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
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81019,310,466 - 19,314,405 (-)NCBIGRCr8
mRatBN7.21018,806,292 - 18,810,231 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1018,806,308 - 18,810,231 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1023,561,038 - 23,564,983 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01023,049,575 - 23,053,518 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01018,529,590 - 18,533,542 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01019,160,566 - 19,164,505 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1019,160,582 - 19,164,505 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01019,039,086 - 19,043,025 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41019,185,917 - 19,189,856 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11019,188,079 - 19,190,836 (-)NCBI
Celera1018,438,984 - 18,442,923 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction 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. 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 (-)NCBIGRCr8
mRatBN7.21018,806,292 - 18,810,231 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1018,806,308 - 18,810,231 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1023,561,038 - 23,564,983 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01023,049,575 - 23,053,518 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01018,529,590 - 18,533,542 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01019,160,566 - 19,164,505 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1019,160,582 - 19,164,505 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01019,039,086 - 19,043,025 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41019,185,917 - 19,189,856 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11019,188,079 - 19,190,836 (-)NCBI
Celera1018,438,984 - 18,442,923 (-)NCBICelera
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 (+)EnsemblGRCh38hg38GRCh38
GRCh375169,532,901 - 169,536,741 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365169,465,495 - 169,469,307 (+)NCBINCBI36Build 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 Ensembl
GRCm381134,204,341 - 34,208,089 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1134,204,338 - 34,208,089 (-)EnsemblGRCm38mm10GRCm38
MGSCv371134,104,341 - 34,108,089 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha441,713,210 - 41,717,202 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0442,137,160 - 42,141,152 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473319,860,586 - 19,864,522 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Foxi1
31 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
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)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
737823Alc12Alcohol consumption QTL 124.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)101724551319388279Rat
631532Cm50Cardiac mass QTL 506.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)101790711351786432Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat


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

circulatory system endocrine system hemolymphoid system integumental system musculoskeletal system renal system reproductive system respiratory system appendage
High
Medium 21
Low 2 2 10 7
Below cutoff 2 3 3 1 1 2 10 2 1

Sequence


RefSeq Acc Id: ENSRNOT00000009058   ⟹   ENSRNOP00000009058
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
RefSeq 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
  ENSRNOT00000009058.7 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: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