FOXD3 Gene (Protein Coding)

Forkhead Box D3

GC01P063323
GIFtS:
42
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] See more...

Aliases for FOXD3 Gene

Aliases for FOXD3 Gene

  • Forkhead Box D3 2 3 5
  • HFH2 2 3 4
  • HNF3/FH Transcription Factor Genesis 3 4
  • Forkhead Box Protein D3 3 4
  • Genesis 2 3
  • VAMAS2 3
  • FOXD3 5
  • AIS1 3

External Ids for FOXD3 Gene

Previous GeneCards Identifiers for FOXD3 Gene

  • GC01P063723
  • GC01P062711
  • GC01P063146
  • GC01P063158
  • GC01P063500
  • GC01P063561
  • GC01P063788
  • GC01P061896

Summaries for FOXD3 Gene

Entrez Gene Summary for FOXD3 Gene

  • 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]

GeneCards Summary for FOXD3 Gene

FOXD3 (Forkhead Box D3) is a Protein Coding gene. Diseases associated with FOXD3 include Autoimmune Disease 1 and Hashimoto Thyroiditis. Among its related pathways are Neural Crest Differentiation and Wnt / Hedgehog / Notch. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription regulatory region DNA binding. An important paralog of this gene is FOXD1.

UniProtKB/Swiss-Prot Summary for FOXD3 Gene

  • 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.

Gene Wiki entry for FOXD3 Gene

Additional gene information for FOXD3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for FOXD3 Gene

Genomics for FOXD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for FOXD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH01J063319 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE 252.3 +1.0 952 7.8 ZBTB10 FEZF1 MNT ETS1 BHLHE40 ZIC2 ZNF610 ZNF623 REST FOXA2 FOXD3 FOXD3-AS1 NONHSAG001697.2 lnc-FOXD3-4 ENSG00000236674 ALG6 HSALNG0004108 MIR6068
GH01J063522 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 10.7 +200.8 200761 3.1 ZSCAN16 CHD2 TBP SP1 ZBTB10 MXD4 FEZF1 CEBPA SIX5 NR2C1 ITGB3BP EFCAB7 ALG6 FOXD3-AS1 FOXD3 ENSG00000235545 ROR1 DOCK7 ENSG00000236674 RF00017-234
GH01J063294 Enhancer 0.8 Ensembl ENCODE dbSUPER 12.3 -27.5 -27466 2.2 ETS1 SP1 SIN3A CEBPB POU5F1 NANOG POLR2A LINC00466 FOXD3 FOXD3-AS1 ENSG00000236674 ALG6 piR-52966-001 ATG4C
GH01J063316 Promoter/Enhancer 1.2 Ensembl ENCODE 0.4 -5.0 -5002 2.8 ZBTB10 ETS1 CTCF ZEB1 ZIC2 ZNF610 SIN3A REST CUX1 VEZF1 LINC00466 HSALNG0004108 ITGB3BP USP1 FOXD3 ATG4C
GH01J063366 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 0.3 +44.9 44943 2.6 ZSCAN16 TBP SMAD5 MBD2 POLR2A ELF1 ZNF610 SIN3A ZNF395 REST ALG6 ITGB3BP LOC441887 FOXD3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FOXD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for FOXD3

Top Transcription factor binding sites by QIAGEN in the FOXD3 gene promoter:
  • CUTL1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • LCR-F1
  • Lhx3a
  • LHX3b

Genomic Locations for FOXD3 Gene

Latest Assembly
chr1:63,322,567-63,325,128
(GRCh38/hg38)
Size:
2,562 bases
Orientation:
Plus strand

Previous Assembly
chr1:63,788,238-63,790,799
(GRCh37/hg19 by Entrez Gene)
Size:
2,562 bases
Orientation:
Plus strand

chr1:63,788,730-63,790,797
(GRCh37/hg19 by Ensembl)
Size:
2,068 bases
Orientation:
Plus strand

Genomic View for FOXD3 Gene

Genes around FOXD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FOXD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FOXD3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for FOXD3 Gene

Proteins for FOXD3 Gene

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  • Protein details for FOXD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UJU5-FOXD3_HUMAN
    Recommended name:
    Forkhead box protein D3
    Protein Accession:
    Q9UJU5
    Secondary Accessions:
    • Q9BYM2
    • Q9UDD1

    Protein attributes for FOXD3 Gene

    Size:
    478 amino acids
    Molecular mass:
    47630 Da
    Quaternary structure:
    • Interacts with POU5F1.

neXtProt entry for FOXD3 Gene

Post-translational modifications for FOXD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FOXD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for FOXD3 Gene

Domains & Families for FOXD3 Gene

Gene Families for FOXD3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for FOXD3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for FOXD3 Gene

GenScript: Design optimal peptide antigens:
  • HNF3/FH transcription factor genesis (FOXD3_HUMAN)
genes like me logo Genes that share domains with FOXD3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for FOXD3 Gene

Function for FOXD3 Gene

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  2. CRISPR products for research
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  6. Cell Lines for research

Molecular function for FOXD3 Gene

UniProtKB/Swiss-Prot 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.
GENATLAS Biochemistry:
transcription factor-like,restrictively expressed in hematopoietic cells,with a Drosophila homeo fork head DNA binding domain,mouse hepatocyte nuclear factor 3 homolog

Phenotypes From GWAS Catalog for FOXD3 Gene

Gene Ontology (GO) - Molecular Function for FOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 22306510
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 22306510
GO:0003677 DNA binding IEA --
genes like me logo Genes that share ontologies with FOXD3: view
genes like me logo Genes that share phenotypes with FOXD3: view

Human Phenotype Ontology for FOXD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for FOXD3 Gene

MGI Knock Outs for FOXD3:

Animal Models for research

miRNA for FOXD3 Gene

miRTarBase miRNAs that target FOXD3

Transcription Factor Targets for FOXD3 Gene

Selected GeneGlobe predicted Target genes for FOXD3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FOXD3

No data available for Enzyme Numbers (IUBMB) and HOMER Transcription for FOXD3 Gene

Localization for FOXD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOXD3 Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FOXD3 gene
Compartment Confidence
nucleus 5
plasma membrane 2
extracellular 2
cytoskeleton 2
cytosol 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for FOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA,ISA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with FOXD3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for FOXD3 Gene

Pathways & Interactions for FOXD3 Gene

genes like me logo Genes that share pathways with FOXD3: view

Pathways by source for FOXD3 Gene

3 Qiagen pathways for FOXD3 Gene
  • Nanog in Mammalian ESC Pluripotency
  • Oct4 in Mammalian ESC Pluripotency
  • Transcriptional Regulatory Network in Embryonic Stem Cell
1 Cell Signaling Technology pathway for FOXD3 Gene

Gene Ontology (GO) - Biological Process for FOXD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA,ISS --
GO:0001701 in utero embryonic development ISS --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with FOXD3: view

No data available for SIGNOR curated interactions for FOXD3 Gene

Drugs & Compounds for FOXD3 Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for FOXD3 Gene

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  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for FOXD3 Gene

1 REFSEQ mRNAs :
2 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FOXD3

Alternative Splicing Database (ASD) splice patterns (SP) for FOXD3 Gene

No ASD Table

Relevant External Links for FOXD3 Gene

GeneLoc Exon Structure for
FOXD3

Expression for FOXD3 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for FOXD3 Gene

mRNA expression in normal human tissues for FOXD3 Gene
mRNA expression by GTEx for FOXD3 GenemRNA expression by BioGPS for FOXD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FOXD3 Gene

This gene is overexpressed in Nerve - Tibial (x20.9) and Colon - Sigmoid (x4.1).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for FOXD3

SOURCE GeneReport for Unigene cluster for FOXD3 Gene:

Hs.546573

mRNA Expression by UniProt/SwissProt for FOXD3 Gene:

Q9UJU5-FOXD3_HUMAN
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.

Evidence on tissue expression from TISSUES for FOXD3 Gene

  • Nervous system(2.7)
  • Skin(2.7)
  • Muscle(2.4)
  • Heart(2.3)
  • Kidney(2.1)
  • Lung(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for FOXD3 Gene

Germ Layers:
  • ectoderm
Systems:
  • integumentary
Regions:
General:
  • skin
genes like me logo Genes that share expression patterns with FOXD3: view

Primer products for research

No data available for Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for FOXD3 Gene

Orthologs for FOXD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for FOXD3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia FOXD3 30 31
  • 99.37 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia FOXD3 30 31
  • 91.01 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia FOXD3 30 31
  • 89.26 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Foxd3 30
  • 87.41 (n)
Mouse
(Mus musculus)
 Mammalia Foxd3 30 17 31
  • 85.91 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia FOXD3 31
  • 71 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia foxd3 30
  • 76.85 (n)
Str.11302 30
African clawed frog
(Xenopus laevis)
 Amphibia foxd3b-A 30
Zebrafish
(Danio rerio)
 Actinopterygii foxd3 30 31
  • 74.98 (n)
 OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.3286 30
Fruit Fly
(Drosophila melanogaster)
 Insecta fd96Cb 32
  • 45 (a)
fd59A 31 32
  • 29 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea unc-130 31 32
  • 35 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.2032 31
  • 29 (a)
 ManyToMany
-- 31
  • 28 (a)
 ManyToMany
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.311 30
Species where no ortholog for FOXD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for FOXD3 Gene

ENSEMBL:
Gene Tree for FOXD3 (if available)
TreeFam:
Gene Tree for FOXD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for FOXD3: view image

Paralogs for FOXD3 Gene

Paralogs for FOXD3 Gene

(8) SIMAP similar genes for FOXD3 Gene using alignment to 1 proteins:

  • FOXD3_HUMAN
genes like me logo Genes that share paralogs with FOXD3: view

Variants for FOXD3 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for FOXD3 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs114453593 Benign: not provided 63,323,697(+) C/T
NM_012183.3(FOXD3):c.639C>T (p.Asn213=) 		SYNONYMOUS

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for FOXD3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for FOXD3 Gene

Variant ID Type Subtype PubMed ID
nsv461672 CNV gain 19166990
nsv470714 CNV gain 18288195
nsv546433 CNV gain 21841781

Variation tolerance for FOXD3 Gene

Gene Damage Index Score: 4.26; 62.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FOXD3 Gene

Human Gene Mutation Database (HGMD)
FOXD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
FOXD3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FOXD3 Gene

Disorders for FOXD3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for FOXD3 Gene - From: OMI, CVR, GTR, COP, and GCD

Disorder Aliases PubMed IDs
autoimmune disease 1
  • autoimmune disease, susceptibility to, 1
hashimoto thyroiditis
  • ht
charcot-marie-tooth disease, axonal, type 2e
  • cmt2e
waardenburg's syndrome
  • van der hoeve halbertsona waardenburg syndrome
persistent hyperplastic primary vitreous
  • congenital retinal detachment
- elite association - COSMIC cancer census association via MalaCards
Search FOXD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

FOXD3_HUMAN
  • Autoimmune disease 1 (AIS1) [MIM:607836]: An autoimmune disorder characterized by the association of vitiligo with autoimmune thyroiditis (Hashimoto thyroiditis). {ECO:0000269 PubMed:16098053}. Note=Disease susceptibility is associated with variants affecting the gene represented in this entry.

Additional Disease Information for FOXD3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with FOXD3: view

No data available for Genatlas for FOXD3 Gene

Publications for FOXD3 Gene

  1. Candidate functional promoter variant in the FOXD3 melanoblast developmental regulator gene in autosomal dominant vitiligo. (PMID: 16098053) Alkhateeb A … Spritz RA (The Journal of investigative dermatology 2005) 3 4 74
  2. Drosophila forkhead homologues are expressed in a lineage-restricted manner in human hematopoietic cells. (PMID: 8499623) Hromas R … Klemsz M (Blood 1993) 2 3 4
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  4. The embryonic stem cell transcription factors Oct-4 and FoxD3 interact to regulate endodermal-specific promoter expression. (PMID: 11891324) Guo Y … Hromas R (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 4
  5. LncRNA FOXD3-AS1 Mediates AKT Pathway to Promote Growth and Invasion in Hepatocellular Carcinoma Through Regulating RICTOR. (PMID: 32191537) Liu C … Zhang R (Cancer biotherapy & radiopharmaceuticals 2020) 3

ExternalLinks

View latest publications for FOXD3 gene in Mastermind

Products for FOXD3 Gene

  • Addgene plasmids for FOXD3

Sources for FOXD3 Gene