Foxf1 (forkhead box F1) - Rat Genome Database

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Gene: Foxf1 (forkhead box F1) Rattus norvegicus
Analyze
Symbol: Foxf1
Name: forkhead box F1
RGD ID: 1584229
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including circulatory system development; digestive tract development; and regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including mesenchyme morphogenesis; regulation of transcription by RNA polymerase II; and respiratory system development. Predicted to be active in nucleus. 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; 6-propyl-2-thiouracil; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: forkhead box protein F1; LOC687536; similar to Forkhead box protein F1 (Forkhead-related protein FKHL5) (Forkhead-related transcription factor 1) (FREAC-1) (Hepatocyte nuclear factor 3 forkhead homolog 8) (HFH-8)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81966,062,635 - 66,066,427 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1966,062,369 - 66,066,428 (+)EnsemblGRCr8
mRatBN7.21949,153,949 - 49,157,741 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1949,153,699 - 49,157,738 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1955,945,226 - 55,949,016 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01956,628,949 - 56,632,741 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01958,843,413 - 58,847,205 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01953,012,306 - 53,016,100 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1953,012,332 - 53,016,086 (+)Ensemblrn6Rnor6.0
Rnor_5.01963,756,636 - 63,760,430 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera1948,400,056 - 48,404,066 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component
nucleus  (IBA,IEA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:7958446   PMID:8626802   PMID:9486531   PMID:9769171   PMID:11124112   PMID:11437453   PMID:11493558   PMID:11809759   PMID:12500195   PMID:15987774   PMID:16439479   PMID:16691571  
PMID:17261592   PMID:17881493   PMID:18421012   PMID:19500772   PMID:35642703  


Genomics

Comparative Map Data
Foxf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81966,062,635 - 66,066,427 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1966,062,369 - 66,066,428 (+)EnsemblGRCr8
mRatBN7.21949,153,949 - 49,157,741 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1949,153,699 - 49,157,738 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1955,945,226 - 55,949,016 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01956,628,949 - 56,632,741 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01958,843,413 - 58,847,205 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01953,012,306 - 53,016,100 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1953,012,332 - 53,016,086 (+)Ensemblrn6Rnor6.0
Rnor_5.01963,756,636 - 63,760,430 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera1948,400,056 - 48,404,066 (+)NCBICelera
Cytogenetic Map19q12NCBI
FOXF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381686,510,527 - 86,515,422 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1686,510,527 - 86,515,422 (+)Ensemblhg38GRCh38
GRCh371686,544,133 - 86,549,028 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361685,101,634 - 85,105,571 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341685,101,658 - 85,105,548NCBI
Celera1670,844,972 - 70,848,909 (+)NCBICelera
Cytogenetic Map16q24.1NCBI
HuRef1672,283,842 - 72,287,779 (+)NCBIHuRef
CHM1_11687,955,849 - 87,959,786 (+)NCBICHM1_1
T2T-CHM13v2.01692,578,744 - 92,583,639 (+)NCBIT2T-CHM13v2.0
Foxf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398121,811,100 - 121,814,883 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8121,811,125 - 121,814,883 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm388121,084,386 - 121,088,154 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8121,084,386 - 121,088,144 (+)Ensemblmm10GRCm38
MGSCv378123,608,374 - 123,610,779 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368123,970,451 - 123,972,856 (+)NCBIMGSCv36mm8
Celera8125,302,426 - 125,304,831 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map870.31NCBI
Foxf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555411,317,114 - 1,346,590 (+)Ensembl
ChiLan1.0NW_0049555411,341,715 - 1,345,397 (+)NCBIChiLan1.0ChiLan1.0
FOXF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21896,269,228 - 96,274,680 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan116102,186,430 - 102,190,920 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01667,183,416 - 67,188,211 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11686,515,150 - 86,519,949 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1686,516,119 - 86,519,949 (+)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha566,355,810 - 66,359,808 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0566,565,325 - 66,569,328 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl566,566,196 - 66,569,484 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1566,588,163 - 66,592,141 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0566,423,363 - 66,427,352 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0566,836,698 - 66,840,702 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Foxf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244082614 - 1,756 (-)NCBIHiC_Itri_2
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 (-)EnsemblsusScr11Sscrofa11.1
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl571,898,786 - 71,903,661 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660473,803,343 - 3,807,492 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Foxf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247462,599,106 - 2,603,336 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247462,599,211 - 2,603,031 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Foxf1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11740,734,186 - 40,737,957 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:58
Interacting mature miRNAs:67
Transcripts:ENSRNOT00000073858
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)196124916174246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat

Markers in Region
Foxf1a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21949,154,344 - 49,154,787 (+)MAPPERmRatBN7.2
Rnor_6.01953,012,690 - 53,013,132NCBIRnor6.0
Rnor_5.01963,757,020 - 63,757,462UniSTSRnor5.0
Celera1948,400,656 - 48,401,098UniSTS
Foxf1a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21949,154,761 - 49,154,944 (+)MAPPERmRatBN7.2
Rnor_6.01953,013,107 - 53,013,289NCBIRnor6.0
Rnor_5.01963,757,437 - 63,757,619UniSTSRnor5.0
Celera1948,401,073 - 48,401,255UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 7 67 149 87 90 59 30 59 6 272 125 10 129 68 92 31 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000073858   ⟹   ENSRNOP00000065868
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1966,062,369 - 66,066,428 (+)Ensembl
mRatBN7.2 Ensembl1949,153,699 - 49,157,738 (+)Ensembl
Rnor_6.0 Ensembl1953,012,332 - 53,016,086 (+)Ensembl
RefSeq Acc Id: NM_001401006   ⟹   NP_001387935
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81966,062,635 - 66,066,427 (+)NCBI
mRatBN7.21949,153,949 - 49,157,741 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001387935 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92712 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000065868
  ENSRNOP00000065868.2
Ensembl Acc Id: ENSRNOP00000065868   ⟸   ENSRNOT00000073858
RefSeq Acc Id: NP_001387935   ⟸   NM_001401006
- UniProtKB: A6IZN4 (UniProtKB/TrEMBL)
Protein Domains
Fork-head

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R8R8-F1-model_v2 AlphaFold M0R8R8 1-378 view protein structure

Transcriptome

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

Promoters
RGD ID:13701194
Promoter ID:EPDNEW_R11712
Type:multiple initiation site
Name:Foxf1_1
Description:forkhead box F1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01953,012,287 - 53,012,347EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1584229 AgrOrtholog
BioCyc Gene G2FUF-5455 BioCyc
Ensembl Genes ENSRNOG00000049906 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073858 ENTREZGENE
  ENSRNOT00000073858.4 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro Forkhead_box_regulator UniProtKB/TrEMBL
  TF_fork_head UniProtKB/TrEMBL
  TF_fork_head_CS UniProtKB/TrEMBL
  TF_fork_head_CS_2 UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene 687536 ENTREZGENE
PANTHER FORKHEAD BOX PROTEIN BINIOU UniProtKB/TrEMBL
  FORKHEAD BOX PROTEIN F1 UniProtKB/TrEMBL
Pfam Fork_head UniProtKB/TrEMBL
PhenoGen Foxf1 PhenoGen
PRINTS FORKHEAD UniProtKB/TrEMBL
PROSITE FORK_HEAD_1 UniProtKB/TrEMBL
  FORK_HEAD_2 UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000049906 RatGTEx
SMART SM00339 UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A6IZN4 ENTREZGENE, UniProtKB/TrEMBL
  M0R8R8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-16 Foxf1  forkhead box F1  LOC687536  similar to Forkhead box protein F1 (Forkhead-related protein FKHL5) (Forkhead-related transcription factor 1) (FREAC-1) (Hepatocyte nuclear factor 3 forkhead homolog 8) (HFH-8)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC687536  similar to Forkhead box protein F1 (Forkhead-related protein FKHL5) (Forkhead-related transcription factor 1) (FREAC-1) (Hepatocyte nuclear factor 3 forkhead homolog 8) (HFH-8)      Symbol and Name status set to provisional 70820 PROVISIONAL