Foxn4 (forkhead box N4) - Rat Genome Database

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Gene: Foxn4 (forkhead box N4) Rattus norvegicus
Analyze
Symbol: Foxn4
Name: forkhead box N4
RGD ID: 1306389
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; chromatin binding activity; and cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II; retina layer formation; and ventral spinal cord interneuron fate commitment. Predicted to act upstream of or within amacrine cell differentiation and neuron fate commitment. Predicted to be active in nucleus. Orthologous to human FOXN4 (forkhead box N4); INTERACTS WITH acetamide; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: forkhead box protein N4; LOC288736
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
GRCr81247,997,308 - 48,020,526 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1248,000,257 - 48,020,526 (+)EnsemblGRCr8
mRatBN7.21242,336,706 - 42,359,932 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1242,340,323 - 42,359,921 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1243,508,097 - 43,528,395 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01244,121,690 - 44,141,988 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01243,182,198 - 43,202,496 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01248,101,012 - 48,121,281 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1248,101,673 - 48,121,270 (+)Ensemblrn6Rnor6.0
Rnor_5.01249,887,275 - 49,907,303 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41243,372,586 - 43,381,544 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1243,948,971 - 43,969,762 (+)NCBICelera
RGSC_v3.11243,232,259 - 43,243,592 (+)NCBI
Cytogenetic Map12q16NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,IEA,ISO)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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
Additional References at PubMed
PMID:15363391   PMID:16020526   PMID:17728344   PMID:21701787   PMID:22323600   PMID:23652001  


Genomics

Comparative Map Data
Foxn4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81247,997,308 - 48,020,526 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1248,000,257 - 48,020,526 (+)EnsemblGRCr8
mRatBN7.21242,336,706 - 42,359,932 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1242,340,323 - 42,359,921 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1243,508,097 - 43,528,395 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01244,121,690 - 44,141,988 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01243,182,198 - 43,202,496 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01248,101,012 - 48,121,281 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1248,101,673 - 48,121,270 (+)Ensemblrn6Rnor6.0
Rnor_5.01249,887,275 - 49,907,303 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41243,372,586 - 43,381,544 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1243,948,971 - 43,969,762 (+)NCBICelera
RGSC_v3.11243,232,259 - 43,243,592 (+)NCBI
Cytogenetic Map12q16NCBI
FOXN4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812109,277,978 - 109,309,284 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl12109,277,978 - 109,309,284 (-)Ensemblhg38GRCh38
GRCh3712109,715,783 - 109,747,089 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612108,200,167 - 108,231,408 (-)NCBIBuild 36Build 36hg18NCBI36
Celera12109,340,232 - 109,371,435 (-)NCBICelera
Cytogenetic Map12q24.11NCBI
HuRef12106,733,988 - 106,765,245 (-)NCBIHuRef
CHM1_112109,683,689 - 109,714,932 (-)NCBICHM1_1
T2T-CHM13v2.012109,252,960 - 109,284,245 (-)NCBIT2T-CHM13v2.0
Foxn4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395114,392,225 - 114,412,486 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5114,392,225 - 114,411,868 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm385114,254,164 - 114,274,418 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5114,254,164 - 114,273,807 (-)Ensemblmm10GRCm38
MGSCv375114,704,173 - 114,723,770 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv365114,515,163 - 114,534,760 (-)NCBIMGSCv36mm8
Celera5111,360,917 - 111,380,534 (-)NCBICelera
Cytogenetic Map5FNCBI
cM Map555.99NCBI
Foxn4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554559,183,475 - 9,210,506 (+)Ensembl
ChiLan1.0NW_0049554559,182,405 - 9,210,365 (+)NCBIChiLan1.0ChiLan1.0
FOXN4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210117,344,767 - 117,376,042 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112117,341,165 - 117,372,442 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012106,855,308 - 106,886,508 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.112110,250,547 - 110,280,876 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12110,251,449 - 110,280,025 (-)EnsemblpanPan2panpan1.1
FOXN4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12617,730,638 - 17,757,173 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2617,728,878 - 17,755,602 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2618,044,121 - 18,070,855 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02618,073,809 - 18,100,778 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2618,072,097 - 18,099,008 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12618,253,264 - 18,279,991 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02618,064,663 - 18,091,420 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02618,083,721 - 18,110,688 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Foxn4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118144,395,447 - 144,415,277 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367691,062,061 - 1,080,444 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367691,061,907 - 1,081,350 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11441,589,128 - 41,614,488 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21444,135,477 - 44,145,796 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FOXN4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111104,499,654 - 104,536,338 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl11104,499,633 - 104,534,275 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666037140,572,888 - 140,604,649 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Foxn4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474711,123,615 - 11,149,571 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474711,122,463 - 11,149,505 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Foxn4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11639,689,191 - 39,707,076 (+)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:166
Count of miRNA genes:117
Interacting mature miRNAs:143
Transcripts:ENSRNOT00000065060
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
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122480502252308831Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121120049452308831Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122871771850386405Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122598935552308831Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12348941648489416Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121847304152308831Rat
1300162Bp188Blood pressure QTL 1883.19arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123776414551558799Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049752308831Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121526424852308831Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)121174352852308831Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)121120049452308831Rat
1300175Cm5Cardiac mass QTL 53.78heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)123370043251558799Rat
1331786Kidm11Kidney mass QTL 113.571kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)121618743852308831Rat
8693658Alc33Alcohol consumption QTL 332.10.68drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122871771849212240Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121613502952308831Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121618743851213550Rat
1331763Wbc2White blood cell count QTL 23.162leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)121120049452308831Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)61120049452308831Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121847304152308831Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)12308718048087180Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
7243862Mcs30Mammary carcinoma susceptibility QTL 308.62mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)12563330650633306Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121613502952308831Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)121120049452308831Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)124413955852308831Rat


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
4 1 11 81 39 52 33 4 33 1 132 21 5 75 74 54 19 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000065060   ⟹   ENSRNOP00000061358
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1242,340,323 - 42,359,921 (+)Ensembl
Rnor_6.0 Ensembl1248,101,673 - 48,121,270 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000094488   ⟹   ENSRNOP00000090152
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1248,000,257 - 48,020,526 (+)Ensembl
mRatBN7.2 Ensembl1242,340,323 - 42,359,921 (+)Ensembl
RefSeq Acc Id: NM_001389259   ⟹   NP_001376188
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81248,000,257 - 48,020,526 (+)NCBI
mRatBN7.21242,339,662 - 42,359,932 (+)NCBI
RefSeq Acc Id: XM_039089275   ⟹   XP_038945203
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81247,997,308 - 48,020,526 (+)NCBI
mRatBN7.21242,336,706 - 42,359,932 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001376188 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945203 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM13945 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000090152
  ENSRNOP00000090152.2
Ensembl Acc Id: ENSRNOP00000061358   ⟸   ENSRNOT00000065060
RefSeq Acc Id: XP_038945203   ⟸   XM_039089275
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AB90 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001376188   ⟸   NM_001389259
- UniProtKB: A0A8I6AB90 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000090152   ⟸   ENSRNOT00000094488

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M4N5-F1-model_v2 AlphaFold F1M4N5 1-476 view protein structure

Transcriptome

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

Promoters
RGD ID:13698713
Promoter ID:EPDNEW_R9237
Type:single initiation site
Name:Foxn4_1
Description:forkhead box N4
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_6.01248,101,699 - 48,101,759EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306389 AgrOrtholog
BioCyc Gene G2FUF-18942 BioCyc
Ensembl Genes ENSRNOG00000000691 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000094488 ENTREZGENE
  ENSRNOT00000094488.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro FOXN1_4 UniProtKB/TrEMBL
  TF_fork_head UniProtKB/TrEMBL
  TF_fork_head_CS_2 UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene 288736 ENTREZGENE
PANTHER FORKHEAD BOX PROTEIN N1 UniProtKB/TrEMBL
  FORKHEAD BOX PROTEIN N4 UniProtKB/TrEMBL
Pfam Fork_head UniProtKB/TrEMBL
PhenoGen Foxn4 PhenoGen
PRINTS FORKHEAD UniProtKB/TrEMBL
PROSITE FORK_HEAD_2 UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000691 RatGTEx
SMART SM00339 UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A0A8I6AB90 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Foxn4  forkhead box N4   Foxn4_predicted  forkhead box N4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Foxn4_predicted  forkhead box N4 (predicted)      Symbol and Name status set to approved 70820 APPROVED