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FOXN4 forkhead box N4 [ Homo sapiens (human) ]

Gene ID: 121643, updated on 3-Apr-2024

Summary

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Official Symbol
FOXN4provided by HGNC
Official Full Name
forkhead box N4provided by HGNC
Primary source
HGNC:HGNC:21399
See related
Ensembl:ENSG00000139445 MIM:609429; AllianceGenome:HGNC:21399
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Restricted expression toward testis (RPKM 2.5) See more
Orthologs
mouse all
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Genomic context

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Location:
12q24.11
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (109277978..109309284, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (109252960..109284245, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (109715783..109747089, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109548634-109549184 Neighboring gene uncharacterized LOC105369974 Neighboring gene uracil DNA glycosylase Neighboring gene acetyl-CoA carboxylase beta Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4839 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109677215-109677716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109677717-109678216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6984 Neighboring gene Sharpr-MPRA regulatory region 176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109722785-109723628 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:109725470-109725629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109725794-109726403 Neighboring gene MPRA-validated peak1938 silencer Neighboring gene Sharpr-MPRA regulatory region 9197 Neighboring gene MPRA-validated peak1941 silencer Neighboring gene myosin IH Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6985 Neighboring gene long intergenic non-protein coding RNA 1486 Neighboring gene MPRA-validated peak1943 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109871570-109872074 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109896331-109897136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109897944-109898749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109898750-109899556 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109900363-109901169 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:109914018-109914753 Neighboring gene potassium channel tetramerization domain containing 10

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Characterization of human FOXN4 gene in silico. Katoh M, et al. Int J Mol Med, 2004 Nov. PMID 15492871
  2. Expression of the winged helix/forkhead gene, foxn4, during zebrafish development. Danilova N, et al. Brain Res Dev Brain Res, 2004 Oct 15. PMID 15464224
  3. Foxn4 controls the genesis of amacrine and horizontal cells by retinal progenitors. Li S, et al. Neuron, 2004 Sep 16. PMID 15363391
  4. Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors. Luo H, et al. Proc Natl Acad Sci U S A, 2012 Feb 28. PMID 22323600, Free PMC Article
  5. Rnf220 cooperates with Zc4h2 to specify spinal progenitor domains. Kim J, et al. Development, 2018 Sep 3. PMID 30177510

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FOXN4 affects myocardial ischemia-reperfusion injury through HIF-1alpha/MMP2-mediated ferroptosis of cardiomyocytes.
    Title: FOXN4 affects myocardial ischemia-reperfusion injury through HIF-1α/MMP2-mediated ferroptosis of cardiomyocytes.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ35967

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
  
enables chromatin binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables cis-regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in amacrine cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in atrioventricular canal development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in heart looping ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of heart contraction ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in retina layer formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in ventral spinal cord interneuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in ventral spinal cord interneuron fate commitment ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
forkhead box protein N4
Names
forkhead/winged helix transcription factor FOXN4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_213596.3 → NP_998761.2  forkhead box protein N4

    See identical proteins and their annotated locations for NP_998761.2

    Status: VALIDATED

    Source sequence(s)
    AA421288, AC012384, AF425596, AK131519, BC146825
    Consensus CDS
    CCDS9126.2
    UniProtKB/Swiss-Prot
    Q6ZMR4, Q96NZ0, Q96NZ1
    UniProtKB/TrEMBL
    A6H901
    Related
    ENSP00000299162.5, ENST00000299162.10
    Conserved Domains (2) summary
    pfam00250
    Location:193 → 280
    Forkhead; Forkhead domain
    pfam14650
    Location:317 → 397
    FAM75; FAM75 family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    109277978..109309284 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537922.3 → XP_011536224.1  forkhead box protein N4 isoform X1

    See identical proteins and their annotated locations for XP_011536224.1

    UniProtKB/TrEMBL
    A6H901
    Conserved Domains (2) summary
    pfam00250
    Location:194 → 281
    Forkhead; Forkhead domain
    pfam14650
    Location:318 → 398
    FAM75; FAM75 family

  2. XM_047428311.1 → XP_047284267.1  forkhead box protein N4 isoform X3

  3. XM_017018818.2 → XP_016874307.1  forkhead box protein N4 isoform X2

    UniProtKB/TrEMBL
    A6H901

  4. XM_011537923.3 → XP_011536225.1  forkhead box protein N4 isoform X4

    Conserved Domains (1) summary
    pfam00250
    Location:194 → 281
    Forkhead; Forkhead domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    109252960..109284245 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371121.1 → XP_054227096.1  forkhead box protein N4 isoform X1

  2. XM_054371123.1 → XP_054227098.1  forkhead box protein N4 isoform X3

  3. XM_054371122.1 → XP_054227097.1  forkhead box protein N4 isoform X2

  4. XM_054371124.1 → XP_054227099.1  forkhead box protein N4 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96NZ1.2 GenPept UniProtKB/Swiss-Prot:Q96NZ1

Gene LinkOut

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