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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
  • DNA Binding Protein RFX3 3
  • Regulatory Factor X 3 4

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. 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 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

Additional gene information for RFX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFX3 Gene

Genomics for RFX3 Gene

GeneHancer (GH) Regulatory Elements for RFX3 Gene

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 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.7 -687 6.4 PKNOX1 FOXA2 SMAD1 MLX ARID4B NEUROD1 SIN3A DMAP1 ZNF2 YY1 RFX3-AS1 RFX3 PUM3 GC09P003267
GH09J003473 Promoter/Enhancer 0.9 EPDnew ENCODE 650.2 +52.4 52393 0.2 MAX SPI1 PIR60517 GC09P003471 RFX3 GC09P003267
GH09J002630 Enhancer 0.5 ENCODE 11.9 +895.7 895748 0.2 ZNF316 MAFF ZNF157 MAFG EMSY MAFK RFX3 PUM3 PIR48978 VLDLR VLDLR-AS1
GH09J004499 Enhancer 0.9 ENCODE dbSUPER 6.1 -975.7 -975730 3.8 FOXA2 NFIB MAX RAD21 YY1 EGR1 HNF4G RXRA REST GABPA RFX3 SLC1A1 GC09P004528 GC09P004427
GH09J003507 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 2.4 +17.2 17155 3.1 SMAD1 FEZF1 YBX1 ZNF2 ZNF213 ATF7 RUNX3 TSHZ1 ZNF488 ZNF592 RFX3 GC09P003480 GC09P003267
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for RFX3 Gene

Genomic Locations for RFX3 Gene
chr9:3,218,297-3,526,004
(GRCh38/hg38)
Size:
307,708 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

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:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA --
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding TAS 8600444
GO:0003700 DNA binding transcription factor activity NAS 8600444
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding TAS 8289803
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

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

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
cytosol 2
cytoskeleton 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 20413507
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

No Data Available

Gene Ontology (GO) - Biological Process for RFX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003309 type B pancreatic cell differentiation IBA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated ISS --
GO:0006357 regulation of transcription by RNA polymerase II IBA --
GO:0007275 multicellular organism development 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

Unigene Clusters for RFX3 Gene

Regulatory factor X, 3 (influences HLA class II expression):
Representative Sequences:

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
ECgene alternative splicing isoforms for
RFX3

Expression for RFX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of RFX3 Gene:

RFX3

SOURCE GeneReport for Unigene cluster for RFX3 Gene:

Hs.136829

Evidence on tissue expression from TISSUES for RFX3 Gene

  • Nervous system(4.4)
  • Muscle(4.2)
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 34
  • 99 (a)
OneToOne
LOC538070 33
  • 95.82 (n)
chimpanzee
(Pan troglodytes)
Mammalia RFX3 33
  • 98.11 (n)
oppossum
(Monodelphis domestica)
Mammalia RFX3 34
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RFX3 34
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RFX3 34 33
  • 94.08 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rfx3 16 34 33
  • 92.48 (n)
chicken
(Gallus gallus)
Aves RFX3 34 33
  • 88.87 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFX3 34
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rfx3 33
  • 84.4 (n)
zebrafish
(Danio rerio)
Actinopterygii rfx3 34 33
  • 69.68 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003943 33
  • 58.14 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rfx 34 35 33
  • 52.74 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea daf-19 33
  • 51.29 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 45 (a)
OneToMany
Cin.4580 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4580 33
Species where no ortholog for RFX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 from dbSNP and Humsavar for RFX3 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000006808 -- 3,428,113(-) C/G genic_upstream_transcript_variant, intron_variant
rs1000010243 -- 3,221,010(-) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000035033 -- 3,254,534(-) C/A/G genic_downstream_transcript_variant, intron_variant
rs1000035398 -- 3,526,635(-) T/C upstream_transcript_variant
rs1000053327 -- 3,396,539(-) C/G genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

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

Additional Disease Information for RFX3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RFX3 Gene.

No data available for MalaCards , 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 58
  2. Rfx6 directs islet formation and insulin production in mice and humans. (PMID: 20148032) Smith SB … German MS (Nature 2010) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4 58
  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 58

Products for RFX3 Gene

Sources for RFX3 Gene

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