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. Mu... See more...

Aliases for RFX3 Gene

Aliases for RFX3 Gene

  • Regulatory Factor X3 2 3 5
  • Regulatory Factor X, 3 (Influences HLA Class II Expression) 2 3
  • Transcription Factor RFX3 3 4
  • DNA Binding Protein RFX3 3
  • Regulatory Factor X 3 4
  • RFX3 5

External Ids for RFX3 Gene

Previous GeneCards Identifiers for RFX3 Gene

  • GC09M003378
  • GC09M003205

Summaries for RFX3 Gene

Entrez Gene Summary for RFX3 Gene

  • 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]

GeneCards Summary for RFX3 Gene

RFX3 (Regulatory Factor X3) is a Protein Coding gene. Diseases associated with RFX3 include Cellular Ependymoma and Visceral Heterotaxy. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and transcription regulatory region DNA binding. An important paralog of this gene is RFX2.

UniProtKB/Swiss-Prot Summary for RFX3 Gene

  • Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Regulates the expression of genes involved in ciliary assembly (DYNC2LI1, FOXJ1 and BBS4) and genes involved in ciliary motility (DNAH11, DNAH9 and DNAH5) (By similarity). Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP (polypeptide-producing) cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes (PubMed:20148032). Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells (PubMed:12411430).

Gene Wiki entry for RFX3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RFX3 Gene

Genomics for RFX3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RFX3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J003523 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 0.0 -25 6.7 SP1 HNRNPL CREB1 ZNF629 PRDM10 REST RFX1 SOX13 NFKBIZ POLR2A RFX3 RFX3-AS1 piR-48209-683 GLIS3
GH09J003473 Promoter/Enhancer 0.7 EPDnew ENCODE 600.2 +52.9 52918 0.2 SPI1 MAX CTCF piR-37472-010 RFX3 lnc-KCNV2-7 PUM3
GH09J002630 Enhancer 0.6 Ensembl ENCODE 11.9 +896.3 896328 0.8 ZNF157 ZNF316 MAFF MAFK MAFG EMSY RFX3 PUM3 piR-54979 VLDLR VLDLR-AS1 KCNV2
GH09J004499 Enhancer 1 Ensembl ENCODE dbSUPER 6.1 -975.2 -975205 3.8 REST SP1 FOXA2 ATF3 YY1 GABPA ZBTB33 JUND NFIC NFIB RFX3 SLC1A1 piR-57176-628 PLPP6
GH09J003507 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 2.4 +17.7 17680 3.1 PRDM10 RFX1 PRDM1 RELA ZSCAN4 ZNF24 IKZF2 BRD9 ZNF501 TRIM22 RFX3 lnc-KCNV2-9 lnc-KCNV2-8 PUM3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RFX3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RFX3

Top Transcription factor binding sites by QIAGEN in the RFX3 gene promoter:
  • AREB6
  • C/EBPalpha
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • FOXD3
  • Nkx2-5

Genomic Locations for RFX3 Gene

Genomic Locations for RFX3 Gene
chr9:3,218,297-3,526,529
(GRCh38/hg38)
Size:
308,233 bases
Orientation:
Minus strand
chr9:3,218,297-3,526,004
(GRCh37/hg19)
Size:
307,708 bases
Orientation:
Minus strand

Genomic View for RFX3 Gene

Genes around RFX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RFX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RFX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RFX3 Gene

Proteins for RFX3 Gene

  • Protein details for RFX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P48380-RFX3_HUMAN
    Recommended name:
    Transcription factor RFX3
    Protein Accession:
    P48380
    Secondary Accessions:
    • A8K0H5
    • D3DRH8
    • D3DRH9
    • Q5JTL7
    • Q5JTL8
    • Q6NW13
    • Q8WTU4
    • Q95HL5
    • Q95HL6

    Protein attributes for RFX3 Gene

    Size:
    749 amino acids
    Molecular mass:
    83530 Da
    Quaternary structure:
    • Heterodimer; heterodimerizes with RFX1 and RFX2, and RFX6.

    Alternative splice isoforms for RFX3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RFX3 Gene

Post-translational modifications for RFX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RFX3 Gene

Domains & Families for RFX3 Gene

Gene Families for RFX3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for RFX3 Gene

InterPro:
Blocks:
  • DNA-binding RFX
  • RFX1 transcription activation region
ProtoNet:

Suggested Antigen Peptide Sequences for RFX3 Gene

GenScript: Design optimal peptide antigens:
  • Regulatory factor X, 3 (Influences HLA class II expression) (B1ANP5_HUMAN)
  • Regulatory factor X, 3 (Influences HLA class II expression) (B1ANP6_HUMAN)
  • Regulatory factor X, 3 (Influences HLA class II expression) (B1ANP7_HUMAN)
  • Regulatory factor X, 3 (Influences HLA class II expression) (Q5JTM0_HUMAN)
  • Regulatory factor X, 3 (Influences HLA class II expression) (Q5JTM1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P48380

UniProtKB/Swiss-Prot:

RFX3_HUMAN :
  • Belongs to the RFX family.
Family:
  • Belongs to the RFX family.
genes like me logo Genes that share domains with RFX3: view

Function for RFX3 Gene

Molecular function for RFX3 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Regulates the expression of genes involved in ciliary assembly (DYNC2LI1, FOXJ1 and BBS4) and genes involved in ciliary motility (DNAH11, DNAH9 and DNAH5) (By similarity). Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP (polypeptide-producing) cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes (PubMed:20148032). Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells (PubMed:12411430).
GENATLAS Biochemistry:
transactivating DNA binding regulator 3,involved in MHC class II expression,binding the MHC promoter box X

Phenotypes From GWAS Catalog for RFX3 Gene

Gene Ontology (GO) - Molecular Function for RFX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IDA 20148032
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific TAS,ISM 19274049
GO:0003677 DNA binding TAS 8600444
GO:0003700 DNA-binding transcription factor activity NAS,IBA 21873635
genes like me logo Genes that share ontologies with RFX3: view
genes like me logo Genes that share phenotypes with RFX3: view

Animal Models for RFX3 Gene

MGI Knock Outs for RFX3:
  • Rfx3 Rfx3<tm1.1Wrth>
  • Rfx3 Rfx3<tm2.1Wrth>

Animal Model Products

CRISPR Products

Targeted motifs for RFX3 Gene
HOMER Transcription Factor Regulatory Elements motif RFX3
  • Consensus sequence: CGGTTGCCATGGCAAC Submotif: canonical Cell Type: K562 GEO ID: SRA012198

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFX3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for RFX3 Gene

Localization for RFX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFX3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RFX3 gene
Compartment Confidence
nucleus 5
extracellular 3
cytoskeleton 2
plasma membrane 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RFX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA,ISA --
GO:0005576 extracellular region IEA --
GO:0005634 nucleus TAS,IC 12411430
GO:0005667 transcription factor complex IC 20413507
genes like me logo Genes that share ontologies with RFX3: view

Pathways & Interactions for RFX3 Gene

PathCards logo

SuperPathways for RFX3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RFX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated ISS --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007368 determination of left/right symmetry IEA --
genes like me logo Genes that share ontologies with RFX3: view

No data available for Pathways by source and SIGNOR curated interactions for RFX3 Gene

Drugs & Compounds for RFX3 Gene

No Compound Related Data Available

Transcripts for RFX3 Gene

mRNA/cDNA for RFX3 Gene

5 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFX3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RFX3 Gene

No ASD Table

Relevant External Links for RFX3 Gene

GeneLoc Exon Structure for
RFX3

Expression for RFX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RFX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RFX3 Gene

This gene is overexpressed in Blymphocyte (30.8), Testis (16.6), Fetal Brain (12.3), and CD8 Tcells (9.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RFX3 Gene



Protein tissue co-expression partners for RFX3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RFX3

SOURCE GeneReport for Unigene cluster for RFX3 Gene:

Hs.136829

Evidence on tissue expression from TISSUES for RFX3 Gene

  • Nervous system(4.5)
  • Muscle(4.3)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with RFX3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RFX3 Gene

Orthologs for RFX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RFX3 Gene

Organism Taxonomy Gene Similarity Type Details
Cow
(Bos Taurus)
Mammalia RFX3 31
  • 99 (a)
OneToOne
LOC538070 30
  • 95.82 (n)
Chimpanzee
(Pan troglodytes)
Mammalia RFX3 30
  • 98.11 (n)
Oppossum
(Monodelphis domestica)
Mammalia RFX3 31
  • 98 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RFX3 31
  • 97 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia RFX3 30 31
  • 94.08 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rfx3 30 17 31
  • 92.48 (n)
OneToOne
Chicken
(Gallus gallus)
Aves RFX3 30 31
  • 88.87 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RFX3 31
  • 96 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rfx3 30
  • 84.4 (n)
Zebrafish
(Danio rerio)
Actinopterygii rfx3 30 31
  • 69.68 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003943 30
  • 58.14 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta Rfx 30 31 32
  • 52.74 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea daf-19 30
  • 51.29 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 45 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4580 30
Species where no ortholog for RFX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for RFX3 Gene

ENSEMBL:
Gene Tree for RFX3 (if available)
TreeFam:
Gene Tree for RFX3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RFX3: view image

Paralogs for RFX3 Gene

Paralogs for RFX3 Gene

(3) SIMAP similar genes for RFX3 Gene using alignment to 9 proteins:

  • RFX3_HUMAN
  • A9Z1Z2_HUMAN
  • F6UGA0_HUMAN
  • F6USP3_HUMAN
  • F6UV76_HUMAN
  • F6XM74_HUMAN
  • H0Y790_HUMAN
  • H0Y7W5_HUMAN
  • H0Y7Z4_HUMAN
genes like me logo Genes that share paralogs with RFX3: view

Variants for RFX3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RFX3 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
768277 Benign: not provided 3,257,053(-) A/G SYNONYMOUS_VARIANT
776762 Likely Benign: not provided 3,248,035(-) G/A SYNONYMOUS_VARIANT
778032 Benign: not provided 3,228,838(-) G/A INTRON_VARIANT
778377 Benign: not provided 3,257,122(-) C/T SYNONYMOUS_VARIANT
788672 Benign: not provided 3,271,018(-) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for RFX3 Gene

Structural Variations from Database of Genomic Variants (DGV) for RFX3 Gene

Variant ID Type Subtype PubMed ID
esv1255308 CNV insertion 17803354
esv2477708 CNV deletion 19546169
esv2659402 CNV deletion 23128226
esv2762782 CNV loss 21179565
esv3331489 CNV insertion 20981092
esv3544440 CNV deletion 23714750
esv3619307 CNV loss 21293372
esv3619310 CNV loss 21293372
esv3619312 CNV loss 21293372
nsv1017474 CNV gain 25217958
nsv1077086 CNV deletion 25765185
nsv1136013 CNV deletion 24896259
nsv1148671 CNV deletion 26484159
nsv415859 CNV insertion 16902084
nsv416089 CNV insertion 16902084
nsv466091 CNV loss 19166990
nsv522711 CNV gain 19592680
nsv613145 CNV loss 21841781
nsv613146 CNV loss 21841781
nsv613147 CNV loss 21841781
nsv950831 CNV duplication 24416366
nsv956145 CNV deletion 24416366
nsv972292 CNV duplication 23825009

Variation tolerance for RFX3 Gene

Residual Variation Intolerance Score: 5.93% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.92; 19.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RFX3 Gene

Human Gene Mutation Database (HGMD)
RFX3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFX3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFX3 Gene

Disorders for RFX3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RFX3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
cellular ependymoma
  • epithelial ependymoma
visceral heterotaxy
  • heterotaxia
primary ciliary dyskinesia
  • pcd
- elite association - COSMIC cancer census association via MalaCards
Search RFX3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RFX3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RFX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RFX3 Gene

Publications for RFX3 Gene

  1. RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. (PMID: 8289803) Reith W … Mach B (Molecular and cellular biology 1994) 2 3 4
  2. Rfx6 directs islet formation and insulin production in mice and humans. (PMID: 20148032) Smith SB … German MS (Nature 2010) 3 4
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for RFX3 Gene

Sources for RFX3 Gene