RFX3 Gene

Name	regulatory factor X, 3 (influences HLA class II expression)
Description	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]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nRFX3 plays a critical role in ciliogenesis by coordinating the expression of genes required for both ciliary assembly and motility. In multiciliated cells, RFX3 is essential for the proper growth and beating efficiency of motile cilia, acting in part via the regulation of the FOXJ1 transcription factor and by directly binding and activating promoters of axonemal dynein genes. Furthermore, its activity is fine‐tuned by posttranslational modifications – notably S‐fatty acylation at a conserved cysteine – which is necessary for RFX3 homodimerization and full activation of downstream ciliary gene expression, ultimately affecting signaling pathways such as Hedgehog. (See"}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": ")\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its role in ciliogenesis, RFX3 functions as a versatile transcriptional regulator in diverse cellular contexts. In non‐neuronal cells, for example, it participates in the repression of the MAP1A 5′ promoter, thereby contributing to cell type–specific gene expression patterns. In neural stem/progenitor cells and glioblastoma stem cells, RFX3 collaborates with RFX2 to bind a critical cis‐acting element in the FGF-1B promoter, ultimately influencing neurosphere formation and stem cell maintenance. In addition, RFX3 has been implicated in the modulation of Ras-dependent transcriptional responses in epithelial cells through binding to specific regulatory elements, and it even associates with viral genome regulatory sequences to regulate adeno-associated virus–mediated transgene expression. (See"}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "7"}]}, {"type": "t", "text": ")\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nEmerging evidence also points to novel roles of RFX3 in cancer biology. Notably, elevated levels of circRFX3 have been detected in glioma, suggesting that aberrant regulation of the RFX3 transcript may contribute to tumorigenesis and tumor progression in the brain. (See"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": ")\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Loubna El Zein, Aouatef Ait-Lounis, Laurette Morlé, et al. "}, {"type": "b", "children": [{"type": "t", "text": "RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.048348"}], "href": "https://doi.org/10.1242/jcs.048348"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19671664"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19671664"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Lukas Didon, Rachel K Zwick, Ion Wa Chao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "RFX3 modulation of FOXJ1 regulation of cilia genes in the human airway epithelium."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Respir Res (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/1465-9921-14-70"}], "href": "https://doi.org/10.1186/1465-9921-14-70"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23822649"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23822649"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Baoen Chen, Jixiao Niu, Johannes Kreuzer, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Auto-fatty acylation of transcription factor RFX3 regulates ciliogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1800949115"}], "href": "https://doi.org/10.1073/pnas.1800949115"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30127002"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30127002"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Atsuo Nakayama, Hideki Murakami, Naomi Maeyama, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Role for RFX transcription factors in non-neuronal cell-specific inactivation of the microtubule-associated protein MAP1A promoter."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M209574200"}], "href": "https://doi.org/10.1074/jbc.M209574200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12411430"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12411430"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Susann Maijgren, Inderpreet Sur, Mats Nilsson, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Involvement of RFX proteins in transcriptional activation from a Ras-responsive enhancer element."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Arch Dermatol Res (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00403-004-0456-5"}], "href": "https://doi.org/10.1007/s00403-004-0456-5"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15024578"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15024578"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Yi-Chao Hsu, Chien-Yu Kao, Yu-Fen Chung, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Ciliogenic RFX transcription factors regulate FGF1 gene promoter."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biochem (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcb.24127"}], "href": "https://doi.org/10.1002/jcb.24127"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22415835"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22415835"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Laura Julien, Julie Chassagne, Cécile Peccate, et al. "}, {"type": "b", "children": [{"type": "t", "text": "RFX1 and RFX3 Transcription Factors Interact with the D Sequence of Adeno-Associated Virus Inverted Terminal Repeat and Regulate AAV Transduction."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41598-017-18604-3"}], "href": "https://doi.org/10.1038/s41598-017-18604-3"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29317724"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29317724"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Yu Qian, Baochun Cheng, Jing Luo, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CircRFX3 Up-regulates Its Host Gene RFX3 to Facilitate Tumorigenesis and Progression of Glioma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Mol Neurosci (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s12031-022-02005-x"}], "href": "https://doi.org/10.1007/s12031-022-02005-x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35416616"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35416616"}]}]}]}
Proteins	RFX3_HUMAN
NCBI Gene ID	5991
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

RFX3 has 7,023 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 114 datasets.

Click the + buttons to view associations for RFX3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

RFX3 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of RFX3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of RFX3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of RFX3 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of RFX3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of RFX3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of RFX3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of RFX3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of RFX3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of RFX3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of RFX3 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of RFX3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of RFX3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with RFX3 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of RFX3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of RFX3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of RFX3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with RFX3 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing RFX3 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of RFX3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing RFX3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing RFX3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing RFX3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing RFX3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with RFX3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with RFX3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of RFX3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with RFX3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with RFX3 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with RFX3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of RFX3 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by RFX3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with RFX3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with RFX3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with RFX3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with RFX3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with RFX3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at RFX3 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of RFX3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of RFX3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing RFX3 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.