U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    RFX4 regulatory factor X4 [ Homo sapiens (human) ]

    Gene ID: 5992, updated on 18-Sep-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    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

    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)

    NEW Try the new Transcript table

    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_001206691.2NP_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:68141
      RFX_DNA_binding; RFX DNA-binding domain
    2. NM_032491.6NP_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_213594.3NP_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:59132
      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.