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    RFX1 regulatory factor X1 [ Homo sapiens (human) ]

    Gene ID: 5989, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RFX1provided by HGNC
    Official Full Name
    regulatory factor X1provided by HGNC
    Primary source
    HGNC:HGNC:9982
    See related
    Ensembl:ENSG00000132005 MIM:600006; AllianceGenome:HGNC:9982
    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
    EFC; RFX
    Summary
    This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has been shown to regulate a wide variety of genes involved in immunity and cancer, including the MHC class II genes and genes that may be involved in cancer progression. This gene exhibits altered expression in glioblastoma and the autoimmune disease systemic lupus erythematosis (SLE). [provided by RefSeq, Jul 2016]
    Expression
    Broad expression in testis (RPKM 5.4), spleen (RPKM 2.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RFX1 in Genome Data Viewer
    Location:
    19p13.12
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13961530..14006816, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14087814..14133810, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (14072342..14117132, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10218 Neighboring gene coiled-coil and C2 domain containing 1A Neighboring gene MPRA-validated peak3378 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14046993-14047750 Neighboring gene podocan like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14069830-14070403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14070404-14070976 Neighboring gene DDB1 and CUL4 associated factor 15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14090312-14090838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14090839-14091365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14091366-14091891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14093768-14094294 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14096053-14096944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14097836-14098726 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14116358-14116886 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14116887-14117414 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14117415-14117942 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14134324-14134824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14134825-14135325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14152 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10224 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10225 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14153631-14154131 Neighboring gene interleukin 27 receptor subunit alpha Neighboring gene relaxin 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of an epigenetically silenced gene, RFX1, in human glioma cells using restriction landmark genomic scanning. Ohashi Y, et al. Oncogene, 2004 Oct 14. PMID 15334059
    2. Downregulation of RFX1 predicts poor prognosis of patients with small hepatocellular carcinoma. Liu Y, et al. Eur J Surg Oncol, 2018 Jul. PMID 29764705
    3. Epigenetics and SLE: RFX1 downregulation causes CD11a and CD70 overexpression by altering epigenetic modifications in lupus CD4+ T cells. Zhao M, et al. J Autoimmun, 2010 Aug. PMID 20223637
    4. The transcription factor RFX protects MHC class II genes against epigenetic silencing by DNA methylation. Seguín-Estévez Q, et al. J Immunol, 2009 Aug 15. PMID 19620312
    5. Nuclear import and DNA-binding activity of RFX1. Evidence for an autoinhibitory mechanism. Katan-Khaykovich Y, et al. Eur J Biochem, 2001 May. PMID 11358531

    See all (92) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RXR agonist, Bexarotene, effectively reduces drug resistance via regulation of RFX1 in embryonic carcinoma cells.
      Title: RXR agonist, Bexarotene, effectively reduces drug resistance via regulation of RFX1 in embryonic carcinoma cells.
    2. RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells.
      Title: RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells.
    3. RFX1-mediated CCN3 induction that may support chondrocyte survival under starved conditions.
      Title: RFX1-mediated CCN3 induction that may support chondrocyte survival under starved conditions.
    4. the recruitment of PP1c to promoters may be a mechanism by which RFX1 regulates the target genes.
      Title: Recruitment of the protein phosphatase-1 catalytic subunit to promoters by the dual-function transcription factor RFX1.
    5. Results show that RFX1 expression deficiency leads to the overexpression of TLR4 and the activation of CD14(+) monocytes in coronary artery disease (CAD) patients by regulating DNA methylation and histone modifications, which highlights the vital role of RFX1 in the pathogenesis of CAD.
      Title: RFX1 downregulation contributes to TLR4 overexpression in CD14(+) monocytes via epigenetic mechanisms in coronary artery disease.
    6. RFX1 interacts with the D sequence of adeno-associated virus inverted terminal repeat and regulates AAV transduction.
      Title: RFX1 and RFX3 Transcription Factors Interact with the D Sequence of Adeno-Associated Virus Inverted Terminal Repeat and Regulate AAV Transduction.
    7. RFX1 expression was significantly lower in HCC tissues compared to the corresponding non-tumor tissues. In vitro studies suggested that knocking down RFX1 facilitated HCC cell invasion, while overexpression of RFX1 reduced the invasion of HCC cells. RFX1 regulated expression of some epithelial-mesenchymal transition markers.
      Title: Downregulation of RFX1 predicts poor prognosis of patients with small hepatocellular carcinoma.
    8. Findings indicate that RFX1 functions downstream of STAT3 and phosphorylated STAT3 can inhibit RFX1 expression and suggest a unique role for RFX1 in Th17-related autoimmune diseases.
      Title: IL-6/STAT3 pathway induced deficiency of RFX1 contributes to Th17-dependent autoimmune diseases via epigenetic regulation.
    9. Results show that reduced miRNA-124 improved microglia activation and up-regulated its downstream target RFX1, indicating that RFX1, as one of the target transcripts, facilitates microglial activation by miR-124 regulation; identified the binding site through which RFX1 directly regulates ApoE, may explain the missing link between decreased miRNA-124 and ineffective Abeta uptaking during aging.
      Title: Regulatory factor X1 depresses ApoE-dependent Aβ uptake by miRNA-124 in microglial response to oxidative stress.
    10. induction of ciliogenesis increases the expression of RFX and dyslexia candidate genes
      Title: Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs.
    Submit: New GeneRIF Correction See all GeneRIFs (33)

    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

    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 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 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 immune response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    MHC class II regulatory factor RFX1
    Names
    MHC class II regulatory factor RFX
    enhancer factor C
    regulatory factor X, 1 (influences HLA class II expression)
    trans-acting regulatory factor 1
    transcription factor RFX1

    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_051220.1 RefSeqGene

      Range
      6195..50985
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002918.5 → NP_002909.4  MHC class II regulatory factor RFX1

      See identical proteins and their annotated locations for NP_002909.4

      Status: REVIEWED

      Source sequence(s)
      AC020916, AK309824, BC049826, BM662273
      Consensus CDS
      CCDS12301.1
      UniProtKB/Swiss-Prot
      P22670
      Related
      ENSP00000254325.3, ENST00000254325.9
      Conserved Domains (3) summary
      pfam02257
      Location:435 → 511
      RFX_DNA_binding; RFX DNA-binding domain
      pfam03153
      Location:75 → 285
      TFIIA; Transcription factor IIA, alpha/beta subunit
      pfam04589
      Location:224 → 371
      RFX1_trans_act; RFX1 transcription activation region

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      13961530..14006816 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528170.3 → XP_011526472.1  MHC class II regulatory factor RFX1 isoform X3

      See identical proteins and their annotated locations for XP_011526472.1

      Conserved Domains (2) summary
      pfam02257
      Location:436 → 512
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:115 → 372
      RFX1_trans_act; RFX1 transcription activation region

    2. XM_047439194.1 → XP_047295150.1  MHC class II regulatory factor RFX1 isoform X4

      UniProtKB/Swiss-Prot
      P22670

    3. XM_011528167.3 → XP_011526469.1  MHC class II regulatory factor RFX1 isoform X1

      See identical proteins and their annotated locations for XP_011526469.1

      Conserved Domains (3) summary
      pfam02257
      Location:545 → 621
      RFX_DNA_binding; RFX DNA-binding domain
      pfam03153
      Location:75 → 280
      TFIIA; Transcription factor IIA, alpha/beta subunit
      pfam04589
      Location:224 → 481
      RFX1_trans_act; RFX1 transcription activation region

    4. XM_047439195.1 → XP_047295151.1  MHC class II regulatory factor RFX1 isoform X5

    5. XM_047439193.1 → XP_047295149.1  MHC class II regulatory factor RFX1 isoform X4

      UniProtKB/Swiss-Prot
      P22670

    6. XM_047439192.1 → XP_047295148.1  MHC class II regulatory factor RFX1 isoform X2

    7. XM_011528166.3 → XP_011526468.1  MHC class II regulatory factor RFX1 isoform X1

      See identical proteins and their annotated locations for XP_011526468.1

      Conserved Domains (3) summary
      pfam02257
      Location:545 → 621
      RFX_DNA_binding; RFX DNA-binding domain
      pfam03153
      Location:75 → 280
      TFIIA; Transcription factor IIA, alpha/beta subunit
      pfam04589
      Location:224 → 481
      RFX1_trans_act; RFX1 transcription activation region

    8. XM_011528169.3 → XP_011526471.1  MHC class II regulatory factor RFX1 isoform X3

      See identical proteins and their annotated locations for XP_011526471.1

      Conserved Domains (2) summary
      pfam02257
      Location:436 → 512
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:115 → 372
      RFX1_trans_act; RFX1 transcription activation region

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_021160022.1 Reference GRCh38.p14 PATCHES

      Range
      173371..219355 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332705.1 → XP_054188680.1  MHC class II regulatory factor RFX1 isoform X4

      UniProtKB/Swiss-Prot
      P22670

    2. XM_054332702.1 → XP_054188677.1  MHC class II regulatory factor RFX1 isoform X3

    3. XM_054332700.1 → XP_054188675.1  MHC class II regulatory factor RFX1 isoform X1

    4. XM_054332703.1 → XP_054188678.1  MHC class II regulatory factor RFX1 isoform X3

    5. XM_054332706.1 → XP_054188681.1  MHC class II regulatory factor RFX1 isoform X5

    6. XM_054332704.1 → XP_054188679.1  MHC class II regulatory factor RFX1 isoform X4

      UniProtKB/Swiss-Prot
      P22670

    7. XM_054332701.1 → XP_054188676.1  MHC class II regulatory factor RFX1 isoform X2

    8. XM_054332699.1 → XP_054188674.1  MHC class II regulatory factor RFX1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      14087814..14133810 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321679.1 → XP_054177654.1  MHC class II regulatory factor RFX1 isoform X4

    2. XM_054321676.1 → XP_054177651.1  MHC class II regulatory factor RFX1 isoform X3

    3. XM_054321674.1 → XP_054177649.1  MHC class II regulatory factor RFX1 isoform X1

    4. XM_054321677.1 → XP_054177652.1  MHC class II regulatory factor RFX1 isoform X3

    5. XM_054321680.1 → XP_054177655.1  MHC class II regulatory factor RFX1 isoform X5

    6. XM_054321678.1 → XP_054177653.1  MHC class II regulatory factor RFX1 isoform X4

    7. XM_054321675.1 → XP_054177650.1  MHC class II regulatory factor RFX1 isoform X2

    8. XM_054321673.1 → XP_054177648.1  MHC class II regulatory factor RFX1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P22670.2 GenPept UniProtKB/Swiss-Prot:P22670

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