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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
  • 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. Diseases associated with RFX3 include Testicular Lymphoma and Pineal Gland Cancer. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding 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

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

Genomics for RFX3 Gene

Regulatory Elements for RFX3 Gene

Enhancers for RFX3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09G004499 0.9 ENCODE dbSUPER 6.1 -975.7 -975730 3.8 NFIB MAX RAD21 FOXA1 YY1 GABPA NFIC JUND ATF3 HNF4G RFX3 SLC1A1 GC09P004528
GH09G003507 1.8 FANTOM5 Ensembl ENCODE dbSUPER 2.4 +17.2 17155 3.1 YBX1 FEZF1 ZNF2 GATA2 ZNF488 TSHZ1 TBX21 ZNF592 ZNF610 SMARCA4 RFX3 GC09P003480
GH09G003523 1.4 ENCODE dbSUPER 0.7 -0.7 -688 6.4 FOXA2 PKNOX1 CREB3L1 MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 PUM3 RFX3-AS1 RFX3
GH09G003522 0.8 ENCODE dbSUPER 0.7 +3.7 3701 0.5 POLR2A SMARCA4 IKZF1 RELB TBX21 IKZF2 RFX3 GC09P003480
GH09G003511 1 Ensembl dbSUPER 0.4 +14.4 14404 0.4 SOX13 FOXA2 CHAMP1 FOSL1 NR2F6 SMARCE1 SOX5 GATAD2A NR2F1 JUNB RFX3 GC09P003480
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RFX3 on UCSC Golden Path with GeneCards custom track

Promoters for RFX3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000232624 104 3801 FOXA2 PKNOX1 CREB3L1 MLX WRNIP1 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for RFX3 Gene

Chromosome:
9
Start:
3,218,297 bp from pter
End:
3,526,004 bp from pter
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

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

GENATLAS Biochemistry:
transactivating DNA binding regulator 3,involved in MHC class II expression,binding the MHC promoter box X
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).

Gene Ontology (GO) - Molecular Function for RFX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IBA --
GO:0003677 DNA binding TAS 8600444
GO:0003700 transcription factor activity, sequence-specific DNA binding NAS 8600444
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding TAS 8289803
GO:0005515 protein binding IPI 16189514
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:

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

Flow Cytometry 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

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: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

Transcripts for RFX3 Gene

Unigene Clusters for RFX3 Gene

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

CRISPR Products

Inhibitory RNA Products

Flow Cytometry 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, PaxDb, 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

Primer Products

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 35
  • 99 (a)
OneToOne
LOC538070 34
  • 95.82 (n)
chimpanzee
(Pan troglodytes)
Mammalia RFX3 34
  • 98.11 (n)
oppossum
(Monodelphis domestica)
Mammalia RFX3 35
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RFX3 35
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RFX3 34 35
  • 94.08 (n)
mouse
(Mus musculus)
Mammalia Rfx3 34 16 35
  • 92.48 (n)
chicken
(Gallus gallus)
Aves RFX3 34 35
  • 88.87 (n)
lizard
(Anolis carolinensis)
Reptilia RFX3 35
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rfx3 34
  • 84.4 (n)
zebrafish
(Danio rerio)
Actinopterygii rfx3 34 35
  • 69.68 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003943 34
  • 58.14 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rfx 36 34 35
  • 52.74 (n)
worm
(Caenorhabditis elegans)
Secernentea daf-19 34
  • 51.29 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 45 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4580 34
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)

Paralogs for RFX3 Gene

Paralogs for RFX3 Gene

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

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 Sequence Context AA Info Type
rs1000006808 -- 3,428,113(+) GTTGC(C/G)TCATA intron-variant
rs1000010243 -- 3,221,010(+) TCTCA(C/T)CTCAA utr-variant-3-prime
rs1000035033 -- 3,254,534(+) AATAT(C/G)TGAAA intron-variant
rs1000035398 -- 3,526,635(+) CCGCC(C/T)CCTGA upstream-variant-2KB
rs1000053327 -- 3,396,539(+) ATAAT(C/G)CTTTG intron-variant, upstream-variant-2KB

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)

Relevant External Links for RFX3 Gene

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

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

Disorders for RFX3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for RFX3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
testicular lymphoma
  • lymphoma of the testis
pineal gland cancer
  • malignant pineal region tumor
- elite association - COSMIC cancer census association via MalaCards
Search RFX3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RFX3

Genetic Association Database (GAD)
RFX3
Human Genome Epidemiology (HuGE) Navigator
RFX3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RFX3
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. (Mol. Cell. Biol. 1994) 2 3 4 64
  2. Rfx6 directs islet formation and insulin production in mice and humans. (PMID: 20148032) Smith S.B. … German M.S. (Nature 2010) 3 4 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray S.J. … Dunham I. (Nature 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for RFX3 Gene

Sources for RFX3 Gene

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