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    Rfx4 regulatory factor X, 4 (influences HLA class II expression) [ Mus musculus (house mouse) ]

    Gene ID: 71137, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Rfx4provided by MGI
    Official Full Name
    regulatory factor X, 4 (influences HLA class II expression)provided by MGI
    Primary source
    MGI:MGI:1918387
    See related
    Ensembl:ENSMUSG00000020037 AllianceGenome:MGI:1918387
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    NYD-sp10; 4933412G19Rik
    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. Acts upstream of or within several processes, including cilium assembly; negative regulation of smoothened signaling pathway; and regulation of gene expression. Located in nucleus. Is expressed in several structures, including central nervous system; eye; future brain; genitourinary system; and liver. Orthologous to human RFX4 (regulatory factor X4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis adult (RPKM 21.4), CNS E11.5 (RPKM 8.8) and 7 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rfx4 in Genome Data Viewer
    Location:
    10 C1; 10 41.63 cM
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (84591895..84742402)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (84756036..84906538)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E3905 Neighboring gene STARR-seq mESC enhancer starr_27418 Neighboring gene predicted gene, 25657 Neighboring gene predicted gene, 17249 Neighboring gene polymerase (RNA) III (DNA directed) polypeptide B Neighboring gene STARR-seq mESC enhancer starr_27420 Neighboring gene STARR-seq mESC enhancer starr_27422 Neighboring gene STARR-seq mESC enhancer starr_27426 Neighboring gene STARR-seq mESC enhancer starr_27427 Neighboring gene STARR-positive B cell enhancer ABC_E8354 Neighboring gene STARR-positive B cell enhancer ABC_E6894 Neighboring gene predicted gene, 53596 Neighboring gene predicted gene, 40728 Neighboring gene STARR-seq mESC enhancer starr_27430 Neighboring gene STARR-seq mESC enhancer starr_27432 Neighboring gene STARR-positive B cell enhancer ABC_E2956 Neighboring gene RIC8 guanine nucleotide exchange factor B Neighboring gene predicted gene, 34633 Neighboring gene STARR-seq mESC enhancer starr_27436 Neighboring gene STARR-seq mESC enhancer starr_27437 Neighboring gene predicted gene, 51826

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Regulatory factor X4 variant 3: a transcription factor involved in brain development and disease. Zhang D, et al. J Neurosci Res, 2007 Dec. PMID 17510980, Free PMC Article
    2. Restricted expression and photic induction of a novel mouse regulatory factor X4 transcript in the suprachiasmatic nucleus. Araki R, et al. J Biol Chem, 2004 Mar 12. PMID 14701801
    3. Conditional ablation of the RFX4 isoform 1 transcription factor: Allele dosage effects on brain phenotype. Xu P, et al. PLoS One, 2018. PMID 29298325, Free PMC Article
    4. Enhanced postischemic functional recovery in CYP2J2 transgenic hearts involves mitochondrial ATP-sensitive K+ channels and p42/p44 MAPK pathway. Seubert J, et al. Circ Res, 2004 Sep 3. PMID 15256482
    5. Differential expression of Rfx1-4 during mouse spermatogenesis. Kistler WS, et al. Gene Expr Patterns, 2009 Oct. PMID 19596083, Free PMC Article

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. provide a novel conditional KO animal model in which to investigate the downstream genes directly and/or indirectly regulated by RFX4 isoform 1. This model could provide new insights into the pathogenesis of obstructive hydrocephalus and holoprosencephaly in humans, both relatively common and disabling birth defects
      Title: Conditional ablation of the RFX4 isoform 1 transcription factor: Allele dosage effects on brain phenotype.
    2. the dominant Rfx4 transcript present begins at a downstream exon and lacks the DNA binding domain
      Title: Differential expression of Rfx1-4 during mouse spermatogenesis.
    3. Rfx4 is a regionally specific transcriptional regulator of ciliogenesis and thus is also a regionally specific modulator of Shh signaling during development of the central nervous system.
      Title: The Rfx4 transcription factor modulates Shh signaling by regional control of ciliogenesis.
    4. GPS2 interacts with RFX4_v3 to modulate transactivation of genes involved in brain morphogenesis, including Cx3Cl1
      Title: G-protein pathway suppressor 2 (GPS2) interacts with the regulatory factor X4 variant 3 (RFX4_v3) and functions as a transcriptional co-activator.
    5. mouse regulatory factor X4 transcript is expressed in the suprachiasmatic nucleus and regulated by light
      Title: Restricted expression and photic induction of a novel mouse regulatory factor X4 transcript in the suprachiasmatic nucleus.
    6. Data implicate the RFX4_v3 variant transcript as being crucial for early brain development, as well as for the genesis of the subcommissural organ.
      Title: Graded phenotypic response to partial and complete deficiency of a brain-specific transcript variant of the winged helix transcription factor RFX4.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of smoothened signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within telencephalon development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transcription factor RFX4
    Names
    regulatory factor X 4 protein
    winged-helix transcription factor RFX4

    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_001024918.1 → NP_001020089.1  transcription factor RFX4 isoform 1

      See identical proteins and their annotated locations for NP_001020089.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB086957, BB595996
      Consensus CDS
      CCDS24082.1
      UniProtKB/Swiss-Prot
      B2RS52, Q3V158, Q76KT2, Q7TNK1, Q8HWA6, Q9D453
      Related
      ENSMUSP00000051107.7, ENSMUST00000060397.13
      Conserved Domains (1) summary
      pfam02257
      Location:59 → 134
      RFX_DNA_binding; RFX DNA-binding domain

    2. NM_027689.3 → NP_081965.2  transcription factor RFX4 isoform 2

      See identical proteins and their annotated locations for NP_081965.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC122349
      Consensus CDS
      CCDS24083.1
      UniProtKB/Swiss-Prot
      Q7TNK1
      Related
      ENSMUSP00000093035.5, ENSMUST00000095388.5

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      84591895..84742402
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030245278.2 → XP_030101138.1  transcription factor RFX4 isoform X3

      Conserved Domains (1) summary
      pfam02257
      Location:59 → 134
      RFX_DNA_binding; RFX DNA-binding domain

    2. XM_006514115.5 → XP_006514178.1  transcription factor RFX4 isoform X4

      See identical proteins and their annotated locations for XP_006514178.1

      Conserved Domains (1) summary
      pfam02257
      Location:2 → 51
      RFX_DNA_binding; RFX DNA-binding domain

    3. XM_030245279.2 → XP_030101139.1  transcription factor RFX4 isoform X4

      Conserved Domains (1) summary
      pfam02257
      Location:2 → 51
      RFX_DNA_binding; RFX DNA-binding domain

    4. XM_006514113.5 → XP_006514176.1  transcription factor RFX4 isoform X1

      Conserved Domains (1) summary
      pfam02257
      Location:69 → 144
      RFX_DNA_binding; RFX DNA-binding domain

    5. XM_006514114.5 → XP_006514177.1  transcription factor RFX4 isoform X2

      Conserved Domains (1) summary
      pfam02257
      Location:69 → 144
      RFX_DNA_binding; RFX DNA-binding domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7TNK1.1 GenPept UniProtKB/Swiss-Prot:Q7TNK1

    Gene LinkOut

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

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