Foxf1 (forkhead box F1) - Rat Genome Database

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Gene: Foxf1 (forkhead box F1) Mus musculus
Analyze
Symbol: Foxf1
Name: forkhead box F1
RGD ID: 1616863
MGI Page MGI
Description: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including animal organ development; chordate embryonic development; and regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including alimentary system; brain; embryo mesenchyme; extraembryonic component; and genitourinary system. Used to study persistent fetal circulation syndrome. Human ortholog(s) of this gene implicated in persistent fetal circulation syndrome. Orthologous to human FOXF1 (forkhead box F1); PARTICIPATES IN forkhead class A signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-di-tert-butyl-4-methylphenol; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: AI450827; forkhead box F1a; forkhead box protein F1; forkhead-related protein FKHL5; forkhead-related transcription factor 1; Foxf; Foxf1a; FREA; Freac; Freac-1; FREAC1; hepatocyte nuclear factor 3 forkhead homolog 8; HFH-8; Hfh8; HNF-3/forkhead homolog 8
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398121,811,125 - 121,814,893 (+)NCBIGRCm39mm39
GRCm39 Ensembl8121,811,125 - 121,814,883 (+)Ensembl
GRCm388121,084,386 - 121,088,154 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8121,084,386 - 121,088,144 (+)EnsemblGRCm38mm10GRCm38
MGSCv378123,608,374 - 123,610,779 (+)NCBIGRCm37mm9NCBIm37
MGSCv368123,970,451 - 123,972,856 (+)NCBImm8
Celera8125,302,426 - 125,304,831 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map870.31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ morphogenesis  (IBA,IMP)
blood vessel development  (ISO)
cardiac left ventricle morphogenesis  (ISO)
cell-cell adhesion  (IMP)
cellular response to cytokine stimulus  (IDA)
cellular response to organic cyclic compound  (IMP)
detection of wounding  (IMP)
determination of left/right symmetry  (IMP)
digestive tract development  (ISO)
ductus arteriosus closure  (ISO)
embryonic digestive tract development  (IGI)
embryonic digestive tract morphogenesis  (ISO)
embryonic ectodermal digestive tract morphogenesis  (ISO)
embryonic foregut morphogenesis  (IMP)
endocardial cushion development  (ISO)
epithelial cell differentiation involved in mammary gland alveolus development  (IGI)
epithelial tube branching involved in lung morphogenesis  (IMP)
establishment of epithelial cell apical/basal polarity  (IGI)
extracellular matrix organization  (IGI)
heart development  (ISO)
in utero embryonic development  (IMP,ISO)
lateral mesodermal cell differentiation  (IMP)
lung alveolus development  (IMP)
lung development  (IMP,ISO)
lung lobe morphogenesis  (IMP)
lung morphogenesis  (IMP)
lung vasculature development  (ISO)
mesenchyme migration  (IMP)
mesoderm development  (IGI,IMP)
midgut development  (ISO)
morphogenesis of a branching structure  (ISO)
negative regulation of inflammatory response  (IMP)
negative regulation of mast cell degranulation  (IMP)
negative regulation of transcription by RNA polymerase II  (IMP)
pancreas development  (ISO)
positive regulation of cell migration  (IMP)
positive regulation of cell-substrate adhesion  (IMP)
positive regulation of mesenchymal cell proliferation  (IMP)
positive regulation of transcription by RNA polymerase II  (IDA,IMP,ISO)
positive regulation of transcription, DNA-templated  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (IEA)
respiratory tube development  (ISO)
right lung morphogenesis  (IMP)
smooth muscle cell differentiation  (IGI,IMP)
smoothened signaling pathway  (IDA)
somitogenesis  (IMP)
trachea development  (IMP,ISO)
ureter development  (ISO)
vasculogenesis  (IMP)
venous blood vessel development  (ISO)

Cellular Component
nucleus  (IBA,IDA)

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal allantois morphology  (IAGP)
abnormal amnion morphology  (IAGP)
abnormal developmental patterning  (IAGP)
abnormal embryonic tissue morphology  (IAGP)
abnormal esophageal smooth muscle morphology  (IAGP)
abnormal extraembryonic mesoderm development  (IAGP)
abnormal extraembryonic tissue morphology  (IAGP)
abnormal gallbladder morphology  (IAGP)
abnormal hindgut morphology  (IAGP)
abnormal intestinal smooth muscle morphology  (IAGP)
abnormal lateral plate mesoderm morphology  (IAGP)
abnormal lung bud morphology  (IAGP)
abnormal lung development  (IAGP)
abnormal lung morphology  (IAGP)
abnormal lung saccule morphology  (IAGP)
abnormal lung vasculature morphology  (IAGP)
abnormal posterior primitive streak morphology  (IAGP)
abnormal pulmonary alveolus morphology  (IAGP)
abnormal pulmonary artery morphology  (IAGP)
abnormal pulmonary vein morphology  (IAGP)
abnormal somite development  (IAGP)
abnormal surfactant secretion  (IAGP)
abnormal vascular branching morphogenesis  (IAGP)
abnormal visceral yolk sac mesenchyme morphology  (IAGP)
abnormal visceral yolk sac morphology  (IAGP)
absent gallbladder  (IAGP)
absent midgut  (IAGP)
absent vitelline blood vessels  (IAGP)
decreased angiogenesis  (IAGP)
decreased lung endothelial cell proliferation  (IAGP)
decreased vascular endothelial cell number  (IAGP)
delayed somite formation  (IAGP)
dilated esophagus  (IAGP)
embryonic lethality during organogenesis, complete penetrance  (IAGP)
embryonic lethality, complete penetrance  (IAGP)
failure of chorioallantoic fusion  (IAGP)
failure of initiation of embryo turning  (IAGP)
fused right lung lobes  (IAGP)
impaired contractility of intestinal smooth muscle  (IAGP)
impaired lung alveolus development  (IAGP)
lethality throughout fetal growth and development, complete penetrance  (IAGP)
lethality, incomplete penetrance  (IAGP)
lung hemorrhage  (IAGP)
lung inflammation  (IAGP)
neonatal lethality, complete penetrance  (IAGP)
neonatal lethality, incomplete penetrance  (IAGP)
perinatal lethality, complete penetrance  (IAGP)
postnatal lethality, incomplete penetrance  (IAGP)
premature death  (IAGP)
pulmonary hypoplasia  (IAGP)
respiratory distress  (IAGP)
small allantois  (IAGP)
small lung  (IAGP)
weight loss  (IAGP)
References

Additional References at PubMed
PMID:7683413   PMID:7789972   PMID:7957066   PMID:7958446   PMID:8626802   PMID:9486531   PMID:10349636   PMID:10822266   PMID:11042159   PMID:11076861   PMID:11124112   PMID:11217851  
PMID:11290504   PMID:11313147   PMID:11437453   PMID:11493558   PMID:11804790   PMID:11809759   PMID:11943666   PMID:12003781   PMID:12361961   PMID:12466851   PMID:12477932   PMID:12500195  
PMID:12711542   PMID:12812790   PMID:14607778   PMID:14681479   PMID:14745957   PMID:15107405   PMID:15136151   PMID:15196959   PMID:15618518   PMID:15809042   PMID:15817462   PMID:15987774  
PMID:16141072   PMID:16141073   PMID:16144835   PMID:16439479   PMID:16691571   PMID:16916379   PMID:16943278   PMID:16989802   PMID:17261592   PMID:17496152   PMID:17881493   PMID:17962963  
PMID:18287559   PMID:18324732   PMID:18421012   PMID:18483557   PMID:18990706   PMID:19000842   PMID:19020777   PMID:19049965   PMID:19304890   PMID:19877281   PMID:19879143   PMID:20097443  
PMID:20233876   PMID:21267068   PMID:21331042   PMID:21558373   PMID:21873635   PMID:21905163   PMID:22627279   PMID:22678773   PMID:22711520   PMID:23023706   PMID:23063659   PMID:23369715  
PMID:23884445   PMID:23946491   PMID:23975021   PMID:24393341   PMID:24633704   PMID:24722050   PMID:24790087   PMID:24939938   PMID:24952961   PMID:25091710   PMID:25356765   PMID:25619889  
PMID:25631042   PMID:26238476   PMID:26294094   PMID:26329601   PMID:26625197   PMID:26745863   PMID:26930384   PMID:27072135   PMID:27095594   PMID:27165781   PMID:27166834   PMID:27180663  
PMID:27320915   PMID:27425595   PMID:27638768   PMID:27736991   PMID:28069742   PMID:28286175   PMID:28501478   PMID:28797033   PMID:28878348   PMID:28939119   PMID:29412136   PMID:29642003  
PMID:30153454   PMID:30352852   PMID:30478225   PMID:30565344   PMID:30670377   PMID:30728831   PMID:30916783   PMID:31199666   PMID:31323030   PMID:31486675   PMID:32616504   PMID:32855415  
PMID:32855417   PMID:32968282   PMID:33328171  


Genomics

Comparative Map Data
Foxf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398121,811,125 - 121,814,893 (+)NCBIGRCm39mm39
GRCm39 Ensembl8121,811,125 - 121,814,883 (+)Ensembl
GRCm388121,084,386 - 121,088,154 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8121,084,386 - 121,088,144 (+)EnsemblGRCm38mm10GRCm38
MGSCv378123,608,374 - 123,610,779 (+)NCBIGRCm37mm9NCBIm37
MGSCv368123,970,451 - 123,972,856 (+)NCBImm8
Celera8125,302,426 - 125,304,831 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map870.31NCBI
FOXF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1686,510,527 - 86,515,422 (+)EnsemblGRCh38hg38GRCh38
GRCh381686,510,527 - 86,515,422 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371686,544,133 - 86,549,028 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361685,101,634 - 85,105,571 (+)NCBINCBI36hg18NCBI36
Build 341685,101,658 - 85,105,548NCBI
Celera1670,844,972 - 70,848,909 (+)NCBI
Cytogenetic Map16q24.1NCBI
HuRef1672,283,842 - 72,287,779 (+)NCBIHuRef
CHM1_11687,955,849 - 87,959,786 (+)NCBICHM1_1
Foxf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21949,153,729 - 49,157,741 (+)NCBImRatBN7.2
Rnor_6.0 Ensembl1953,012,332 - 53,016,086 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01953,012,306 - 53,016,100 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01963,756,636 - 63,760,430 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1948,400,056 - 48,404,066 (+)NCBICelera
Cytogenetic Map19q12NCBI
Foxf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555411,317,114 - 1,346,590 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555411,341,715 - 1,345,397 (+)NCBIChiLan1.0ChiLan1.0
FOXF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11686,515,150 - 86,519,949 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1686,516,119 - 86,519,949 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01667,183,416 - 67,188,211 (+)NCBIMhudiblu_PPA_v0panPan3
FOXF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1566,343,776 - 66,347,785 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl566,345,150 - 66,347,935 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha566,355,810 - 66,359,808 (-)NCBI
ROS_Cfam_1.0566,565,325 - 66,569,328 (-)NCBI
UMICH_Zoey_3.1566,588,163 - 66,592,141 (-)NCBI
UNSW_CanFamBas_1.0566,423,363 - 66,427,352 (-)NCBI
UU_Cfam_GSD_1.0566,836,698 - 66,840,702 (-)NCBI
Foxf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244082614 - 1,756 (-)NCBI
SpeTri2.0NW_0049438834 - 1,756 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl62,592,993 - 2,597,659 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.162,579,348 - 2,598,122 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.262,799,092 - 2,801,627 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FOXF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1571,898,473 - 71,902,624 (+)NCBI
ChlSab1.1 Ensembl571,898,786 - 71,903,661 (+)Ensembl
Vero_WHO_p1.0NW_0236660473,803,343 - 3,807,492 (-)NCBI
Foxf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247462,599,211 - 2,603,031 (+)NCBI

Position Markers
UniSTS:236022  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm388121,087,024 - 121,087,246UniSTSGRCm38
MGSCv378123,610,924 - 123,611,146UniSTSGRCm37
Celera8125,304,976 - 125,305,198UniSTS
Cytogenetic Map8E1UniSTS
cM Map867.0UniSTS
AI450827  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm388121,087,989 - 121,088,088UniSTSGRCm38
MGSCv378123,611,889 - 123,611,988UniSTSGRCm37
Celera8125,305,941 - 125,306,040UniSTS
Cytogenetic Map8E1UniSTS
cM Map867.0UniSTS
Whitehead/MRC_RH81416.7UniSTS
Foxf1a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm388121,084,757 - 121,085,199UniSTSGRCm38
MGSCv378123,608,657 - 123,609,099UniSTSGRCm37
Celera8125,302,709 - 125,303,151UniSTS
Cytogenetic Map8E1UniSTS
cM Map870.31UniSTS
cM Map867.0UniSTS
Foxf1a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm388121,085,174 - 121,085,356UniSTSGRCm38
Celera8125,303,126 - 125,303,308UniSTS
Cytogenetic Map8E1UniSTS
Foxf1a  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map8E1UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142023W3q5_mweight 3 weeks QTL 5 (mouse)Not determined71287817123895615Mouse
10412274Leci1_mleukocyte endothelial cell interactions 1 (mouse)Not determined8109688333129401213Mouse
11532691Sluc38_msusceptibility to lung cancer 38 (mouse)8104307238129401213Mouse
12904938Edlmmq7_mextensor digitorum longus muscle mass QTL 7 (mouse)8110755016129401213Mouse
1301316Dntcs1_mdental caries susceptibility 1 (mouse)Not determined8102716921127055036Mouse
11532692Sluc38a_msusceptibility to lung cancer 38a (mouse)8104307238129401213Mouse
1357708Orq1_movulation rate QTL 1 (mouse)Not determined871287817123895615Mouse
1301481Lith11_mlithogenic gene 11 (mouse)Not determined897836895129401213Mouse
12880431Fgf23lq2_mFGF23 serum level QTL 2 (mouse)896900000129401213Mouse
4141435Fbtq3_mfemoral bone trait QTL 3 (mouse)Not determined8100238570129401213Mouse
1301080Sluc9_msusceptibility to lung cancer 9 (mouse)Not determined899101792129401213Mouse
11252141Fdr2_mfat response to dietary restriction 2 (mouse)897663894129401213Mouse
12904960Gmmq6_mgastrocnemius muscle mass QTL 6 (mouse)8110755016129401213Mouse
26884375Skwq2_mskull length QTL 2, 5 week (mouse)8120000000131200000Mouse
27226796Scvln16_msacral vertebrae length 2, 16 week (mouse)889000000130800000Mouse
1302105Im1_mImmunoregulatory 1 (mouse)Not determined899101792129401213Mouse
4141546Mrdq3_mmodifier of retinal degeneration QTL 3 (mouse)Not determined113712788125329141Mouse
10412273Fcd1_mfunctional capillary density 1 (mouse)Not determined8109688333129401213Mouse
14746994Manh65_mmandible shape 65 (mouse)8105762890129401213Mouse
27095912Pglq14_mpelvic girdle length QTL 14, 16 week (mouse)873400000126100000Mouse
1357494Obsty2_mobesity 2 (mouse)Not determined895518613129018580Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:709
Count of miRNA genes:412
Interacting mature miRNAs:497
Transcripts:ENSMUST00000050684, ENSMUST00000181504
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


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000181504   ⟹   ENSMUSP00000137662
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl8121,084,386 - 121,088,144 (+)Ensembl
RefSeq Acc Id: NM_010426   ⟹   NP_034556
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm398121,811,125 - 121,814,893 (+)NCBI
GRCm388121,084,386 - 121,088,154 (+)NCBI
MGSCv378123,608,374 - 123,610,779 (+)RGD
Celera8125,302,338 - 125,306,106 (+)NCBI
cM Map8 ENTREZGENE
Sequence:
Reference Sequences
RefSeq Acc Id: NP_034556   ⟸   NM_010426
- UniProtKB: Q61080 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000137662   ⟸   ENSMUST00000181504

Promoters
RGD ID:8668475
Promoter ID:EPDNEW_M12268
Type:multiple initiation site
Name:Foxf1_1
Description:Mus musculus forkhead box F1 , 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
GRCm388121,084,361 - 121,084,421EPDNEW
RGD ID:6843193
Promoter ID:MM_KWN:55955
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   Lung
Transcripts:NM_010426
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv368123,607,496 - 123,608,747 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1347470 AgrOrtholog
Ensembl Genes ENSMUSG00000042812 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000137662 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000181504 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.10.10 UniProtKB/Swiss-Prot
InterPro Fork_head_dom UniProtKB/Swiss-Prot
  TF_fork_head_CS_1 UniProtKB/Swiss-Prot
  TF_fork_head_CS_2 UniProtKB/Swiss-Prot
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot
  WH_DNA-bd_sf UniProtKB/Swiss-Prot
KEGG Report mmu:15227 UniProtKB/Swiss-Prot
MGD MGI:1347470 ENTREZGENE
NCBI Gene 15227 ENTREZGENE
Pfam Forkhead UniProtKB/Swiss-Prot
PhenoGen Foxf1 PhenoGen
PRINTS FORKHEAD UniProtKB/Swiss-Prot
PROSITE FORK_HEAD_1 UniProtKB/Swiss-Prot
  FORK_HEAD_2 UniProtKB/Swiss-Prot
  FORK_HEAD_3 UniProtKB/Swiss-Prot
SMART SM00339 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot
UniProt FOXF1_MOUSE UniProtKB/Swiss-Prot
  Q3U0R0_MOUSE UniProtKB/TrEMBL
  Q61080 ENTREZGENE
UniProt Secondary B2RSC1 UniProtKB/Swiss-Prot
  Q61661 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-06-26 Foxf1  forkhead box F1  Foxf1a  forkhead box F1a  Symbol and/or name change 5135510 APPROVED