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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81966,062,635 - 66,066,427 (+)NCBIGRCr8
mRatBN7.21949,153,949 - 49,157,741 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1949,153,699 - 49,157,738 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1955,945,226 - 55,949,016 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01956,628,949 - 56,632,741 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01958,843,413 - 58,847,205 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01953,012,306 - 53,016,100 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1953,012,332 - 53,016,086 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01963,756,636 - 63,760,430 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1948,400,056 - 48,404,066 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

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

Cellular Component
nucleus  (IBA,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 (+)NCBIGRCr8
mRatBN7.21949,153,949 - 49,157,741 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1949,153,699 - 49,157,738 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1955,945,226 - 55,949,016 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01956,628,949 - 56,632,741 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01958,843,413 - 58,847,205 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01953,012,306 - 53,016,100 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1953,012,332 - 53,016,086 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01963,756,636 - 63,760,430 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1948,400,056 - 48,404,066 (+)NCBICelera
Cytogenetic Map19q12NCBI
FOXF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381686,510,527 - 86,515,422 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1686,510,527 - 86,515,422 (+)EnsemblGRCh38hg38GRCh38
GRCh371686,544,133 - 86,549,028 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361685,101,634 - 85,105,571 (+)NCBINCBI36Build 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 Ensembl
GRCm388121,084,386 - 121,088,154 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8121,084,386 - 121,088,144 (+)EnsemblGRCm38mm10GRCm38
MGSCv378123,608,374 - 123,610,779 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)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
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 (+)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0566,565,325 - 66,569,328 (-)NCBIROS_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_1.0
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 (-)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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl571,898,786 - 71,903,661 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247462,599,211 - 2,603,031 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Foxf1
12 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat

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
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 3 6 6 6 7 11
Low 16 34 34 3 34 1 60 17 30
Below cutoff 27 13 1 16 1 4 5 14 17 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000073858   ⟹   ENSRNOP00000065868
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
Reference Protein Sequences
RefSeq 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
  ENSRNOT00000073858.3 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro 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
KEGG Report rno:687536 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