Foxi3 (forkhead box I3) - Rat Genome Database

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Gene: Foxi3 (forkhead box I3) Mus musculus
Analyze
Symbol: Foxi3
Name: forkhead box I3
RGD ID: 9586081
MGI Page MGI
Description: Enables DNA-binding transcription factor activity, RNA polymerase II-specific. Involved in several processes, including otic placode development; parathyroid gland development; and pharyngeal system development. Is active in nucleus. Is expressed in several structures, including alimentary system; branchial arch; exocrine system; integumental system; and sensory organ. Used to study Goldenhar syndrome. Orthologous to human FOXI3 (forkhead box I3).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: forkhead box protein I3
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39670,933,590 - 70,938,050 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl670,933,515 - 70,938,050 (+)EnsemblGRCm39 Ensembl
GRCm38670,956,606 - 70,961,066 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl670,956,531 - 70,961,066 (+)EnsemblGRCm38mm10GRCm38
MGSCv37670,906,600 - 70,911,060 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36670,886,038 - 70,890,642 (+)NCBIMGSCv36mm8
Celera673,035,029 - 73,039,489 (+)NCBICelera
Cytogenetic Map6C1NCBI
cM Map632.14NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IDA,ISO)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal cranium morphology  (IAGP)
abnormal facial morphology  (IAGP)
abnormal geniculate ganglion morphology  (IAGP)
abnormal mandible morphology  (IAGP)
abnormal maxilla morphology  (IAGP)
abnormal Meckel's cartilage morphology  (IAGP)
abnormal middle ear morphology  (IAGP)
abnormal nervous system development  (IAGP)
abnormal neurocranium morphology  (IAGP)
abnormal otic placode morphology  (IAGP)
abnormal palatine bone morphology  (IAGP)
abnormal pharyngeal pouch morphology  (IAGP)
abnormal respiration  (IAGP)
abnormal retrotympanic process morphology  (IAGP)
abnormal stapes morphology  (IAGP)
abnormal temporal bone morphology  (IAGP)
abnormal temporal bone squamous part morphology  (IAGP)
abnormal trigeminal ganglion morphology  (IAGP)
abnormal vestibulocochlear ganglion morphology  (IAGP)
abnormal zygomatic bone morphology  (IAGP)
absent incus  (IAGP)
absent inner ear  (IAGP)
absent malleus  (IAGP)
absent mouth  (IAGP)
absent outer ear  (IAGP)
absent pharyngeal arches  (IAGP)
absent stapes  (IAGP)
absent tympanic ring  (IAGP)
absent vibrissae  (IAGP)
absent zygomatic bone  (IAGP)
athymia  (IAGP)
cleft palate  (IAGP)
craniofacial asymmetry  (IAGP)
cranioschisis  (IAGP)
decreased birth body size  (IAGP)
decreased birth weight  (IAGP)
decreased body weight  (IAGP)
decreased mouth size  (IAGP)
embryonic lethality during organogenesis, incomplete penetrance  (IAGP)
increased cranial neural crest cell apoptosis  (IAGP)
increased embryonic tissue cell apoptosis  (IAGP)
neonatal lethality, complete penetrance  (IAGP)
no abnormal phenotype detected  (IAGP)
postnatal lethality, complete penetrance  (IAGP)
pterygoid bone hypoplasia  (IAGP)
small ears  (IAGP)
small face  (IAGP)
syngnathia  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Mouse MP Annotation Import Pipeline RGD automated import pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12466851   PMID:15376323   PMID:16530750   PMID:18787161   PMID:20171206   PMID:21873635   PMID:23441037   PMID:24650709   PMID:26450968   PMID:26550799   PMID:26581094   PMID:26952977  
PMID:26992132   PMID:30467319   PMID:31412026   PMID:34432485   PMID:37041148   PMID:37307487   PMID:37543988   PMID:37756587   PMID:38113115   PMID:38433559  


Genomics

Comparative Map Data
Foxi3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39670,933,590 - 70,938,050 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl670,933,515 - 70,938,050 (+)EnsemblGRCm39 Ensembl
GRCm38670,956,606 - 70,961,066 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl670,956,531 - 70,961,066 (+)EnsemblGRCm38mm10GRCm38
MGSCv37670,906,600 - 70,911,060 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36670,886,038 - 70,890,642 (+)NCBIMGSCv36mm8
Celera673,035,029 - 73,039,489 (+)NCBICelera
Cytogenetic Map6C1NCBI
cM Map632.14NCBI
FOXI3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38288,446,787 - 88,452,693 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl288,446,787 - 88,452,693 (-)EnsemblGRCh38hg38GRCh38
GRCh37288,746,306 - 88,752,211 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36288,520,284 - 88,539,630 (-)NCBINCBI36Build 36hg18NCBI36
Celera288,034,019 - 88,038,349 (+)NCBICelera
Cytogenetic Map2p11.2NCBI
HuRef287,669,933 - 87,673,975 (-)NCBIHuRef
CHM1_1288,677,039 - 88,681,361 (-)NCBICHM1_1
T2T-CHM13v2.0288,458,787 - 88,464,693 (-)NCBIT2T-CHM13v2.0
Foxi3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84104,491,834 - 104,496,008 (+)NCBIGRCr8
mRatBN7.24102,933,487 - 102,937,655 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4102,933,409 - 102,937,655 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4108,324,289 - 108,328,469 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04104,099,378 - 104,103,558 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04102,703,383 - 102,707,551 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0498,775,908 - 98,780,082 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl498,775,908 - 98,780,082 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04163,554,654 - 163,558,828 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44104,145,540 - 104,149,714 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera492,109,460 - 92,113,635 (+)NCBICelera
Cytogenetic Map4q32NCBI
Foxi3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955424356,951 - 358,221 (+)NCBIChiLan1.0ChiLan1.0
FOXI3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21238,850,151 - 38,858,814 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A38,852,932 - 38,861,563 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A87,578,732 - 87,585,111 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A89,488,473 - 89,493,839 (-)NCBIpanpan1.1PanPan1.1panPan2
FOXI3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11738,032,479 - 38,036,424 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1738,032,479 - 38,037,630 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1737,717,638 - 37,721,642 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01738,764,819 - 38,768,812 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1738,764,363 - 38,770,015 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11737,931,650 - 37,935,639 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01737,967,970 - 37,971,967 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01738,315,971 - 38,319,969 (+)NCBIUU_Cfam_GSD_1.0
Foxi3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629280,335,534 - 80,340,880 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936712517,562 - 522,925 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936712517,566 - 522,709 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FOXI3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl357,586,485 - 57,590,344 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1357,586,669 - 57,590,366 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2360,254,441 - 60,256,594 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FOXI3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11418,310,904 - 18,317,115 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1418,312,661 - 18,317,033 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660801,456,094 - 1,463,940 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Foxi3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474916,033,767 - 16,039,249 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474916,033,754 - 16,041,679 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Foxi3
231 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:142
Count of miRNA genes:65
Interacting mature miRNAs:70
Transcripts:ENSMUST00000069634, ENSMUST00000163089
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396633110Mouse
1301266Lmr4_mleishmaniasis resistance 4 (mouse)Not determined64209335876093500Mouse
26884441Sklq3_mskull length QTL 3, 5 week (mouse)6760000080576983Mouse
12910785Pwgrq16_mpost-weaning growth rate QTL 16 (mouse)64380374777788506Mouse
4140983Srilp_msleep response to influenza, light phase (mouse)Not determined4870349075424693Mouse
10412119Stv_mstriatal volumne (mouse)Not determined660026991100026967Mouse
12910798Pwgrq5_mpre-weaning growth rate QTL 5 (mouse)64380374777788506Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46912919136400690Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648696934125336963Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396633110Mouse
14746995Manh60_mmandible shape 60 (mouse)63720266271202662Mouse
12910807Pwbwq11_mpost-weaning body weight QTL 11 (mouse)64380374777788506Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648696934148351498Mouse
1301254Skts11_mskin tumor susceptibility 11 (mouse)Not determined65115613485156284Mouse
1357442Dbts1_mdiabetes 1 (mouse)Not determined61823414773364675Mouse
1558977Skmw10_mskeletal muscle weight 10 (mouse)Not determined65842456692424693Mouse
12910802Pwbwq12_mpost-weaning body weight QTL 12 (mouse)64380374777788506Mouse
1300618Pgia19_mproteoglycan induced arthritis 19 (mouse)Not determined64529099387403016Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648703490125333748Mouse
4141028Mclr_mmethylcholanthrene lymphoma resistance (mouse)Not determined5435041188356155Mouse
12910809Pwbwq10_mpost-weaning body weight QTL 10 (mouse)64380374777788506Mouse
1301326Trbv4c2_mT cell receptor beta variable 4 (mouse)Not determined64086823071356155Mouse
10043972Obq28_mobesity QTL 28 (mouse)Not determined65851741692517416Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487403016Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63864656092584431Mouse
12910820Ogrq3_moverall growth rate QTL 3 (mouse)64380374777788506Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645290993128811995Mouse
25440480Moaq2_mmodifier of alien QTL 2 (mouse)63050001117476961Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139076998Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396633110Mouse
1301813Skl3_mskeletal size (tail length) 3 (mouse)Not determined670402880104403016Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396633110Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652138693116132228Mouse
1301876Bits2_mbitterness sensitivity 2 (mouse)Not determined670402880104403016Mouse
15039373Adip28_madiposity 28 (mouse)65628519490285194Mouse
4141782Mrdq5_mmodifier of retinal degeneration QTL 5 (mouse)Not determined3282758578215957Mouse
15039375Bw41_mbody weight QTL 41 (mouse)65628519490285194Mouse
1301369Im4_mimmunoregulatory 4 (mouse)Not determined66346172197461888Mouse
10412213Sxbq2_mSGC/Knj cross B6 QTL 2 (mouse)Not determined61991268571299759Mouse
12880424V25Dq4_mvitamin D inactive form serum level QTL 4 (mouse)64157698575576985Mouse
11040600Lmr4c_mleishmaniasis resistance 4c (mouse)64209335876093500Mouse
11040601Lmr4a_mleishmaniasis resistance 4a (mouse)64209335876093500Mouse
11533915Mts4_mmammary tumor susceptibility 4 (mouse)64209335876093500Mouse
10043885Cia6c_mcollagen induced arthritis QTL 6c (mouse)Not determined64444280571096451Mouse
1300650Bw18_mbody weight QTL 18 (mouse)Not determined666690851100691013Mouse
1301034Egrm2_mearly growth rate (mouse)Not determined670402880104403016Mouse
13208564Bmiq7_mbody mass index QTL 7 (mouse)62499999979976983Mouse
1301740Bwq2_mbody weight QTL 2 (mouse)Not determined66003466394034782Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000069634   ⟹   ENSMUSP00000065664
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl670,933,590 - 70,938,050 (+)Ensembl
GRCm38.p6 Ensembl670,956,606 - 70,961,066 (+)Ensembl
Ensembl Acc Id: ENSMUST00000163089   ⟹   ENSMUSP00000125380
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl670,933,515 - 70,938,047 (+)Ensembl
GRCm38.p6 Ensembl670,956,531 - 70,961,063 (+)Ensembl
RefSeq Acc Id: NM_001101464   ⟹   NP_001094934
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39670,933,590 - 70,938,050 (+)NCBI
GRCm38670,956,606 - 70,961,066 (+)NCBI
Celera673,035,029 - 73,039,489 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001094934 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3Z120 (Get FASTA)   NCBI Sequence Viewer  
  EDK98929 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000065664
  ENSMUSP00000065664.6
  ENSMUSP00000125380.2
RefSeq Acc Id: NP_001094934   ⟸   NM_001101464
- UniProtKB: E0CZH3 (UniProtKB/Swiss-Prot),   D3Z120 (UniProtKB/Swiss-Prot),   A0A9S4I865 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000125380   ⟸   ENSMUST00000163089
Ensembl Acc Id: ENSMUSP00000065664   ⟸   ENSMUST00000069634
Protein Domains
Fork-head

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E0CZH3-F1-model_v2 AlphaFold E0CZH3 1-425 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3511278 AgrOrtholog
Ensembl Genes ENSMUSG00000055874 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000069634 ENTREZGENE
  ENSMUST00000069634.6 UniProtKB/Swiss-Prot
  ENSMUST00000163089.2 UniProtKB/TrEMBL
Gene3D-CATH Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Fork_head_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FOX_domain-containing UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_fork_head_CS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_fork_head_CS_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:232077 UniProtKB/Swiss-Prot
MGD MGI:3511278 ENTREZGENE
NCBI Gene Foxi3 ENTREZGENE
PANTHER FORKHEAD BOX PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FORKHEAD BOX PROTEIN I3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Forkhead UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Foxi3 PhenoGen
PRINTS FORKHEAD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE FORK_HEAD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FORK_HEAD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FORK_HEAD_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00339 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Winged helix' DNA-binding domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A9S4I865 ENTREZGENE, UniProtKB/TrEMBL
  D3Z120 ENTREZGENE
  E0CZH3 ENTREZGENE
  FOXI3_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary E0CZH3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-05-18 Foxi3  forkhead box I3  Foxi3  forkhead box I3  Data merged from RGD:1608238 737654 PROVISIONAL