Human Gene FOXI1 (uc003mai.4) Description and Page Index
  Description: Homo sapiens forkhead box I1 (FOXI1), transcript variant 1, mRNA.
RefSeq Summary (NM_012188): This gene belongs to the forkhead family of transcription factors, which is characterized by a distinct forkhead domain. This gene may play an important role in the development of the cochlea and vestibulum, as well as in embryogenesis. The encoded protein has been found to be required for the transcription of four subunits of a proton pump found in the inner ear, the kidney, and the epididymis. Mutations in this gene have been associated with deafness, autosomal recessive 4. [provided by RefSeq, Jan 2017].
Transcript (Including UTRs)
   Position: hg19 chr5:169,532,917-169,536,729 Size: 3,813 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr5:169,532,962-169,535,615 Size: 2,654 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr5:169,532,917-169,536,729)mRNA (may differ from genome)Protein (378 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Forkhead box protein I1; AltName: Full=Forkhead-related protein FKHL10; AltName: Full=Forkhead-related transcription factor 6; Short=FREAC-6; AltName: Full=Hepatocyte nuclear factor 3 forkhead homolog 3; Short=HFH-3; Short=HNF-3/fork-head homolog 3;
FUNCTION: Transcriptional activator required for the development of normal hearing, sense of balance and kidney function. Required for the expression of SLC26A4/PDS, JAG1 and COCH in a subset of epithelial cells and the development of the endolymphatic system in the inner ear. Also required for the expression of SLC4A1/AE1, SLC4A9/AE4, ATP6V1B1 and the differentiation of intercalated cells in the epithelium of distal renal tubules (By similarity).
TISSUE SPECIFICITY: Expressed in kidney.
SIMILARITY: Contains 1 fork-head DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAB50574.1; Type=Erroneous initiation; Sequence=AAU12169.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): FOXI1
CDC HuGE Published Literature: FOXI1

-  MalaCards Disease Associations
  MalaCards Gene Search: FOXI1
Diseases sorted by gene-association score: deafness, autosomal recessive 4, with enlarged vestibular aqueduct* (655), pendred syndrome* (548), foxi1-related pendred syndrome* (100), vestibular disease (10), ichthyosis, congenital, autosomal recessive 11 (6), nonsyndromic deafness (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.42 RPKM in Kidney - Cortex
Total median expression: 28.62 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -19.7045-0.438 Picture PostScript Text
3' UTR -379.681114-0.341 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001766 - TF_fork_head
IPR018122 - TF_fork_head_CS
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00250 - Forkhead domain

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q12951
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Protein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0008301 DNA binding, bending
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0009653 anatomical structure morphogenesis
GO:0009792 embryo development ending in birth or egg hatching
GO:0030154 cell differentiation
GO:0042472 inner ear morphogenesis
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0043231 intracellular membrane-bounded organelle

-  Descriptions from all associated GenBank mRNAs
  AK292176 - Homo sapiens cDNA FLJ76677 complete cds, highly similar to Homo sapiens forkhead box I1 (FOXI1), transcript variant 1, mRNA.
BC029778 - Homo sapiens forkhead box I1, mRNA (cDNA clone MGC:34197 IMAGE:5185923), complete cds.
AB464531 - Synthetic construct DNA, clone: pF1KB8982, Homo sapiens FOXI1 gene for forkhead box I1, without stop codon, in Flexi system.
KJ896821 - Synthetic construct Homo sapiens clone ccsbBroadEn_06215 FOXI1 gene, encodes complete protein.
KR712034 - Synthetic construct Homo sapiens clone CCSBHm_00034979 FOXI1 (FOXI1) mRNA, encodes complete protein.
L13203 - Homo sapiens forkhead box L1 (Foxl1) mRNA, complete cds.
AY707089 - Homo sapiens FOXI1 protein mRNA, complete cds.
JD224192 - Sequence 205216 from Patent EP1572962.
JD442702 - Sequence 423726 from Patent EP1572962.
JD050616 - Sequence 31640 from Patent EP1572962.
JD097241 - Sequence 78265 from Patent EP1572962.
JD313595 - Sequence 294619 from Patent EP1572962.
JD535128 - Sequence 516152 from Patent EP1572962.
JD280479 - Sequence 261503 from Patent EP1572962.
JD449138 - Sequence 430162 from Patent EP1572962.
JD308561 - Sequence 289585 from Patent EP1572962.
JD228123 - Sequence 209147 from Patent EP1572962.
JD064724 - Sequence 45748 from Patent EP1572962.
JD291821 - Sequence 272845 from Patent EP1572962.
JD243790 - Sequence 224814 from Patent EP1572962.
JD046770 - Sequence 27794 from Patent EP1572962.
JD060110 - Sequence 41134 from Patent EP1572962.
JD364014 - Sequence 345038 from Patent EP1572962.
JD563640 - Sequence 544664 from Patent EP1572962.
JD450696 - Sequence 431720 from Patent EP1572962.
JD420055 - Sequence 401079 from Patent EP1572962.
JD063954 - Sequence 44978 from Patent EP1572962.
JD102298 - Sequence 83322 from Patent EP1572962.
JD558660 - Sequence 539684 from Patent EP1572962.
JD283547 - Sequence 264571 from Patent EP1572962.
JD121647 - Sequence 102671 from Patent EP1572962.
JD281882 - Sequence 262906 from Patent EP1572962.
JD380533 - Sequence 361557 from Patent EP1572962.
JD457103 - Sequence 438127 from Patent EP1572962.
JD511961 - Sequence 492985 from Patent EP1572962.
JD343306 - Sequence 324330 from Patent EP1572962.
JD456644 - Sequence 437668 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: FKHL10, FOXI1_HUMAN, FREAC6, NM_012188, NP_036320, Q12951, Q14518, Q66SR7, Q8N6L8
UCSC ID: uc003mai.4
RefSeq Accession: NM_012188
Protein: Q12951 (aka FOXI1_HUMAN or FXI1_HUMAN)
CCDS: CCDS4372.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene FOXI1:
hered-drta (Hereditary Distal Renal Tubular Acidosis)
pendred (Pendred Syndrome/Nonsyndromic Enlarged Vestibular Aqueduct)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_012188.4
exon count: 2CDS single in 3' UTR: no RNA size: 2296
ORF size: 1137CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2474.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.