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RFX5 regulatory factor X5 [ Homo sapiens (human) ]

Gene ID: 5993, updated on 3-Apr-2024

Summary

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Official Symbol
RFX5provided by HGNC
Official Full Name
regulatory factor X5provided by HGNC
Primary source
HGNC:HGNC:9986
See related
Ensembl:ENSG00000143390 MIM:601863; AllianceGenome:HGNC:9986
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
Summary
A lack of MHC-II expression results in a severe immunodeficiency syndrome called MHC-II deficiency, or the bare lymphocyte syndrome (BLS; MIM 209920). At least 4 complementation groups have been identified in B-cell lines established from patients with BLS. The molecular defects in complementation groups B, C, and D all lead to a deficiency in RFX, a nuclear protein complex that binds to the X box of MHC-II promoters. The lack of RFX binding activity in complementation group C results from mutations in the RFX5 gene encoding the 75-kD subunit of RFX (Steimle et al., 1995). RFX5 is the fifth member of the growing family of DNA-binding proteins sharing a novel and highly characteristic DNA-binding domain called the RFX motif. Multiple alternatively spliced transcript variants have been found but the full-length natures of only two have been determined. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 26.5), spleen (RPKM 21.2) and 24 other tissues See more
Orthologs
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Genomic context

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See RFX5 in Genome Data Viewer
Location:
1q21.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151340640..151347252, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150464344..150470955, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151313116..151319728, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151253738-151254622 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151254623-151255508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1717 Neighboring gene ZNF687 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151261481-151262132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151262133-151262782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151262783-151263433 Neighboring gene zinc finger protein 687 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151266030-151267013 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151267014-151267998 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:151267999-151268981 Neighboring gene phosphatidylinositol 4-kinase beta Neighboring gene RNA, 7SL, cytoplasmic 444, pseudogene Neighboring gene Sharpr-MPRA regulatory region 1421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151299400-151300324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151315395-151315895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1718 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:151318990-151320189 Neighboring gene MPRA-validated peak412 silencer Neighboring gene RFX5 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:151332077-151332231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151342446-151343117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:151343118-151343788 Neighboring gene selenium binding protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151344535-151345118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151345119-151345702 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151371406-151372128 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151372129-151372850 Neighboring gene proteasome 20S subunit beta 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. Identification of RFX5 as prognostic biomarker and associated with immune infiltration in stomach adenocarcinoma. Guo L, et al. Eur J Med Res, 2022 Aug 31. PMID 36045400, Free PMC Article
  2. RFX5 regulates gene expression of the Pcdhα cluster. Wang N, et al. Yi Chuan, 2020 Aug 20. PMID 32952112
  3. Mutation in a winged-helix DNA-binding motif causes atypical bare lymphocyte syndrome. Nekrep N, et al. Nat Immunol, 2002 Nov. PMID 12368908
  4. Molecular analysis of an MHC class II deficiency patient reveals a novel mutation in the RFX5 gene. Peijnenburg A, et al. Immunogenetics, 1999 Apr. PMID 10079298
  5. Regulatory factor X, a bare lymphocyte syndrome transcription factor, is a multimeric phosphoprotein complex. Moreno CS, et al. J Immunol, 1997 Jun 15. PMID 9190936

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of RFX5 as prognostic biomarker and associated with immune infiltration in stomach adenocarcinoma.
    Title: Identification of RFX5 as prognostic biomarker and associated with immune infiltration in stomach adenocarcinoma.
  2. RFX5 promotes the progression of hepatocellular carcinoma through transcriptional activation of KDM4A.
    Title: RFX5 promotes the progression of hepatocellular carcinoma through transcriptional activation of KDM4A.
  3. RFX5 regulates gene expression of the Pcdhalpha cluster.
    Title: RFX5 regulates gene expression of the Pcdhα cluster.
  4. RFX5 acts as a direct positive transcriptional regulator of TPP1 in hepatocellular carcinoma.
    Title: The transcription factor RFX5 is a transcriptional activator of the TPP1 gene in hepatocellular carcinoma.
  5. Data show arginine methyltransferase PRMT6 methylates the AT-hook motif of regulatory factor RFX5 and downregulates HLA-DQ expression.
    Title: Differential regulation of MHCII genes by PRMT6, via an AT-hook motif of RFX5.
  6. these data have identified as novel pathway whereby SIRT1 maintains COL1A2 synthesis in SMCs by modulating RFX5 activity.
    Title: SIRT1 deacetylates RFX5 and antagonizes repression of collagen type I (COL1A2) transcription in smooth muscle cells.
  7. RFXAP(C) consists of two alpha-helices that form a V-shaped structure that packs within the RFX5(N)(2) staple.
    Title: Solution structure of the heterotrimeric complex between the interaction domains of RFX5 and RFXAP from the RFX gene regulatory complex.
  8. TSA treatment enhances the association of CIITA with the transcription factor RFX5, which ameliorates the down-regulation of CIITA recruitment to target promoters by HDAC2.
    Title: HDAC2 deacetylates class II transactivator and suppresses its activity in macrophages and smooth muscle cells.
  9. RFXAP and RFXB have roles in relieving autoinhibition of RFX5
    Title: Assembly of the RFX complex on the MHCII promoter: role of RFXAP and RFXB in relieving autoinhibition of RFX5.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association between the SERPING1 gene and age-related macular degeneration: a two-stage case-control study.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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

Associated conditions

Description Tests
MHC class II deficiency
MedGen: C2931418 OMIM: 209920 GeneReviews: Not available
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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

Pathways from PubChem

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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 activator activity, RNA polymerase II-specific IGI
Inferred from Genetic Interaction
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 transcription 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 DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of MHC class II biosynthetic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
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 RNA polymerase II transcription regulator complex IPI
Inferred from Physical Interaction
more info
 PubMed 
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
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA-binding protein RFX5
Names
regulatory factor X 5
regulatory factor X, 5 (influences HLA class II expression)

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_007576.1 RefSeqGene

    Range
    5001..11654
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_101

mRNA and Protein(s)

  1. NM_000449.4 → NP_000440.1  DNA-binding protein RFX5 isoform 1

    See identical proteins and their annotated locations for NP_000440.1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Related
    ENSP00000290524.4, ENST00000290524.8
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  2. NM_001025603.2 → NP_001020774.1  DNA-binding protein RFX5 isoform 1

    See identical proteins and their annotated locations for NP_001020774.1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Related
    ENSP00000389130.2, ENST00000452671.7
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  3. NM_001379412.1 → NP_001366341.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  4. NM_001379413.1 → NP_001366342.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  5. NM_001379414.1 → NP_001366343.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  6. NM_001379415.1 → NP_001366344.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  7. NM_001379416.1 → NP_001366345.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Related
    ENSP00000376502.3, ENST00000392746.7
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  8. NM_001379417.1 → NP_001366346.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  9. NM_001379418.1 → NP_001366347.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3
    UniProtKB/TrEMBL
    B2R5R9
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 86
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:95 → 166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407 → 614
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  10. NM_001379419.1 → NP_001366348.1  DNA-binding protein RFX5 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL391069
    UniProtKB/TrEMBL
    B2R5R9
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 78
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:80 → 126
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:367 → 574
    RFX5_DNA_bdg; RFX5 DNA-binding domain

  11. NM_001379420.1 → NP_001366349.1  DNA-binding protein RFX5 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL391069
    UniProtKB/TrEMBL
    B2R5R9
    Conserved Domains (3) summary
    pfam18326
    Location:28 → 78
    RFX5_N; RFX5 N-terminal domain
    pfam02257
    Location:80 → 126
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:367 → 574
    RFX5_DNA_bdg; RFX5 DNA-binding domain

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    151340640..151347252 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426951.1 → XP_047282907.1  DNA-binding protein RFX5 isoform X1

    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3

  2. XM_024448791.2 → XP_024304559.1  DNA-binding protein RFX5 isoform X2

    UniProtKB/TrEMBL
    Q9UG77
    Conserved Domains (1) summary
    pfam14621
    Location:236 → 443
    RFX5_DNA_bdg; RFX5 DNA-binding domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    150464344..150470955 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338039.1 → XP_054194014.1  DNA-binding protein RFX5 isoform X1

    UniProtKB/Swiss-Prot
    B7Z848, D3DV19, E9PFU4, P48382, Q5VWC3

  2. XM_054338040.1 → XP_054194015.1  DNA-binding protein RFX5 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P48382.1 GenPept UniProtKB/Swiss-Prot:P48382

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