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Aliases for FOXN4 Gene

Aliases for FOXN4 Gene

  • Forkhead Box N4 2 3 5

External Ids for FOXN4 Gene

Previous GeneCards Identifiers for FOXN4 Gene

  • GC12M108775
  • GC12M109554
  • GC12M108180
  • GC12M108178
  • GC12M109715
  • GC12M106733

Summaries for FOXN4 Gene

Entrez Gene Summary for FOXN4 Gene

  • Members of the winged-helix/forkhead family of transcription factors, such as FOXN4, are characterized by a 110-amino acid DNA-binding domain that can fold into a variant of the helix-turn-helix motif consisting of 3 alpha helices flanked by 2 large loops or wings. These transcription factors are involved in a variety of biologic processes as key regulators in development and metabolism (Li et al., 2004 [PubMed 15363391]).[supplied by OMIM, Mar 2008]

GeneCards Summary for FOXN4 Gene

FOXN4 (Forkhead Box N4) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and chromatin binding. An important paralog of this gene is FOXN1.

UniProtKB/Swiss-Prot for FOXN4 Gene

  • Transcription factor essential for neural and some non-neural tissues development, such as retina and lung respectively. Binds to an 11-bp consensus sequence containing the invariant tetranucleotide 5-ACGC-3. During development of the central nervous system, is required to specify the amacrine and horizontal cell fates from multipotent retinal progenitors while suppressing the alternative photoreceptor cell fates through activating DLL4-NOTCH signaling. Also acts synergistically with ASCL1/MASH1 to activate DLL4-NOTCH signaling and drive commitment of p2 progenitors to the V2b interneuron fates during spinal cord neurogenesis. In development of non-neural tissues, plays an essential role in the specification of the atrioventricular canal and is indirectly required for patterning the distal airway during lung development (By similarity).

Additional gene information for FOXN4 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FOXN4 Gene

Genomics for FOXN4 Gene

GeneHancer (GH) Regulatory Elements for FOXN4 Gene

Promoters and enhancers for FOXN4 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
GH12I109310 Promoter 1.1 Ensembl 550.8 +0.5 489 0.4 ZNF2 ZNF335 ZNF213 ZNF416 KLF13 EGR2 SP3 ZNF398 SMARCB1 ZFP69B FOXN4 SART3 TCHP UBE3B PIR60835
GH12I109309 Promoter 0.9 EPDnew 550.8 +1.2 1228 0.1 SP3 L3MBTL2 NRF1 SIN3A REST ZNF335 GLIS2 PATZ1 ZBTB26 ZXDB FOXN4 PIR60835
GH12I109311 Enhancer 0.7 ENCODE 550.8 -1.5 -1521 0.2 NCOA3 PKNOX1 CLOCK NFIB ZNF133 BMI1 CTBP1 GATA3 ZSCAN5C ZNF600 FOXN4 MYO1H ENSG00000255655
GH12I108626 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.6 +671.6 671626 24.2 HDGF PKNOX1 SMAD1 ARNT FEZF1 IRF4 POLR2B ZNF766 CBX5 ZNF207 SELPLG PWP1 SART3 PRDM4 UBE3B RNU4-32P CORO1C FICD LOC101929162 TMEM119
GH12I109347 Enhancer 0.8 FANTOM5 ENCODE 15.9 -37.5 -37513 1.1 CTCF MEIS2 PKNOX1 TEAD4 TAL1 CBFA2T3 DPF2 TCF12 NCOR1 SMARCA4 MYO1H FOXN4 LINC01486
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around FOXN4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FOXN4 gene promoter:

Genomic Locations for FOXN4 Gene

Genomic Locations for FOXN4 Gene
chr12:109,277,978-109,310,490
(GRCh38/hg38)
Size:
32,513 bases
Orientation:
Minus strand
chr12:109,715,783-109,747,025
(GRCh37/hg19)

Genomic View for FOXN4 Gene

Genes around FOXN4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FOXN4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FOXN4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FOXN4 Gene

Proteins for FOXN4 Gene

  • Protein details for FOXN4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96NZ1-FOXN4_HUMAN
    Recommended name:
    Forkhead box protein N4
    Protein Accession:
    Q96NZ1
    Secondary Accessions:
    • Q6ZMR4
    • Q96NZ0

    Protein attributes for FOXN4 Gene

    Size:
    517 amino acids
    Molecular mass:
    55215 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for FOXN4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for FOXN4 Gene

Post-translational modifications for FOXN4 Gene

No Post-translational modifications

Other Protein References for FOXN4 Gene

No data available for DME Specific Peptides for FOXN4 Gene

Domains & Families for FOXN4 Gene

Gene Families for FOXN4 Gene

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

Protein Domains for FOXN4 Gene

Suggested Antigen Peptide Sequences for FOXN4 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FOXN4: view

No data available for UniProtKB/Swiss-Prot for FOXN4 Gene

Function for FOXN4 Gene

Molecular function for FOXN4 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor essential for neural and some non-neural tissues development, such as retina and lung respectively. Binds to an 11-bp consensus sequence containing the invariant tetranucleotide 5-ACGC-3. During development of the central nervous system, is required to specify the amacrine and horizontal cell fates from multipotent retinal progenitors while suppressing the alternative photoreceptor cell fates through activating DLL4-NOTCH signaling. Also acts synergistically with ASCL1/MASH1 to activate DLL4-NOTCH signaling and drive commitment of p2 progenitors to the V2b interneuron fates during spinal cord neurogenesis. In development of non-neural tissues, plays an essential role in the specification of the atrioventricular canal and is indirectly required for patterning the distal airway during lung development (By similarity).

Phenotypes From GWAS Catalog for FOXN4 Gene

Gene Ontology (GO) - Molecular Function for FOXN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001158 enhancer sequence-specific DNA binding ISS --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IEA,ISS 22323600
GO:0003700 DNA binding transcription factor activity ISS,IBA --
GO:0005515 protein binding IPI 27107012
genes like me logo Genes that share ontologies with FOXN4: view
genes like me logo Genes that share phenotypes with FOXN4: view

Animal Models for FOXN4 Gene

MGI Knock Outs for FOXN4:

Animal Model Products

miRNA for FOXN4 Gene

miRTarBase miRNAs that target FOXN4

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for FOXN4 Gene

Localization for FOXN4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOXN4 Gene

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 FOXN4 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitochondria (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FOXN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS,IBA --
genes like me logo Genes that share ontologies with FOXN4: view

Pathways & Interactions for FOXN4 Gene

SuperPathways for FOXN4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for FOXN4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001947 heart looping ISS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated ISS --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with FOXN4: view

No data available for Pathways by source and SIGNOR curated interactions for FOXN4 Gene

Drugs & Compounds for FOXN4 Gene

No Compound Related Data Available

Transcripts for FOXN4 Gene

mRNA/cDNA for FOXN4 Gene

Unigene Clusters for FOXN4 Gene

Forkhead box N4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FOXN4 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11
SP1: -
SP2: - -
SP3:
SP4: - - -

Relevant External Links for FOXN4 Gene

GeneLoc Exon Structure for
FOXN4
ECgene alternative splicing isoforms for
FOXN4

Expression for FOXN4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FOXN4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FOXN4 Gene

This gene is overexpressed in Testis (x29.6) and Cervix - Ectocervix (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of FOXN4 Gene:

FOXN4

SOURCE GeneReport for Unigene cluster for FOXN4 Gene:

Hs.528316

Evidence on tissue expression from TISSUES for FOXN4 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with FOXN4: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for FOXN4 Gene

Orthologs for FOXN4 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for FOXN4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia FOXN4 33 34
  • 99.55 (n)
dog
(Canis familiaris)
Mammalia FOXN4 34 33
  • 88.85 (n)
OneToOne
cow
(Bos Taurus)
Mammalia FOXN4 34 33
  • 88.78 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Foxn4 33
  • 82.31 (n)
mouse
(Mus musculus)
Mammalia Foxn4 33 16 34
  • 81.3 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia FOXN4 34
  • 57 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 12 (a)
ManyToMany
chicken
(Gallus gallus)
Aves FOXN4 33 34
  • 71.36 (n)
lizard
(Anolis carolinensis)
Reptilia FOXN4 34
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia foxn4 33
  • 65.14 (n)
zebrafish
(Danio rerio)
Actinopterygii foxn4 33 34
  • 63.51 (n)
fruit fly
(Drosophila melanogaster)
Insecta jumu 34
  • 19 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FHL1 34
  • 9 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 72 (a)
OneToMany
Species where no ortholog for FOXN4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for FOXN4 Gene

ENSEMBL:
Gene Tree for FOXN4 (if available)
TreeFam:
Gene Tree for FOXN4 (if available)

Paralogs for FOXN4 Gene

Paralogs for FOXN4 Gene

(14) SIMAP similar genes for FOXN4 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with FOXN4: view

Variants for FOXN4 Gene

Sequence variations from dbSNP and Humsavar for FOXN4 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000034527 -- 109,290,698(-) A/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000057991 -- 109,284,644(-) G/A 3_prime_UTR_variant, intron_variant
rs1000206568 -- 109,308,504(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000237766 -- 109,307,989(-) A/C genic_upstream_transcript_variant, intron_variant
rs1000286606 -- 109,284,398(-) G/C 3_prime_UTR_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for FOXN4 Gene

Variant ID Type Subtype PubMed ID
nsv1070126 CNV deletion 25765185
nsv1136154 CNV deletion 24896259

Variation tolerance for FOXN4 Gene

Residual Variation Intolerance Score: 74% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.74; 46.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FOXN4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
FOXN4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FOXN4 Gene

Disorders for FOXN4 Gene

Additional Disease Information for FOXN4

No disorders were found for FOXN4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for FOXN4 Gene

Publications for FOXN4 Gene

  1. The finished DNA sequence of human chromosome 12. (PMID: 16541075) Scherer SE … Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team (Nature 2006) 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. Expression of the winged helix/forkhead gene, foxn4, during zebrafish development. (PMID: 15464224) Danilova N … Steiner LA (Brain research. Developmental brain research 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Pooled-matrix protein interaction screens using Barcode Fusion Genetics. (PMID: 27107012) Yachie N … Roth FP (Molecular systems biology 2016) 3 58

Products for FOXN4 Gene

Sources for FOXN4 Gene

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