Foxi1 (forkhead box I1) - Rat Genome Database

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Gene: Foxi1 (forkhead box I1) Rattus norvegicus
Analyze
Symbol: Foxi1
Name: forkhead box I1
RGD ID: 1307421
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 anatomical structure morphogenesis; cell differentiation; and regulation of DNA-templated transcription. Predicted to act upstream of or within inner ear morphogenesis and positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleolus. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 4. Orthologous to human FOXI1 (forkhead box I1); INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: forkhead box protein I1; LOC287185
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
GRCr81019,310,466 - 19,314,405 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1019,310,482 - 19,314,405 (-)EnsemblGRCr8
mRatBN7.21018,806,292 - 18,810,231 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1018,806,308 - 18,810,231 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1023,561,038 - 23,564,983 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01023,049,575 - 23,053,518 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01018,529,590 - 18,533,542 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01019,160,566 - 19,164,505 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1019,160,582 - 19,164,505 (-)Ensemblrn6Rnor6.0
Rnor_5.01019,039,086 - 19,043,025 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41019,185,917 - 19,189,856 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1018,438,984 - 18,442,923 (-)NCBICelera
RGSC_v3.11019,188,079 - 19,190,836 (-)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleolus  (IEA,ISO)
nucleus  (IEA)

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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7958446   PMID:12642503   PMID:16159312   PMID:19214237  


Genomics

Comparative Map Data
Foxi1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81019,310,466 - 19,314,405 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1019,310,482 - 19,314,405 (-)EnsemblGRCr8
mRatBN7.21018,806,292 - 18,810,231 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1018,806,308 - 18,810,231 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1023,561,038 - 23,564,983 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01023,049,575 - 23,053,518 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01018,529,590 - 18,533,542 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01019,160,566 - 19,164,505 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1019,160,582 - 19,164,505 (-)Ensemblrn6Rnor6.0
Rnor_5.01019,039,086 - 19,043,025 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41019,185,917 - 19,189,856 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1018,438,984 - 18,442,923 (-)NCBICelera
RGSC_v3.11019,188,079 - 19,190,836 (-)NCBI
Cytogenetic Map10q12NCBI
FOXI1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385170,105,897 - 170,109,737 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5170,105,897 - 170,109,734 (+)Ensemblhg38GRCh38
GRCh375169,532,901 - 169,536,741 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365169,465,495 - 169,469,307 (+)NCBIBuild 36Build 36hg18NCBI36
Build 345169,465,494 - 169,469,302NCBI
Celera5165,564,551 - 165,568,363 (+)NCBICelera
Cytogenetic Map5q35.1NCBI
HuRef5164,630,964 - 164,634,777 (+)NCBIHuRef
CHM1_15168,965,387 - 168,969,200 (+)NCBICHM1_1
T2T-CHM13v2.05170,644,375 - 170,648,215 (+)NCBIT2T-CHM13v2.0
Foxi1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391134,154,341 - 34,158,089 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1134,154,338 - 34,158,089 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381134,204,341 - 34,208,089 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1134,204,338 - 34,208,089 (-)Ensemblmm10GRCm38
MGSCv371134,104,341 - 34,108,089 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361134,104,341 - 34,108,089 (-)NCBIMGSCv36mm8
Celera1136,615,688 - 36,619,447 (-)NCBICelera
Cytogenetic Map11A4NCBI
cM Map1119.65NCBI
Foxi1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540823,074,850 - 23,078,815 (+)Ensembl
ChiLan1.0NW_00495540823,074,876 - 23,078,766 (+)NCBIChiLan1.0ChiLan1.0
FOXI1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24165,265,610 - 165,271,144 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15163,405,187 - 163,410,687 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05165,468,600 - 165,473,088 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15172,228,840 - 172,232,692 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5172,228,840 - 172,232,692 (+)EnsemblpanPan2panpan1.1
FOXI1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1441,760,899 - 41,764,887 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl441,761,016 - 41,764,836 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha441,713,210 - 41,717,202 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0442,137,160 - 42,141,152 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl442,137,277 - 42,141,393 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1441,954,224 - 41,958,215 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0442,141,176 - 42,145,168 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0442,652,030 - 42,656,023 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Foxi1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721395,944,423 - 95,948,631 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366094,667,425 - 4,669,746 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366094,667,425 - 4,694,259 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXI1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1653,835,399 - 53,839,187 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11653,835,350 - 53,839,185 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21658,331,419 - 58,335,249 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FOXI1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12372,319,377 - 72,324,442 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2372,321,483 - 72,325,532 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660346,337,152 - 6,342,295 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Foxi1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473319,859,972 - 19,864,359 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473319,860,586 - 19,864,522 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Foxi1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v197,022,360 - 7,026,413 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Foxi1
16 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:157
Count of miRNA genes:122
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000009058
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
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101577675460776754Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101553301273695498Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
737823Alc12Alcohol consumption QTL 124.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101774978420796344Rat
61332Eau3Experimental allergic uveoretinitis QTL 30.004uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)101803578263035782Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101576223019737486Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)101617552561175525Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101866841963668419Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101803578263035782Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
3 1 3 12 11 14 3 51 3 139 55 12 77 30 11 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000009058   ⟹   ENSRNOP00000009058
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1019,310,482 - 19,314,405 (-)Ensembl
mRatBN7.2 Ensembl1018,806,308 - 18,810,231 (-)Ensembl
Rnor_6.0 Ensembl1019,160,582 - 19,164,505 (-)Ensembl
RefSeq Acc Id: NM_001105776   ⟹   NP_001099246
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81019,310,466 - 19,314,405 (-)NCBI
mRatBN7.21018,806,292 - 18,810,231 (-)NCBI
Rnor_6.01019,160,566 - 19,164,505 (-)NCBI
Rnor_5.01019,039,086 - 19,043,025 (-)NCBI
RGSC_v3.41019,185,917 - 19,189,856 (-)RGD
Celera1018,438,984 - 18,442,923 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099246 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM04085 (Get FASTA)   NCBI Sequence Viewer  
  EDM04086 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000009058
  ENSRNOP00000009058.4
RefSeq Acc Id: NP_001099246   ⟸   NM_001105776
- UniProtKB: D4A7G2 (UniProtKB/TrEMBL),   A6HDI0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000009058   ⟸   ENSRNOT00000009058
Protein Domains
Fork-head

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7G2-F1-model_v2 AlphaFold D4A7G2 1-372 view protein structure

Transcriptome

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

Promoters
RGD ID:13697099
Promoter ID:EPDNEW_R7624
Type:single initiation site
Name:Foxi1_1
Description:forkhead box I1
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_6.01019,164,502 - 19,164,562EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307421 AgrOrtholog
BioCyc Gene G2FUF-25588 BioCyc
Ensembl Genes ENSRNOG00000006293 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009058 ENTREZGENE
  ENSRNOT00000009058.8 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
InterPro FOX_domain-containing 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
KEGG Report rno:287185 UniProtKB/TrEMBL
NCBI Gene 287185 ENTREZGENE
PANTHER FORKHEAD BOX PROTEIN UniProtKB/TrEMBL
  PTHR11829:SF180 UniProtKB/TrEMBL
Pfam Fork_head UniProtKB/TrEMBL
PhenoGen Foxi1 PhenoGen
PRINTS FORKHEAD UniProtKB/TrEMBL
PROSITE FORK_HEAD_1 UniProtKB/TrEMBL
  FORK_HEAD_2 UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006293 RatGTEx
SMART SM00339 UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A6HDI0 ENTREZGENE, UniProtKB/TrEMBL
  D4A7G2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Foxi1  forkhead box I1   Foxi1_predicted  forkhead box I1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Foxi1_predicted  forkhead box I1 (predicted)      Symbol and Name status set to approved 70820 APPROVED