Human Gene FOXD3 (ENST00000371116.4) from GENCODE V44
  Description: Homo sapiens forkhead box D3 (FOXD3), mRNA. (from RefSeq NM_012183)
RefSeq Summary (NM_012183): This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. Mutations in this gene cause autoimmune susceptibility 1. [provided by RefSeq, Nov 2008]. ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000371116.4/ ENSP00000360157.2 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Gencode Transcript: ENST00000371116.4
Gencode Gene: ENSG00000187140.6
Transcript (Including UTRs)
   Position: hg38 chr1:63,322,567-63,325,128 Size: 2,562 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg38 chr1:63,323,059-63,324,495 Size: 1,437 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:63,322,567-63,325,128)mRNA (may differ from genome)Protein (478 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Forkhead box protein D3; AltName: Full=HNF3/FH transcription factor genesis;
FUNCTION: Binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3' and acts as a transcriptional repressor. Also acts as a transcriptional activator. Promotes development of neural crest cells from neural tube progenitors. Restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. Required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis.
INTERACTION: Q01860:POU5F1; NbExp=2; IntAct=EBI-475674, EBI-475687;
TISSUE SPECIFICITY: Expressed in chronic myeloid leukemia, Jurkat T-cell leukemia and teratocarcinoma cell lines, but not in any other cell lines or normal tissues examined.
DISEASE: Defects in FOXD3 are associated with susceptibility to autoimmune disease type 1 (AIS1) [MIM:607836]. AIS1 is a disorder characterized by the association of vitiligo with autoimmune thyroiditis (Hashimoto thyroiditis).
SIMILARITY: Contains 1 fork-head DNA-binding domain.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: FOXD3
Diseases sorted by gene-association score: autoimmune disease 1* (593), senile entropion (16), entropion (9), vestibular nystagmus (9), lymphangitis (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.83 RPKM in Nerve - Tibial
Total median expression: 35.50 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 -238.70492-0.485 Picture PostScript Text
3' UTR -171.90633-0.272 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

ModBase Predicted Comparative 3D Structure on Q9UJU5
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
Genome BrowserNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI Ensembl   
Protein Sequence Protein Sequence   
Alignment Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001701 in utero embryonic development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0009653 anatomical structure morphogenesis
GO:0030154 cell differentiation
GO:0035019 somatic stem cell population maintenance
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm

-  Descriptions from all associated GenBank mRNAs
  LF211952 - JP 2014500723-A/19455: Polycomb-Associated Non-Coding RNAs.
MA447529 - JP 2018138019-A/19455: Polycomb-Associated Non-Coding RNAs.
AB464527 - Synthetic construct DNA, clone: pF1KB9598, Homo sapiens FOXD3 gene for forkhead box D3, without stop codon, in Flexi system.
BC172266 - Synthetic construct Homo sapiens clone IMAGE:100068960, MGC:198971 forkhead box D3 (FOXD3) mRNA, encodes complete protein.
BC172572 - Synthetic construct Homo sapiens clone IMAGE:100069266, MGC:199277 forkhead box D3 (FOXD3) mRNA, encodes complete protein.
L12142 - Homo sapiens forkhead homolog mRNA, partial cds.
JD248959 - Sequence 229983 from Patent EP1572962.
AF086235 - Homo sapiens full length insert cDNA clone ZD20D09.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UJU5 (Reactome details) participates in the following event(s):

R-HSA-2892247 POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
R-HSA-452723 Transcriptional regulation of pluripotent stem cells
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000371116.1, ENST00000371116.2, ENST00000371116.3, FOXD3_HUMAN, HFH2, NM_012183, Q9BYM2, Q9UDD1, Q9UJU5, uc001dax.1, uc001dax.2, uc001dax.3, uc001dax.4
UCSC ID: ENST00000371116.4
RefSeq Accession: NM_012183
Protein: Q9UJU5 (aka FOXD3_HUMAN or FXD3_HUMAN)

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