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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 RFX5.

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 Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFX3 Gene

Genomics for RFX3 Gene

Regulatory Elements for RFX3 Gene

Promoters for RFX3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around RFX3 on UCSC Golden Path with GeneCards custom track

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

Proteomics data for RFX3 Gene at MOPED

Post-translational modifications for RFX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

No data available for DME Specific Peptides for RFX3 Gene

Domains & Families for RFX3 Gene

Gene Families for RFX3 Gene

Protein Domains for RFX3 Gene

Graphical View of Domain Structure for InterPro Entry

P48380

UniProtKB/Swiss-Prot:

RFX3_HUMAN :
  • Contains 1 RFX-type winged-helix DNA-binding domain.
  • Belongs to the RFX family.
Domain:
  • Contains 1 RFX-type winged-helix DNA-binding domain.
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:0005515 protein binding IPI 20148032
GO:0044212 transcription regulatory region DNA binding IDA 20148032
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

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

In Situ Assay 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
Jensen Localization Image for RFX3 Gene COMPARTMENTS Subcellular localization image for RFX3 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

No data available for Gene Ontology (GO) - Cellular Components for RFX3 Gene

Pathways & Interactions for RFX3 Gene

SuperPathways for RFX3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RFX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA,ISS --
GO:0045892 negative regulation of transcription, DNA-templated IDA 12411430
GO:0045893 positive regulation of transcription, DNA-templated IDA 20148032
GO:0048469 cell maturation ISS 20413507
GO:0050796 regulation of insulin secretion ISS 20413507
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:

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 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, MOPED, and MaxQB for RFX3 Gene



SOURCE GeneReport for Unigene cluster for RFX3 Gene Hs.136829

genes like me logo Genes that share expression patterns with RFX3: view

Protein tissue co-expression partners for RFX3 Gene

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 LOC538070 35
  • 95.82 (n)
  • 99.47 (a)
RFX3 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RFX3 35
  • 94.08 (n)
  • 99.47 (a)
RFX3 36
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RFX3 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rfx3 36
  • 99 (a)
OneToOne
Rfx3 16
Rfx3 35
  • 92.48 (n)
  • 98.93 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia RFX3 36
  • 97 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RFX3 35
  • 98.11 (n)
  • 97.56 (a)
chicken
(Gallus gallus)
Aves RFX3 35
  • 88.87 (n)
  • 96.4 (a)
RFX3 36
  • 96 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFX3 36
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rfx3 35
  • 84.4 (n)
  • 93.45 (a)
zebrafish
(Danio rerio)
Actinopterygii rfx3 35
  • 69.68 (n)
  • 76.01 (a)
rfx3 36
  • 75 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Rfx 37
  • 55 (a)
Rfx 35
  • 52.74 (n)
  • 52.63 (a)
Rfx 36
  • 29 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003943 35
  • 58.14 (n)
  • 62.05 (a)
worm
(Caenorhabditis elegans)
Secernentea daf-19 35
  • 51.29 (n)
  • 43.4 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4580 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 45 (a)
OneToMany
Species with no ortholog for RFX3:
  • 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
rs493667 -- 3,234,830(+) AGAAG(A/G)TTTTT intron-variant
rs494348 -- 3,261,665(+) acaag(A/G)agttg intron-variant
rs495665 -- 3,225,608(-) GACTA(C/T)TTTAT intron-variant
rs498371 -- 3,235,352(+) AGAGG(A/T)GGAAG intron-variant
rs499111 -- 3,235,404(+) AAGTC(A/T)TCAAT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv892086 CNV Gain 21882294
nsv892089 CNV Gain 21882294
nsv466091 CNV Loss 19166990
nsv416089 CNV Insertion 16902084
nsv892090 CNV Loss 21882294
esv2659402 CNV Deletion 23128226
nsv892091 CNV Loss 21882294
nsv522711 CNV Gain 19592680
esv1255308 CNV Insertion 17803354
nsv415859 CNV Insertion 16902084
esv2477708 CNV Deletion 19546169

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

HapMap Linkage Disequilibrium report
RFX3
Human Gene Mutation Database (HGMD)
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

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 67
  2. Human regulatory factor X 4 (RFX4) is a testis-specific dimeric DNA- binding protein that cooperates with other human RFX members. (PMID: 11682486) Morotomi-Yano K. … Miki Y. (J. Biol. Chem. 2002) 3 23
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3
  5. RFX3 modulation of FOXJ1 regulation of cilia genes in the human airway epithelium. (PMID: 23822649) Didon L. … Crystal R.G. (Respir. Res. 2013) 3

Products for RFX3 Gene

Sources for RFX3 Gene

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