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    Foxn4 forkhead box N4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 288736, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Foxn4provided by RGD
    Official Full Name
    forkhead box N4provided by RGD
    Primary source
    RGD:1306389
    See related
    Ensembl:ENSRNOG00000000691 AllianceGenome:RGD:1306389
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; chromatin binding activity; and cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in neural retina development; positive regulation of transcription by RNA polymerase II; and ventral spinal cord interneuron fate commitment. Predicted to act upstream of or within neuron fate commitment. Predicted to be active in nucleus. Orthologous to human FOXN4 (forkhead box N4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Kidney (RPKM 4.7), Testes (RPKM 1.5) and 2 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Foxn4 in Genome Data Viewer
    Location:
    12q16
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (47997308..48020526)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (42336706..42359932)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (48101012..48121281)

    Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene ubiquitin protein ligase E3B Neighboring gene potassium channel tetramerization domain containing 10 Neighboring gene myosin IH Neighboring gene uncharacterized LOC134481305 Neighboring gene acetyl-CoA carboxylase beta Neighboring gene uracil-DNA glycosylase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. A regulatory domain is required for Foxn4 activity during retinogenesis. Lelièvre EC, et al. J Mol Neurosci, 2012 Feb. PMID 21701787, Free PMC Article
    2. A regulatory network involving Foxn4, Mash1 and delta-like 4/Notch1 generates V2a and V2b spinal interneurons from a common progenitor pool. Del Barrio MG, et al. Development, 2007 Oct. PMID 17728344, Free PMC Article
    3. Foxn4 acts synergistically with Mash1 to specify subtype identity of V2 interneurons in the spinal cord. Li S, et al. Proc Natl Acad Sci U S A, 2005 Jul 26. PMID 16020526, Free PMC Article
    4. Foxn4 controls the genesis of amacrine and horizontal cells by retinal progenitors. Li S, et al. Neuron, 2004 Sep 16. PMID 15363391
    5. 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

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within amacrine cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron fate commitment ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retina layer formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ventral spinal cord interneuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ventral spinal cord interneuron fate commitment ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    forkhead box protein N4

    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_001389259.1 → NP_001376188.1  forkhead box protein N4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000012
      UniProtKB/TrEMBL
      A0A8I6AB90
      Related
      ENSRNOP00000090152.1, ENSRNOT00000094488.1
      Conserved Domains (2) summary
      COG5025
      Location:143 → 357
      COG5025; Transcription factor of the Forkhead/HNF3 family [Transcription]
      cl00061
      Location:242 → 347
      FH_FOX; Forkhead (FH) domain found in Forkhead box (FOX) family of transcription factors and similar proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086030.1 Reference GRCr8

      Range
      47997308..48020526
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039089275.2 → XP_038945203.1  forkhead box protein N4 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AB90
      Conserved Domains (2) summary
      COG5025
      Location:143 → 357
      COG5025; Transcription factor of the Forkhead/HNF3 family [Transcription]
      cl00061
      Location:242 → 347
      FH_FOX; Forkhead (FH) domain found in Forkhead box (FOX) family of transcription factors and similar proteins

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001105935.1: Suppressed sequence

      Description
      NM_001105935.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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