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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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    See FOXN4 in Genome Data Viewer
    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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