U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    RFX5 regulatory factor X5 [ Homo sapiens (human) ]

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

    Summary

    Go to the top of the page Help
    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
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    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
    		Compare labs

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    DNA-binding protein RFX5
    Names
    regulatory factor X 5
    regulatory factor X, 5 (influences HLA class II expression)

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_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

    Gene LinkOut

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

    Chemical Information
    Medical
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous