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RFX1 regulatory factor X1 [ Homo sapiens (human) ]

Gene ID: 5989, updated on 7-Apr-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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Location:
19p13.12
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13961530..14006816, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14087814..14133810, complement)
105.20220307 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: 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. Downregulation of RFX1 predicts poor prognosis of patients with small hepatocellular carcinoma. Liu Y, et al. Eur J Surg Oncol, 2018 Jul. PMID 29764705
  2. 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
  3. 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
  4. 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
  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 (83) 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)

Genotypes

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
part_of 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_2023_10

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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