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    RFX4 regulatory factor X4 [ Homo sapiens (human) ]

    Gene ID: 5992, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RFX4provided by HGNC
    Official Full Name
    regulatory factor X4provided by HGNC
    Primary source
    HGNC:HGNC:9985
    See related
    Ensembl:ENSG00000111783 MIM:603958; AllianceGenome:HGNC:9985
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NYD-SP10
    Summary
    This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
    Expression
    Restricted expression toward testis (RPKM 40.0) See more
    Orthologs
    mouse all
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    Genomic context

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    See RFX4 in Genome Data Viewer
    Location:
    12q23.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (106583004..106762803)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (106546661..106726445)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (106976782..107156581)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106696289-106697174 Neighboring gene NANOG hESC enhancer GRCh37_chr12:106725081-106725582 Neighboring gene t-complex 11 like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106791431-106791932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106791933-106792432 Neighboring gene RNA polymerase III subunit B Neighboring gene ReSE screen-validated silencer GRCh37_chr12:106838256-106838461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106870783-106871355 Neighboring gene NANOG hESC enhancer GRCh37_chr12:106884667-106885244 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:106887966-106888130 Neighboring gene uncharacterized LOC100287944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106929421-106929920 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106934851-106935440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106944957-106945458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106974861-106975743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106977232-106977816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106979571-106980156 Neighboring gene Sharpr-MPRA regulatory region 8958 Neighboring gene Sharpr-MPRA regulatory region 7289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:107038213-107038714 Neighboring gene uncharacterized LOC100505978 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:107104586-107105785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6948 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:107167609-107168160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6949 Neighboring gene RIC8 guanine nucleotide exchange factor B Neighboring gene uncharacterized LOC105369961 Neighboring gene NANOG hESC enhancer GRCh37_chr12:107270199-107270748 Neighboring gene eukaryotic translation elongation factor 1 beta 2 pseudogene 4

    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. High expression of RFX4 is associated with tumor progression and poor prognosis in patients with glioblastoma. Jeong HY, et al. Int J Neurosci, 2021 Jan. PMID 32075484
    2. Identification of a potential bipolar risk haplotype in the gene encoding the winged-helix transcription factor RFX4. Glaser B, et al. Mol Psychiatry, 2005 Oct. PMID 15940297
    3. Identification of a novel substrate for tyrosine kinase in human testes. Huang X, et al. J Nanosci Nanotechnol, 2005 Aug. PMID 16193984
    4. Identification of glioma-specific RFX4-E and -F isoforms and humoral immune response in patients. Matsushita H, et al. Cancer Sci, 2005 Nov. PMID 16271074, Free PMC Article
    5. Immune transcriptome alterations in the temporal cortex of subjects with autism. Garbett K, et al. Neurobiol Dis, 2008 Jun. PMID 18378158, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RFX4 is an intrinsic factor for neuronal differentiation through induction of proneural genes POU3F2 and NEUROD1.
      Title: RFX4 is an intrinsic factor for neuronal differentiation through induction of proneural genes POU3F2 and NEUROD1.
    2. High expression of RFX4 is associated with tumor progression and poor prognosis in patients with glioblastoma.
      Title: High expression of RFX4 is associated with tumor progression and poor prognosis in patients with glioblastoma.
    3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study confirms BST1 and suggests a locus on 12q24 as the risk loci for Parkinson's disease in the European population.
    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. Observational study of gene-disease association. (HuGE Navigator)
      Title: Case-control association study of 65 candidate genes revealed a possible association of a SNP of HTR5A to be a factor susceptible to bipolar disease in Bulgarian population.
    6. The gene encoding the transcription factor RFX4 represents an excellent neurobiological and positional candidate gene for Bipolar disorder due to the potential involvement of RFX4 proteins in the regulation of circadian rhythms, linked to chromosome 12.
      Title: Identification of a potential bipolar risk haplotype in the gene encoding the winged-helix transcription factor RFX4.
    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

    EBI GWAS Catalog

    Description
    Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.
    EBI GWAS Catalog
    Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
    EBI GWAS Catalog
    Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific 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 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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cilium assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of protein processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in telencephalon development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    transcription factor RFX4
    Names
    regulatory factor X, 4 (influences HLA class II expression)
    testis development protein NYD-SP10
    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.

    Genomic

    1. NG_047074.1 RefSeqGene

      Range
      5098..184897
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001206691.2 → NP_001193620.1  transcription factor RFX4 isoform d

      See identical proteins and their annotated locations for NP_001193620.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4, also known as RFX4_v4) uses an alternate 5' exon and thus differs in the 5' UTR and 5' coding region, compared to variant 3. The encoded isoform (d, also known as RFX4-C) has a distinct N-terminus and is longer than isoform c.
      Source sequence(s)
      AB095365, AI002078, AK074913, AY102009
      Consensus CDS
      CCDS55880.1
      UniProtKB/Swiss-Prot
      Q33E94
      Related
      ENSP00000350552.4, ENST00000357881.8
      Conserved Domains (1) summary
      pfam02257
      Location:68 → 141
      RFX_DNA_binding; RFX DNA-binding domain

    2. NM_032491.6 → NP_115880.2  transcription factor RFX4 isoform a

      See identical proteins and their annotated locations for NP_115880.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as RFX4_v1) differs in the 5' UTR, and lacks several exons in the 5' coding region but includes an alternate 5' coding region, compared to variant 3. The encoded isoform (a, also known as RFX4-A) has a distinct and shorter N-terminus, compared to isoform c.
      Source sequence(s)
      BC028582, BC030644
      Consensus CDS
      CCDS9108.1
      UniProtKB/Swiss-Prot
      Q33E94
      Related
      ENSP00000229387.5, ENST00000229387.6

    3. NM_213594.3 → NP_998759.1  transcription factor RFX4 isoform c

      See identical proteins and their annotated locations for NP_998759.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as RFX4_v3) represents the longest transcript and encodes isoform c, also known as RFX4-D.
      Source sequence(s)
      AB095366, AI002078, AY102009
      Consensus CDS
      CCDS9106.1
      UniProtKB/Swiss-Prot
      A8K5Y0, B2RDW4, Q33DW6, Q33DW7, Q33E94, Q33E95, Q6YM53, Q8MHQ1, Q8NC78, Q8NDF9, Q8SNA1, Q96S80, Q9BXI0
      Related
      ENSP00000376585.1, ENST00000392842.6
      Conserved Domains (1) summary
      pfam02257
      Location:59 → 132
      RFX_DNA_binding; RFX DNA-binding domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      106583004..106762803
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      106546661..106726445
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_002920.3: Suppressed sequence

      Description
      NM_002920.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q33E94.2 GenPept UniProtKB/Swiss-Prot:Q33E94

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
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