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RFX3 regulatory factor X3 [ Homo sapiens (human) ]

Gene ID: 5991, updated on 5-Mar-2024

Summary

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Official Symbol
RFX3provided by HGNC
Official Full Name
regulatory factor X3provided by HGNC
Primary source
HGNC:HGNC:9984
See related
Ensembl:ENSG00000080298 MIM:601337; AllianceGenome:HGNC:9984
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
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, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. Multiple transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]
Expression
Broad expression in testis (RPKM 2.7), brain (RPKM 2.6) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
9p24.2
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (3218297..3526001, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (3222120..3530379, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (3218297..3526001, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene coactivator associated arginine methyltransferase 1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:3181301-3181935 Neighboring gene uncharacterized LOC105375959 Neighboring gene long intergenic non-protein coding RNA 1231 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:3290904-3291705 Neighboring gene VISTA enhancer hs1350 Neighboring gene Sharpr-MPRA regulatory region 5337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28139 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:3478271-3479470 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:3525142-3525758 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28141 Neighboring gene uncharacterized LOC124902110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28142 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:3577789-3577989 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:3674142-3675341 Neighboring gene RFX3 divergent transcript

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. Auto-fatty acylation of transcription factor RFX3 regulates ciliogenesis. Chen B, et al. Proc Natl Acad Sci U S A, 2018 Sep 4. PMID 30127002, Free PMC Article
  2. RFX1 and RFX3 Transcription Factors Interact with the D Sequence of Adeno-Associated Virus Inverted Terminal Repeat and Regulate AAV Transduction. Julien L, et al. Sci Rep, 2018 Jan 9. PMID 29317724, Free PMC Article
  3. RFX3 modulation of FOXJ1 regulation of cilia genes in the human airway epithelium. Didon L, et al. Respir Res, 2013 Jul 3. PMID 23822649, Free PMC Article
  4. CircRFX3 Up-regulates Its Host Gene RFX3 to Facilitate Tumorigenesis and Progression of Glioma. Qian Y, et al. J Mol Neurosci, 2022 Jun. PMID 35416616
  5. RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies. El Zein L, et al. J Cell Sci, 2009 Sep 1. PMID 19671664

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircRFX3 Up-regulates Its Host Gene RFX3 to Facilitate Tumorigenesis and Progression of Glioma.
    Title: CircRFX3 Up-regulates Its Host Gene RFX3 to Facilitate Tumorigenesis and Progression of Glioma.
  2. RFX3 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.
  3. findings reveal a regulation of RFX3 transcription factor and link fatty acid metabolism and protein lipidation to the regulation of ciliogenesis.
    Title: Auto-fatty acylation of transcription factor RFX3 regulates ciliogenesis.
  4. FOXJ1 is an important regulator of cilia gene expression during ciliated cell differentiation, with RFX3 as a transcriptional co-activator to FOXJ1.
    Title: RFX3 modulation of FOXJ1 regulation of cilia genes in the human airway epithelium.
  5. Taken together, this study suggests ciliogenic RFX transcription factors regulate FGF-1B promoter activity and the maintenance of F1BGFP(+) NSPCs and GBM-SCs.
    Title: Ciliogenic RFX transcription factors regulate FGF1 gene promoter.
  6. RFX3 controls the expression of genes involved in primary ciliary dyskinesia.
    Title: RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies.
  7. novel role for the RFX family of transcription factors as modulators of Ras signalling in epithelial cells.
    Title: Involvement of RFX proteins in transcriptional activation from a Ras-responsive enhancer element.
  8. Data show that two regulatory factor for X box (RFX1 and 3) binding sites in exon1 of both the mouse and human microtubule-associated protein (MAP1A) gene are important for effective transcriptional repression in non-neuronal cells.
    Title: Role for RFX transcription factors in non-neuronal cell-specific inactivation of the microtubule-associated protein MAP1A promoter.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide meta-analysis of systolic blood pressure in children with sickle cell disease.
EBI GWAS Catalog

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

Clone Names

  • MGC87155, bA32F11.1

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
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 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 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in cell maturation ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in cilium-dependent cell motility ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in endocrine pancreas development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in epithelial cilium movement involved in determination of left/right asymmetry ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in positive regulation of type B pancreatic cell development ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of insulin secretion ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in type B pancreatic cell maturation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IC
Inferred by Curator
more info
 PubMed 
part_of transcription regulator complex ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
transcription factor RFX3
Names
DNA binding protein RFX3
regulatory factor X, 3 (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.

mRNA and Protein(s)

  1. NM_001282116.2 → NP_001269045.1  transcription factor RFX3 isoform b

    See identical proteins and their annotated locations for NP_001269045.1

    Status: REVIEWED

    Source sequence(s)
    AL133549, AL354941, AL365202
    Consensus CDS
    CCDS6449.1
    UniProtKB/Swiss-Prot
    A8K0H5, D3DRH8, D3DRH9, P48380, Q5JTL7, Q5JTL8, Q6NW13, Q8WTU4, Q95HL5, Q95HL6
    Related
    ENSP00000482598.1, ENST00000617270.5
    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 133
    RFX1_trans_act; RFX1 transcription activation region

  2. NM_001282117.2 → NP_001269046.1  transcription factor RFX3 isoform c

    Status: REVIEWED

    Source sequence(s)
    AL133549, AL354941, AL365202
    Consensus CDS
    CCDS75809.1
    UniProtKB/Swiss-Prot
    P48380
    Related
    ENSP00000303847.2, ENST00000302303.5
    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 133
    RFX1_trans_act; RFX1 transcription activation region

  3. NM_001377999.1 → NP_001364928.1  transcription factor RFX3 isoform d

    Status: REVIEWED

    Source sequence(s)
    AL133549, AL354941, AL365202
    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 134
    RFX1_trans_act; RFX1 transcription activation region

  4. NM_002919.4 → NP_002910.1  transcription factor RFX3 isoform a

    See identical proteins and their annotated locations for NP_002910.1

    Status: REVIEWED

    Source sequence(s)
    AL133549, AL354941, AL365202
    Consensus CDS
    CCDS6450.1
    UniProtKB/Swiss-Prot
    P48380
    Related
    ENSP00000351574.2, ENST00000358730.6
    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 137
    RFX1_trans_act; RFX1 transcription activation region

  5. NM_134428.3 → NP_602304.1  transcription factor RFX3 isoform b

    See identical proteins and their annotated locations for NP_602304.1

    Status: REVIEWED

    Source sequence(s)
    AL133549, BC022191, BM666287, BU170404, DB461398
    Consensus CDS
    CCDS6449.1
    UniProtKB/Swiss-Prot
    A8K0H5, D3DRH8, D3DRH9, P48380, Q5JTL7, Q5JTL8, Q6NW13, Q8WTU4, Q95HL5, Q95HL6
    Related
    ENSP00000371434.3, ENST00000382004.7
    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 133
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    3218297..3526001 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423701.1 → XP_047279657.1  transcription factor RFX3 isoform X13

  2. XM_047423699.1 → XP_047279655.1  transcription factor RFX3 isoform X11

  3. XM_047423696.1 → XP_047279652.1  transcription factor RFX3 isoform X8

  4. XM_024447632.2 → XP_024303400.1  transcription factor RFX3 isoform X4

    Conserved Domains (2) summary
    pfam02257
    Location:190 → 262
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:57 → 143
    RFX1_trans_act; RFX1 transcription activation region

  5. XM_006716844.3 → XP_006716907.1  transcription factor RFX3 isoform X6

    See identical proteins and their annotated locations for XP_006716907.1

    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 134
    RFX1_trans_act; RFX1 transcription activation region

  6. XM_017015000.3 → XP_016870489.1  transcription factor RFX3 isoform X6

    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 134
    RFX1_trans_act; RFX1 transcription activation region

  7. XM_024447631.2 → XP_024303399.1  transcription factor RFX3 isoform X1

    Conserved Domains (2) summary
    pfam02257
    Location:214 → 286
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:81 → 167
    RFX1_trans_act; RFX1 transcription activation region

  8. XM_024447630.2 → XP_024303398.1  transcription factor RFX3 isoform X1

    Conserved Domains (2) summary
    pfam02257
    Location:214 → 286
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:81 → 167
    RFX1_trans_act; RFX1 transcription activation region

  9. XM_024447635.2 → XP_024303403.1  transcription factor RFX3 isoform X6

    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 134
    RFX1_trans_act; RFX1 transcription activation region

  10. XM_047423688.1 → XP_047279644.1  transcription factor RFX3 isoform X1

  11. XM_047423697.1 → XP_047279653.1  transcription factor RFX3 isoform X9

  12. XM_047423695.1 → XP_047279651.1  transcription factor RFX3 isoform X7

  13. XM_006716840.3 → XP_006716903.1  transcription factor RFX3 isoform X2

    Conserved Domains (2) summary
    pfam02257
    Location:194 → 266
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:61 → 147
    RFX1_trans_act; RFX1 transcription activation region

  14. XM_047423694.1 → XP_047279650.1  transcription factor RFX3 isoform X6

  15. XM_024447634.2 → XP_024303402.1  transcription factor RFX3 isoform X6

    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 134
    RFX1_trans_act; RFX1 transcription activation region

  16. XM_047423692.1 → XP_047279648.1  transcription factor RFX3 isoform X6

  17. XM_047423693.1 → XP_047279649.1  transcription factor RFX3 isoform X6

  18. XM_047423698.1 → XP_047279654.1  transcription factor RFX3 isoform X10

  19. XM_047423691.1 → XP_047279647.1  transcription factor RFX3 isoform X5

  20. XM_047423689.1 → XP_047279645.1  transcription factor RFX3 isoform X3

  21. XM_047423687.1 → XP_047279643.1  transcription factor RFX3 isoform X1

  22. XM_011517998.3 → XP_011516300.1  transcription factor RFX3 isoform X6

    See identical proteins and their annotated locations for XP_011516300.1

    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 134
    RFX1_trans_act; RFX1 transcription activation region

  23. XM_006716843.3 → XP_006716906.1  transcription factor RFX3 isoform X6

    See identical proteins and their annotated locations for XP_006716906.1

    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51 → 134
    RFX1_trans_act; RFX1 transcription activation region

  24. XM_047423700.1 → XP_047279656.1  transcription factor RFX3 isoform X12

  25. XM_047423690.1 → XP_047279646.1  transcription factor RFX3 isoform X4

  26. XM_047423702.1 → XP_047279658.1  transcription factor RFX3 isoform X14

  27. XM_006716847.3 → XP_006716910.1  transcription factor RFX3 isoform X16

  28. XM_017015002.3 → XP_016870491.1  transcription factor RFX3 isoform X15

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    3222120..3530379 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363486.1 → XP_054219461.1  transcription factor RFX3 isoform X24

  2. XM_054363474.1 → XP_054219449.1  transcription factor RFX3 isoform X22

  3. XM_054363478.1 → XP_054219453.1  transcription factor RFX3 isoform X22

  4. XM_054363477.1 → XP_054219452.1  transcription factor RFX3 isoform X22

  5. XM_054363467.1 → XP_054219442.1  transcription factor RFX3 isoform X17

  6. XM_054363466.1 → XP_054219441.1  transcription factor RFX3 isoform X17

  7. XM_054363481.1 → XP_054219456.1  transcription factor RFX3 isoform X22

  8. XM_054363482.1 → XP_054219457.1  transcription factor RFX3 isoform X23

  9. XM_054363469.1 → XP_054219444.1  transcription factor RFX3 isoform X18

  10. XM_054363475.1 → XP_054219450.1  transcription factor RFX3 isoform X22

  11. XM_054363476.1 → XP_054219451.1  transcription factor RFX3 isoform X22

  12. XM_054363472.1 → XP_054219447.1  transcription factor RFX3 isoform X21

  13. XM_054363470.1 → XP_054219445.1  transcription factor RFX3 isoform X19

  14. XM_054363479.1 → XP_054219454.1  transcription factor RFX3 isoform X22

  15. XM_054363480.1 → XP_054219455.1  transcription factor RFX3 isoform X22

  16. XM_054363471.1 → XP_054219446.1  transcription factor RFX3 isoform X20

  17. XM_054363489.1 → XP_054219464.1  transcription factor RFX3 isoform X25

  18. XM_054363491.1 → XP_054219466.1  transcription factor RFX3 isoform X27

  19. XM_054363490.1 → XP_054219465.1  transcription factor RFX3 isoform X26

  20. XM_054363488.1 → XP_054219463.1  transcription factor RFX3 isoform X13

  21. XM_054363484.1 → XP_054219459.1  transcription factor RFX3 isoform X8

  22. XM_054363483.1 → XP_054219458.1  transcription factor RFX3 isoform X7

  23. XM_054363485.1 → XP_054219460.1  transcription factor RFX3 isoform X10

  24. XM_054363473.1 → XP_054219448.1  transcription factor RFX3 isoform X3

  25. XM_054363468.1 → XP_054219443.1  transcription factor RFX3 isoform X1

  26. XM_054363487.1 → XP_054219462.1  transcription factor RFX3 isoform X12

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P48380.2 GenPept UniProtKB/Swiss-Prot:P48380

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