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Forkhead_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HNF_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
UniGene Rn.10470 ENTREZGENE
UniProt F1LR25_RAT UniProtKB/TrEMBL
  FOXA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


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