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    Rfx4 regulatory factor X4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 500818, updated on 27-Nov-2024

    Summary

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    Symbol
    Rfx4provided by RGD
    Full Name
    regulatory factor X4provided by RGD
    Primary source
    RGD:1562092
    See related
    EnsemblRapid:ENSRNOG00000051536 AllianceGenome:RGD:1562092
    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
    Also known as
    RGD1562092
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including cilium assembly; negative regulation of smoothened signaling pathway; and regulation of gene expression. Predicted to be located in nucleus. Orthologous to human RFX4 (regulatory factor X4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Testes (RPKM 22.1), Brain (RPKM 8.6) and 7 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rfx4 in Genome Data Viewer
    Location:
    7q13
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (20740760..20903355, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (18853065..19015378, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (25831358..25909976)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene shugoshin 1, pseudogene 1 Neighboring gene RIC8 guanine nucleotide exchange factor B Neighboring gene uncharacterized LOC134479647 Neighboring gene uncharacterized LOC134479648 Neighboring gene RNA polymerase III subunit B Neighboring gene uncharacterized LOC102552828 Neighboring gene t-complex 11 like 2

    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. Transcription factor RFX4 binding to the testis-specific histone H1t promoter in spermatocytes may be important for regulation of H1t gene transcription during spermatogenesis. Wolfe SA, et al. J Cell Biochem, 2008 Sep 1. PMID 18459115
    2. G-protein pathway suppressor 2 (GPS2) interacts with the regulatory factor X4 variant 3 (RFX4_v3) and functions as a transcriptional co-activator. Zhang D, et al. J Biol Chem, 2008 Mar 28. PMID 18218630, Free PMC Article
    3. Graded phenotypic response to partial and complete deficiency of a brain-specific transcript variant of the winged helix transcription factor RFX4. Blackshear PJ, et al. Development, 2003 Oct. PMID 12925582
    4. The Rfx4 transcription factor modulates Shh signaling by regional control of ciliogenesis. Ashique AM, et al. Sci Signal, 2009 Nov 3. PMID 19887680
    5. Identification of potential target genes for RFX4_v3, a transcription factor critical for brain development. Zhang D, et al. J Neurochem, 2006 Aug. PMID 16893423

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. suggest a possible regulatory role for RFX4 in transcription of the histone H1t gene during spermatogenesis
      Title: Transcription factor RFX4 binding to the testis-specific histone H1t promoter in spermatocytes may be important for regulation of H1t gene transcription during spermatogenesis.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    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 sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cilium assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of smoothened signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of protein processing 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
    		  
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within telencephalon development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    regulatory factor X4; transcription factor RFX4
    Names
    regulatory factor X, 4 (influences HLA class II expression)
    transcription factor RFX4-like

    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_001432568.1 → NP_001419497.1  regulatory factor X4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A0A8I5XZT6

    2. NM_001432570.1 → NP_001419499.1  regulatory factor X4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007

    3. NM_001432572.1 → NP_001419501.1  regulatory factor X4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A0A0G2K8F2

    4. NM_001432574.1 → NP_001419503.1  regulatory factor X4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007

    5. NM_001432575.1 → NP_001419504.1  regulatory factor X4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007

    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_086025.1 Reference GRCr8

      Range
      20740760..20903355 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063264402.1 → XP_063120472.1  transcription factor RFX4 isoform X7

    2. XM_039080076.2 → XP_038936004.1  transcription factor RFX4 isoform X5

      Related
      ENSRNOP00000074585.2, ENSRNOT00000091571.3
      Conserved Domains (1) summary
      pfam02257
      Location:59 → 134
      RFX_DNA_binding; RFX DNA-binding domain

    3. XM_039080073.2 → XP_038936001.1  transcription factor RFX4 isoform X1

      Conserved Domains (1) summary
      pfam02257
      Location:79 → 154
      RFX_DNA_binding; RFX DNA-binding domain

    4. XM_063264400.1 → XP_063120470.1  transcription factor RFX4 isoform X4

    5. XM_063264401.1 → XP_063120471.1  transcription factor RFX4 isoform X6

    6. XM_039080075.2 → XP_038936003.1  transcription factor RFX4 isoform X3

      Related
      ENSRNOP00000076359.1, ENSRNOT00000114082.2
      Conserved Domains (1) summary
      pfam02257
      Location:69 → 144
      RFX_DNA_binding; RFX DNA-binding domain

    7. XM_039080077.2 → XP_038936005.1  transcription factor RFX4 isoform X8

      Related
      ENSRNOP00000103734.1, ENSRNOT00000138684.1
      Conserved Domains (1) summary
      pfam02257
      Location:2 → 51
      RFX_DNA_binding; RFX DNA-binding domain

    8. XM_039080074.2 → XP_038936002.1  transcription factor RFX4 isoform X2

      Conserved Domains (1) summary
      pfam02257
      Location:81 → 156
      RFX_DNA_binding; RFX DNA-binding domain

    9. XM_063264403.1 → XP_063120473.1  transcription factor RFX4 isoform X10

    10. XM_063264404.1 → XP_063120474.1  transcription factor RFX4 isoform X11

    11. XM_006241183.5 → XP_006241245.3  transcription factor RFX4 isoform X9

      UniProtKB/TrEMBL
      A0A0G2K3G6
      Related
      ENSRNOP00000072631.2, ENSRNOT00000084955.3
    Nucleotide Protein Strain
    Heading Accession and Version

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