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Aliases for RBFOX3 Gene

Aliases for RBFOX3 Gene

  • RNA Binding Fox-1 Homolog 3 2 3 5
  • RNA Binding Protein, Fox-1 Homolog 3 2 3
  • Hexaribonucleotide Binding Protein 3 2 3
  • Neuronal Nuclei Antigen 3 4
  • Fox-1 Homolog C 3 4
  • NeuN Antigen 3 4
  • RNA Binding Protein, Fox-1 Homolog (C. Elegans) 3 2
  • RNA Binding Protein Fox-1 Homolog 3 3
  • Neuronal Nuclei 2
  • HRNBP3 3
  • FOX-3 3
  • FOX3 3
  • NEUN 3

External Ids for RBFOX3 Gene

Previous GeneCards Identifiers for RBFOX3 Gene

  • GC17M072508
  • GC17M077086

Summaries for RBFOX3 Gene

Entrez Gene Summary for RBFOX3 Gene

  • This gene encodes a member of the RNA-binding FOX protein family which is involved in the regulation of alternative splicing of pre-mRNA. The protein has an N-terminal proline-rich region, an RNA recognition motif (RRM) domain, and a C-terminal alanine-rich region. This gene produces the neuronal nuclei (NeuN) antigen that has been widely used as a marker for post-mitotic neurons. This gene has its highest expression in the central nervous system and plays a prominent role in neural tissue development and regulation of adult brain function. Mutations in this gene have been associated with numerous neurological disorders. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2017]

GeneCards Summary for RBFOX3 Gene

RBFOX3 (RNA Binding Fox-1 Homolog 3) is a Protein Coding gene. Diseases associated with RBFOX3 include Benign Epilepsy With Centrotemporal Spikes and Sella Turcica Neoplasm. Among its related pathways are Neuroscience. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is RBFOX1.

UniProtKB/Swiss-Prot for RBFOX3 Gene

  • Pre-mRNA alternative splicing regulator. Regulates alternative splicing of RBFOX2 to enhance the production of mRNA species that are targeted for nonsense-mediated decay (NMD).

Additional gene information for RBFOX3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RBFOX3 Gene

Genomics for RBFOX3 Gene

GeneHancer (GH) Regulatory Elements for RBFOX3 Gene

Promoters and enhancers for RBFOX3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J080252 Promoter/Enhancer 2.9 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5.2 -648.6 -648598 14.2 CLOCK MLX ZFP64 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF143 MEF2D RNF213 GC17M080259 EIF4A3 ENSG00000262768 ENSG00000262580 CARD14 CEP131 RPL12P37 SLC26A11 RBFOX3
GH17J079149 Enhancer 0.4 FANTOM5 6.8 +461.0 461029 0.2 GLIS2 GLIS1 GC17M079150 RBFOX3 ENSG00000266711
GH17J079219 Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 2 +390.7 390672 2.2 GLIS2 POLR2A ZSCAN4 CTBP2 EZH2 CBX8 RBFOX3 PIR62880 GC17M079268
GH17J079273 Enhancer 0.2 FANTOM5 7.4 +337.2 337162 0.2 GC17M079269 RBFOX3 GC17P079350
GH17J079394 Enhancer 0.5 FANTOM5 2.7 +217.0 217044 0.2 TCF12 CTCF ATF1 NFATC1 CREB1 STAT5A RBFOX3 GC17M079381 PIR34960
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RBFOX3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for RBFOX3 Gene

Genomic Locations for RBFOX3 Gene
521,757 bases
Minus strand
528,124 bases
Minus strand

Genomic View for RBFOX3 Gene

Genes around RBFOX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBFOX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBFOX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RBFOX3 Gene

Proteins for RBFOX3 Gene

  • Protein details for RBFOX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    RNA binding protein fox-1 homolog 3
    Protein Accession:
    Secondary Accessions:
    • B4DEG6
    • B4DF29

    Protein attributes for RBFOX3 Gene

    312 amino acids
    Molecular mass:
    33873 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for RBFOX3 Gene


neXtProt entry for RBFOX3 Gene

Post-translational modifications for RBFOX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RBFOX3 Gene

Domains & Families for RBFOX3 Gene

Gene Families for RBFOX3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RBFOX3 Gene

Suggested Antigen Peptide Sequences for RBFOX3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RBFOX3: view

No data available for UniProtKB/Swiss-Prot for RBFOX3 Gene

Function for RBFOX3 Gene

Molecular function for RBFOX3 Gene

UniProtKB/Swiss-Prot Function:
Pre-mRNA alternative splicing regulator. Regulates alternative splicing of RBFOX2 to enhance the production of mRNA species that are targeted for nonsense-mediated decay (NMD).

Phenotypes From GWAS Catalog for RBFOX3 Gene

Gene Ontology (GO) - Molecular Function for RBFOX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA --
GO:0003729 mRNA binding IBA --
genes like me logo Genes that share ontologies with RBFOX3: view
genes like me logo Genes that share phenotypes with RBFOX3: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RBFOX3 Gene

Localization for RBFOX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBFOX3 Gene

Nucleus. Cytoplasm. Note=Largely restricted to neuronal nuclei. However, significant cytoplasmic localization in neurons from brains from HIV-infected individuals with cognitive impairment. {ECO:0000269 PubMed:24215932}.

Subcellular locations from

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 RBFOX3 gene
Compartment Confidence
nucleus 5
cytoskeleton 3
extracellular 2
mitochondrion 2
cytosol 2
plasma membrane 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RBFOX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IBA --
GO:0043025 neuronal cell body IEA --
GO:0043204 perikaryon IEA --
genes like me logo Genes that share ontologies with RBFOX3: view

Pathways & Interactions for RBFOX3 Gene

SuperPathways for RBFOX3 Gene

SuperPathway Contained pathways
1 Neuroscience
genes like me logo Genes that share pathways with RBFOX3: view

Pathways by source for RBFOX3 Gene

1 Cell Signaling Technology pathway for RBFOX3 Gene

Interacting Proteins for RBFOX3 Gene

Gene Ontology (GO) - Biological Process for RBFOX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000381 regulation of alternative mRNA splicing, via spliceosome IBA --
GO:0006397 mRNA processing IEA --
GO:0007399 nervous system development IBA --
GO:0008380 RNA splicing IEA --
GO:0043484 regulation of RNA splicing IEA --
genes like me logo Genes that share ontologies with RBFOX3: view

No data available for SIGNOR curated interactions for RBFOX3 Gene

Drugs & Compounds for RBFOX3 Gene

No Compound Related Data Available

Transcripts for RBFOX3 Gene

mRNA/cDNA for RBFOX3 Gene

(27) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(2) Selected AceView cDNA sequences:
(12) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RBFOX3 Gene

RNA binding protein, fox-1 homolog (C. elegans) 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RBFOX3 Gene

No ASD Table

Relevant External Links for RBFOX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RBFOX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RBFOX3 Gene

mRNA differential expression in normal tissues according to GTEx for RBFOX3 Gene

This gene is overexpressed in Brain - Cerebellum (x9.0), Brain - Cerebellar Hemisphere (x8.8), Brain - Cortex (x4.4), and Colon - Sigmoid (x4.2).

Protein differential expression in normal tissues from HIPED for RBFOX3 Gene

This gene is overexpressed in Heart (42.3) and Frontal cortex (26.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RBFOX3 Gene

Protein tissue co-expression partners for RBFOX3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RBFOX3 Gene:


SOURCE GeneReport for Unigene cluster for RBFOX3 Gene:


Evidence on tissue expression from TISSUES for RBFOX3 Gene

  • Nervous system(4.8)
  • Eye(2)
genes like me logo Genes that share expression patterns with RBFOX3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RBFOX3 Gene

Orthologs for RBFOX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RBFOX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RBFOX3 34 33
  • 99.79 (n)
(Canis familiaris)
Mammalia RBFOX3 34
  • 82 (a)
(Monodelphis domestica)
Mammalia RBFOX3 34
  • 81 (a)
(Mus musculus)
Mammalia Rbfox3 34
  • 78 (a)
(Bos Taurus)
Mammalia RBFOX3 34
  • 69 (a)
(Gallus gallus)
Aves LOC100857589 33
  • 84.57 (n)
  • 78 (a)
(Anolis carolinensis)
Reptilia RBFOX3 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rbfox3 33
  • 72.68 (n)
(Danio rerio)
Actinopterygii LOC100330510 33
  • 77.47 (n)
RBFOX3 (3 of 3) 34
  • 74 (a)
rbfox3 34
  • 71 (a)
rbfox3l 34
  • 69 (a)
fruit fly
(Drosophila melanogaster)
Insecta A2bp1 34
  • 14 (a)
(Caenorhabditis elegans)
Secernentea fox-1 34
  • 22 (a)
asd-1 34
  • 21 (a)
spn-4 34
  • 18 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3750 34
  • 30 (a)
Species where no ortholog for RBFOX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • 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 RBFOX3 Gene

Gene Tree for RBFOX3 (if available)
Gene Tree for RBFOX3 (if available)
Evolutionary constrained regions (ECRs) for RBFOX3: view image

Paralogs for RBFOX3 Gene

Paralogs for RBFOX3 Gene

(6) SIMAP similar genes for RBFOX3 Gene using alignment to 7 proteins:

  • B4DF29_HUMAN
genes like me logo Genes that share paralogs with RBFOX3: view

Variants for RBFOX3 Gene

Sequence variations from dbSNP and Humsavar for RBFOX3 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1015038952 likely-benign, Idiopathic generalized epilepsy 79,097,297(-) G/A coding_sequence_variant, synonymous_variant
rs150282906 benign, Idiopathic generalized epilepsy 79,106,690(-) G/A coding_sequence_variant, synonymous_variant
rs199891032 uncertain-significance, Idiopathic generalized epilepsy 79,106,664(-) C/T coding_sequence_variant, missense_variant
rs372072435 uncertain-significance, Idiopathic generalized epilepsy 79,101,596(-) G/A/T coding_sequence_variant, missense_variant
rs373093807 likely-benign, Idiopathic generalized epilepsy 79,094,499(-) C/T coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for RBFOX3 Gene

Variant ID Type Subtype PubMed ID
dgv1826e59 CNV duplication 20981092
dgv3286n100 CNV loss 25217958
dgv3287n100 CNV loss 25217958
dgv3288n100 CNV gain 25217958
dgv3289n100 CNV gain 25217958
dgv3290n100 CNV gain 25217958
dgv3291n100 CNV gain 25217958
dgv374n27 CNV gain 19166990
dgv429e201 CNV deletion 23290073
dgv5790n54 CNV gain 21841781
dgv5791n54 CNV loss 21841781
dgv5792n54 CNV gain 21841781
esv1010966 CNV deletion 20482838
esv1067302 CNV insertion 17803354
esv1233971 CNV insertion 17803354
esv1345308 CNV deletion 17803354
esv1382305 CNV insertion 17803354
esv2000452 CNV deletion 18987734
esv2043488 CNV deletion 18987734
esv22826 CNV loss 19812545
esv23168 CNV loss 19812545
esv23358 CNV loss 19812545
esv23359 CNV gain 19812545
esv2657181 CNV deletion 23128226
esv2658402 CNV deletion 23128226
esv2661992 CNV deletion 23128226
esv2664266 CNV deletion 23128226
esv2666578 CNV deletion 23128226
esv2668337 CNV deletion 23128226
esv2676824 CNV deletion 23128226
esv2716325 CNV deletion 23290073
esv2716326 CNV deletion 23290073
esv2716327 CNV deletion 23290073
esv2716328 CNV deletion 23290073
esv2716330 CNV deletion 23290073
esv2716331 CNV deletion 23290073
esv2716332 CNV deletion 23290073
esv2716333 CNV deletion 23290073
esv2716334 CNV deletion 23290073
esv2716335 CNV deletion 23290073
esv2716336 CNV deletion 23290073
esv2716337 CNV deletion 23290073
esv2716338 CNV deletion 23290073
esv2716339 CNV deletion 23290073
esv2716341 CNV deletion 23290073
esv2716342 CNV deletion 23290073
esv2716343 CNV deletion 23290073
esv2758705 CNV loss 17122850
esv2762533 CNV gain 21179565
esv3396156 CNV duplication 20981092
esv3554836 CNV deletion 23714750
esv3554840 CNV deletion 23714750
esv3582921 CNV loss 25503493
esv3641347 CNV loss 21293372
esv3641348 CNV loss 21293372
esv3641349 CNV loss 21293372
esv3641350 CNV gain 21293372
esv3641351 CNV gain 21293372
esv3893047 CNV loss 25118596
esv3893049 CNV gain 25118596
esv998420 CNV deletion 20482838
nsv1055593 CNV gain 25217958
nsv1056733 CNV loss 25217958
nsv1057193 CNV gain 25217958
nsv1057260 CNV gain 25217958
nsv1060644 CNV loss 25217958
nsv1071410 CNV deletion 25765185
nsv1071411 CNV deletion 25765185
nsv1071412 CNV deletion 25765185
nsv1071805 CNV deletion 25765185
nsv1071806 CNV deletion 25765185
nsv1072755 CNV deletion 25765185
nsv1072756 CNV deletion 25765185
nsv1078897 CNV insertion 25765185
nsv1109111 CNV deletion 24896259
nsv1111150 CNV tandem duplication 24896259
nsv1112499 CNV deletion 24896259
nsv1112719 CNV deletion 24896259
nsv1112720 CNV deletion 24896259
nsv1113892 CNV deletion 24896259
nsv1116430 CNV deletion 24896259
nsv1118772 CNV deletion 24896259
nsv1120342 CNV tandem duplication 24896259
nsv112361 CNV insertion 16902084
nsv112374 CNV deletion 16902084
nsv1125203 CNV insertion 24896259
nsv1127602 CNV deletion 24896259
nsv1130709 CNV deletion 24896259
nsv1144819 CNV deletion 24896259
nsv1146757 CNV deletion 26484159
nsv1148784 CNV deletion 26484159
nsv1149217 CNV duplication 26484159
nsv1149737 CNV insertion 26484159
nsv1150166 CNV insertion 26484159
nsv1153059 CNV deletion 26484159
nsv2157 CNV insertion 18451855
nsv442427 CNV gain 18776908
nsv457924 CNV gain 19166990
nsv457966 CNV loss 19166990
nsv470610 CNV loss 18288195
nsv470612 CNV gain 18288195
nsv470613 CNV loss 18288195
nsv470614 CNV gain 18288195
nsv472157 CNV novel sequence insertion 20440878
nsv474394 CNV novel sequence insertion 20440878
nsv513485 CNV insertion 21212237
nsv517744 CNV gain+loss 19592680
nsv518325 CNV loss 19592680
nsv522632 CNV loss 19592680
nsv523650 CNV loss 19592680
nsv524700 CNV loss 19592680
nsv527021 CNV loss 19592680
nsv527752 CNV gain 19592680
nsv527899 CNV loss 19592680
nsv528997 CNV loss 19592680
nsv529010 CNV gain 19592680
nsv576103 CNV loss 21841781
nsv576104 CNV loss 21841781
nsv576105 CNV loss 21841781
nsv576106 CNV loss 21841781
nsv576107 CNV gain 21841781
nsv576115 CNV gain 21841781
nsv817775 CNV loss 17921354
nsv817776 CNV gain 17921354
nsv828115 CNV gain 20364138
nsv833556 CNV loss 17160897
nsv833557 CNV loss 17160897
nsv833558 CNV loss 17160897
nsv833560 CNV loss 17160897
nsv952379 CNV deletion 24416366
nsv9590 CNV gain+loss 18304495
nsv9592 CNV loss 18304495

Variation tolerance for RBFOX3 Gene

Gene Damage Index Score: 1.10; 22.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RBFOX3 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBFOX3 Gene

Disorders for RBFOX3 Gene

MalaCards: The human disease database

(18) MalaCards diseases for RBFOX3 Gene - From: HGMD, ClinVar, and DISEASES

Disorder Aliases PubMed IDs
benign epilepsy with centrotemporal spikes
  • bcects
sella turcica neoplasm
  • tumor of sella turcica
tuberculum sellae meningioma
  • meningioma of the tuberculum sellae
cerebellar liponeurocytoma
  • lipomatous medulloblastoma
spinocerebellar ataxia 36
  • sca36
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RBFOX3

genes like me logo Genes that share disorders with RBFOX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RBFOX3 Gene

Publications for RBFOX3 Gene

  1. Altered subcellular localization of the NeuN/Rbfox3 RNA splicing factor in HIV-associated neurocognitive disorders (HAND). (PMID: 24215932) Lucas CH … Brown A (Neuroscience letters 2014) 3 4 58
  2. Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. (PMID: 16260614) Underwood JG … Black DL (Molecular and cellular biology 2005) 2 3 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. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. RBFOX3 regulates Claudin-1 expression in human lung tissue via attenuation of proteasomal degradation. (PMID: 28126724) Kim YE … Kim KK (Bioscience reports 2017) 3 58

Products for RBFOX3 Gene

Sources for RBFOX3 Gene

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