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    RFX3 regulatory factor X3 [ Homo sapiens (human) ]

    Gene ID: 5991, updated on 2-Nov-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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    See RFX3 in Genome Data Viewer
    Location:
    9p24.2
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (3218297..3526001, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (3222120..3530379, complement)
    RS_2024_09 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 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. Dimeric RFX proteins contribute to the activity and lineage specificity of the interleukin-5 receptor alpha promoter through activation and repression domains. Iwama A, et al. Mol Cell Biol, 1999 Jun. PMID 10330134, Free PMC Article

    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
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in 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_2024_08

    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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