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    Foxp4 forkhead box P4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363185, updated on 30-Mar-2024

    Summary

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    Symbol
    Foxp4provided by RGD
    Full Name
    forkhead box P4provided by RGD
    Primary source
    RGD:1311386
    See related
    Ensembl:ENSRNOG00000022804 AllianceGenome:RGD:1311386
    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 repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including embryonic foregut morphogenesis; lung secretory cell differentiation; and negative regulation of lung goblet cell differentiation. Predicted to be active in nucleus. Orthologous to human FOXP4 (forkhead box P4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 42.8), Spleen (RPKM 25.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Foxp4 in Genome Data Viewer
    Location:
    9q12
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (20556270..20612967)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (13058506..13115406)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (15068378..15124962)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134480268 Neighboring gene uncharacterized LOC102554116 Neighboring gene MyoD family inhibitor Neighboring gene uncharacterized LOC134480340 Neighboring gene transcription factor EB

    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. Expression of Foxp4 in the developing and adult rat forebrain. Takahashi K, et al. J Neurosci Res, 2008 Nov 1. PMID 18561326
    2. Transcriptional genomics associates FOX transcription factors with human heart failure. Hannenhalli S, et al. Circulation, 2006 Sep 19. PMID 16952980
    3. Transcriptional and DNA binding activity of the Foxp1/2/4 family is modulated by heterotypic and homotypic protein interactions. Li S, et al. Mol Cell Biol, 2004 Jan. PMID 14701752, Free PMC Article
    4. Advanced cardiac morphogenesis does not require heart tube fusion. Li S, et al. Science, 2004 Sep 10. PMID 15361625
    5. Foxp1/4 control epithelial cell fate during lung development and regeneration through regulation of anterior gradient 2. Li S, et al. Development, 2012 Jul. PMID 22675208, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within embryonic foregut morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within heart development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within lung secretory cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of lung goblet cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of lung goblet cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    forkhead box protein P4
    Names
    CCR4-NOT transcription complex subunit 3-like
    serine/arginine repetitive matrix protein 1

    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_001389210.1 → NP_001376139.1  forkhead box protein P4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      Conserved Domains (2) summary
      pfam16159
      Location:308 → 375
      FOXP-CC; FOXP coiled-coil domain
      cd20067
      Location:459 → 545
      FH_FOXP4; Forkhead (FH) domain found in Forkhead box protein P4 (FOXP4) 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_086027.1 Reference GRCr8

      Range
      20556270..20612967
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039083810.2 → XP_038939738.1  forkhead box protein P4 isoform X1

      Conserved Domains (3) summary
      COG5025
      Location:374 → 571
      COG5025; Transcription factor of the Forkhead/HNF3 family [Transcription]
      pfam16159
      Location:308 → 375
      FOXP-CC; FOXP coiled-coil domain
      cd20067
      Location:478 → 564
      FH_FOXP4; Forkhead (FH) domain found in Forkhead box protein P4 (FOXP4) and similar proteins

    2. XM_008766868.4 → XP_008765090.1  forkhead box protein P4 isoform X3

      UniProtKB/TrEMBL
      A0A0G2JXI7
      Related
      ENSRNOP00000070287.2
      Conserved Domains (3) summary
      COG5025
      Location:369 → 564
      COG5025; Transcription factor of the Forkhead/HNF3 family [Transcription]
      pfam16159
      Location:308 → 375
      FOXP-CC; FOXP coiled-coil domain
      cd20067
      Location:471 → 557
      FH_FOXP4; Forkhead (FH) domain found in Forkhead box protein P4 (FOXP4) and similar proteins

    3. XM_039083811.2 → XP_038939739.1  forkhead box protein P4 isoform X2

      Conserved Domains (3) summary
      COG5025
      Location:373 → 570
      COG5025; Transcription factor of the Forkhead/HNF3 family [Transcription]
      pfam16159
      Location:307 → 374
      FOXP-CC; FOXP coiled-coil domain
      cd20067
      Location:477 → 563
      FH_FOXP4; Forkhead (FH) domain found in Forkhead box protein P4 (FOXP4) and similar proteins

    4. XM_008766871.4 → XP_008765093.1  forkhead box protein P4 isoform X4

      Conserved Domains (3) summary
      COG5025
      Location:368 → 563
      COG5025; Transcription factor of the Forkhead/HNF3 family [Transcription]
      pfam16159
      Location:307 → 374
      FOXP-CC; FOXP coiled-coil domain
      cd20067
      Location:470 → 556
      FH_FOXP4; Forkhead (FH) domain found in Forkhead box protein P4 (FOXP4) and similar proteins

    5. XM_008766870.4 → XP_008765092.1  forkhead box protein P4 isoform X5

      UniProtKB/TrEMBL
      A0A0G2JXI7
      Conserved Domains (2) summary
      pfam16159
      Location:307 → 374
      FOXP-CC; FOXP coiled-coil domain
      cd20067
      Location:458 → 544
      FH_FOXP4; Forkhead (FH) domain found in Forkhead box protein P4 (FOXP4) and similar proteins

    6. XM_039083812.2 → XP_038939740.1  forkhead box protein P4 isoform X6

      Conserved Domains (3) summary
      COG5025
      Location:297 → 494
      COG5025; Transcription factor of the Forkhead/HNF3 family [Transcription]
      pfam16159
      Location:231 → 298
      FOXP-CC; FOXP coiled-coil domain
      cd20067
      Location:401 → 487
      FH_FOXP4; Forkhead (FH) domain found in Forkhead box protein P4 (FOXP4) and similar proteins

    7. XM_063267354.1 → XP_063123424.1  forkhead box protein P4 isoform X7

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108788.1: Suppressed sequence

      Description
      NM_001108788.1: 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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