FOXA1 (forkhead box A1) - Rat Genome Database

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Pathways
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Gene: FOXA1 (forkhead box A1) Sus scrofa
Analyze
Symbol: FOXA1
Name: forkhead box A1
RGD ID: 13860671
Description: ENCODES a protein that exhibits DNA-binding transcription activator activity, RNA polymerase II-specific (ortholog); double-stranded DNA binding (ortholog); protein domain specific binding (ortholog); INVOLVED IN alveolar secondary septum development (ortholog); anatomical structure formation involved in morphogenesis (ortholog); connective tissue development (ortholog); PARTICIPATES IN forkhead class A signaling pathway; ASSOCIATED WITH Acute Lung Injury (ortholog); brain glioma (ortholog); Brain-Lung-Thyroid Syndrome (ortholog); FOUND IN fibrillar center (inferred); microvillus (inferred); nucleoplasm (inferred); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: MODEL
Previously known as: hepatocyte nuclear factor 3-alpha
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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)
connective tissue development  (IEA,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  (IEA,ISO)
lung epithelial cell differentiation  (IEA,ISO)
lung morphogenesis  (IEA,ISO)
mesenchymal-epithelial cell signaling involved in prostate gland development  (IEA,ISO)
negative regulation of epithelial to mesenchymal transition  (IEA)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
neuron differentiation  (IEA,ISO)
neuron fate specification  (IEA,ISO)
Notch signaling pathway  (IEA,ISO)
positive regulation of apoptotic process  (IEA)
positive regulation of DNA-binding transcription factor activity  (ISO)
positive regulation of dopaminergic neuron differentiation  (IEA,ISO)
positive regulation of hydrogen peroxide-mediated programmed cell death  (ISO)
positive regulation of intracellular estrogen receptor signaling pathway  (IEA)
positive regulation of mitotic cell cycle  (IEA)
positive regulation of smoothened signaling pathway  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
prostate gland epithelium morphogenesis  (IEA,ISO)
prostate gland stromal morphogenesis  (IEA,ISO)
regulation of cell cycle  (IEA,ISO)
regulation of DNA-templated transcription  (IEA)
regulation of gene expression  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
respiratory basal cell differentiation  (IEA,ISO)
response to estradiol  (IEA)
secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development  (IEA,ISO)
smoothened signaling pathway  (IEA,ISO)
tube morphogenesis  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
96 total Variants

Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
8 2 1 5 1 2 1 1

Sequence


Ensembl Acc Id: ENSSSCT00000039247   ⟹   ENSSSCP00000042307
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl762,471,249 - 62,479,220 (+)Ensembl
Ensembl Acc Id: ENSSSCT00000087431   ⟹   ENSSSCP00000064410
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl762,471,228 - 62,478,760 (+)Ensembl
RefSeq Acc Id: XM_001929276   ⟹   XP_001929311
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1762,471,233 - 62,479,638 (+)NCBI
Sequence:
RefSeq Acc Id: XP_001929311   ⟸   XM_001929276
- UniProtKB: A0A287AEQ3 (UniProtKB/TrEMBL),   A0A4X1TF89 (UniProtKB/TrEMBL),   A0A8D0S1P6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSSSCP00000042307   ⟸   ENSSSCT00000039247
Ensembl Acc Id: ENSSSCP00000064410   ⟸   ENSSSCT00000087431
Protein Domains
Fork-head


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000037634 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00025037314 UniProtKB/TrEMBL
  ENSSSCG00030073760 UniProtKB/TrEMBL
  ENSSSCG00035018591 UniProtKB/TrEMBL
  ENSSSCG00040070329 UniProtKB/TrEMBL
  ENSSSCG00045012190 UniProtKB/TrEMBL
  ENSSSCG00050005222 UniProtKB/TrEMBL
  ENSSSCG00055028172 UniProtKB/TrEMBL
  ENSSSCG00060057371 UniProtKB/TrEMBL
  ENSSSCG00065052857 UniProtKB/TrEMBL
  ENSSSCG00070008410 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000039247 ENTREZGENE
  ENSSSCT00000039247.3 UniProtKB/TrEMBL
  ENSSSCT00025050763.1 UniProtKB/TrEMBL
  ENSSSCT00025050772.1 UniProtKB/TrEMBL
  ENSSSCT00030103336.1 UniProtKB/TrEMBL
  ENSSSCT00030103349.1 UniProtKB/TrEMBL
  ENSSSCT00035024005.1 UniProtKB/TrEMBL
  ENSSSCT00035024010.1 UniProtKB/TrEMBL
  ENSSSCT00040096480.1 UniProtKB/TrEMBL
  ENSSSCT00040096517.1 UniProtKB/TrEMBL
  ENSSSCT00045020716.1 UniProtKB/TrEMBL
  ENSSSCT00045020730.1 UniProtKB/TrEMBL
  ENSSSCT00050007138.1 UniProtKB/TrEMBL
  ENSSSCT00050007144.1 UniProtKB/TrEMBL
  ENSSSCT00055055798.1 UniProtKB/TrEMBL
  ENSSSCT00055055828.1 UniProtKB/TrEMBL
  ENSSSCT00060078166.1 UniProtKB/TrEMBL
  ENSSSCT00060078171.1 UniProtKB/TrEMBL
  ENSSSCT00065072365.1 UniProtKB/TrEMBL
  ENSSSCT00065072370.1 UniProtKB/TrEMBL
  ENSSSCT00070016237.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro Fork-head_N UniProtKB/TrEMBL
  Fork_head_dom UniProtKB/TrEMBL
  Forkhead_box_C UniProtKB/TrEMBL
  FOX_domain-containing UniProtKB/TrEMBL
  TF_fork_head_CS_1 UniProtKB/TrEMBL
  TF_fork_head_CS_2 UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report ssc:100156502 UniProtKB/TrEMBL
NCBI Gene FOXA1 ENTREZGENE
PANTHER FORKHEAD BOX PROTEIN UniProtKB/TrEMBL
  HEPATOCYTE NUCLEAR FACTOR 3-ALPHA UniProtKB/TrEMBL
Pfam Forkhead UniProtKB/TrEMBL
  Forkhead_N UniProtKB/TrEMBL
  HNF_C UniProtKB/TrEMBL
PRINTS FORKHEAD UniProtKB/TrEMBL
PROSITE FORK_HEAD_1 UniProtKB/TrEMBL
  FORK_HEAD_2 UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/TrEMBL
SMART SM00339 UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A0A287AEQ3 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1TF89 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0S1P6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0UQ99_PIG UniProtKB/TrEMBL
  A0A8D1H6G0_PIG UniProtKB/TrEMBL
VGNC ID VGNC:88193 ENTREZGENE