{"gene":"RBFOX3","run_date":"2026-04-28T19:45:45","timeline":{"discoveries":[{"year":2009,"finding":"NeuN was identified as the protein product of the Fox-3 (RBFOX3) gene by mass spectrometry of anti-NeuN immunoreactive protein, confirmation with recombinant Fox-3, shRNA knockdown, and overlapping immunostaining. Fox-3/RBFOX3 contains an RNA recognition motif, binds the UGCAUG RNA element, and was demonstrated to function as a splicing regulator using neural cell-specific alternative splicing of non-muscle myosin heavy chain II-B pre-mRNA as a model.","method":"Mass spectrometry, recombinant protein expression, shRNA knockdown, immunostaining, splicing reporter assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods in one study establishing molecular identity and splicing function","pmids":["19713214"],"is_preprint":false},{"year":2010,"finding":"Fox-3/RBFOX3 interacts with polypyrimidine tract binding protein-associated splicing factor (PSF), identified by affinity chromatography. Enhancement of neural cell-specific cassette exon N30 inclusion in NMHC II-B by Fox-3 depends on PSF; Fox-3 is recruited to the UGCAUG element downstream of N30 in a PSF-dependent manner, establishing PSF as a co-activator of Fox-3-mediated splicing activation.","method":"Affinity chromatography, co-immunoprecipitation, splicing reporter assay, chromatin/RNA immunoprecipitation","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 — reciprocal binding assay plus functional splicing validation with multiple methods","pmids":["21177649"],"is_preprint":false},{"year":2011,"finding":"RBFOX3 produces four protein isoforms (~45–50 kDa) via alternative splicing of its own pre-mRNA; one splicing choice adds or removes a short C-terminal extension containing the second half of a bipartite hydrophobic proline-tyrosine nuclear localization signal, thereby determining nuclear vs. cytoplasmic steady-state distribution. Nuclear RBFOX3 isoforms regulate alternative splicing of Rbfox2 pre-mRNA to produce a dominant-negative Rbfox2 form and can also enhance cryptic exon inclusion leading to nonsense-mediated decay of Rbfox2 mRNA.","method":"Immunoprecipitation, mass spectrometry, isoform mapping, NLS mutagenesis analysis, splicing assays, NMD analysis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods establishing isoform-dependent localization and downstream regulatory mechanism","pmids":["21747913"],"is_preprint":false},{"year":2013,"finding":"Rbfox3 is required for neuronal differentiation of postmitotic neurons in the developing chicken spinal cord. Rbfox3 represses inclusion of an alternative exon in Numb pre-mRNA by binding to the UGCAUG element in the upstream intron; depleting the specific Numb splice isoform phenocopies Rbfox3 loss, and forced expression of that isoform rescues differentiation defects caused by Rbfox3 depletion.","method":"siRNA loss-of-function in vivo (chicken spinal cord), splicing assays, rescue experiments with specific Numb isoforms","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — in vivo loss-of-function with specific molecular mechanism and isoform-specific rescue","pmids":["23420872"],"is_preprint":false},{"year":2014,"finding":"Transcriptome-wide PAR-CLIP identified diverse Rbfox3 targets including primary microRNAs lacking the canonical UGCAUG motif. Rbfox3 functions both as a positive and negative regulator of pri-miRNA processing to pre-miRNA; it binds directly to pri-miRNAs and regulates recruitment of the microprocessor complex.","method":"PAR-CLIP, inducible expression/depletion, in vitro pri-miRNA processing assay, direct binding assay","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro reconstitution of miRNA processing regulation combined with transcriptome-wide binding data","pmids":["25240799"],"is_preprint":false},{"year":2014,"finding":"The Rbfox3-d31 isoform (excluding a 93-nt cassette exon within the RRM) is rapidly degraded by the ubiquitin-proteasome pathway in a manner specific to this isoform; suppression of its degradation by MG132 alters subcellular localization of Rbfox2 and attenuates Rbfox2 splicing activity, showing Rbfox3-d31 acts as a repressor of Rbfox family splicing activity.","method":"Proteasome inhibitor treatment (MG132), isoform-specific expression analysis, subcellular fractionation, splicing assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — single lab with orthogonal pharmacological and molecular methods","pmids":["25044120"],"is_preprint":false},{"year":2010,"finding":"NeuN/Fox-3 (RBFOX3) is an intrinsic component of the neuronal nuclear matrix and a marker of nuclear speckles in neurons, as determined by nuclear matrix extraction and immunofluorescence.","method":"Nuclear matrix fractionation, immunofluorescence/confocal microscopy","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 — direct biochemical fractionation with functional implication for nuclear compartmentalization","pmids":["20452351"],"is_preprint":false},{"year":2005,"finding":"NeuN (RBFOX3) is a phosphoprotein; enzymatic dephosphorylation abolishes anti-NeuN immunoreactivity, and both the 46- and 48-kDa isoforms separate into multiple spots by isoelectric focusing, indicating multiple phosphorylated forms. The 48-kDa isoform is preferentially cytoplasmic whereas both isoforms are nuclear, and NeuN is excluded from densely packed chromatin regions.","method":"Isoelectric focusing, enzymatic dephosphorylation, biochemical fractionation, immunohistochemistry","journal":"Journal of neuroscience research","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical characterization with multiple methods in one study","pmids":["15605376"],"is_preprint":false},{"year":2015,"finding":"Rbfox3 knockout mice display increased seizure susceptibility, decreased anxiety, defective synaptic transmission and plasticity in the perforant pathway, increased frequency of excitatory synaptic events in dentate granule cells associated with increased neurotransmitter release probability and dendritic spine density, and increased expression of plasticity genes Egr4 and Arc.","method":"Rbfox3 knockout mouse, electrophysiology, behavioral assays, morphological analysis","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 — clean KO with multiple defined cellular and circuit-level phenotypes","pmids":["26619789"],"is_preprint":false},{"year":2016,"finding":"Rbfox3 homozygous knockout mice exhibit deficits in hippocampal neurogenesis, impaired cognitive abilities, altered synaptic plasticity and density in the hippocampal dentate gyrus. RBFOX3 regulates exons of genes with synapse-related function.","method":"Rbfox3 knockout mouse, neurogenesis assays, synaptic plasticity electrophysiology, electron microscopy of synapses, behavioral tests","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 — KO model with multiple orthogonal phenotypic readouts","pmids":["27701470"],"is_preprint":false},{"year":2022,"finding":"Deletion of Rbfox3 specifically in GABAergic neurons causes spontaneous seizures and high premature mortality via increased presynaptic release, enhanced excitatory GABA action, and reduced VAMP1 (a GABAergic-specific presynaptic protein) expression in hippocampal dentate gyrus. Postnatal restoration of VAMP1 rescued premature mortality. Deletion of Rbfox3 in NPY-expressing GABAergic neurons lowered intrinsic excitability and increased seizure susceptibility.","method":"Cell-type-specific conditional knockout, electrophysiology, viral VAMP1 rescue, bumetanide pharmacology, immunohistochemistry","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 — cell-type-specific KO with defined molecular substrate (VAMP1) and rescue experiment","pmids":["35951651"],"is_preprint":false},{"year":2018,"finding":"Rbfox3/NeuN regulates alternative splicing of SNORD116 (Snord116) primary transcript in neurons; knockdown of Rbfox3 in Snord116+/- neurons reduced splicing of a Snord116 transgene, demonstrating neuron-specific splicing of this locus requires Rbfox3.","method":"Rbfox3 knockdown in primary neurons, RT-PCR splicing assay, RNA FISH","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 — direct knockdown with defined splicing readout in neurons","pmids":["30124848"],"is_preprint":false},{"year":2018,"finding":"Rbfox3/NeuN regulates alternative splicing of tau exon 10 via binding to UGCAUG in tau intron 10; deletion mutants of the RNA recognition motif (RRM) or its three RNA-binding sites abolished exon 10 inclusion enhancement. Intron 10 of tau pre-mRNA co-immunoprecipitated with Rbfox3/NeuN.","method":"RNA immunoprecipitation, splicing minigene assay, RRM deletion mutagenesis","journal":"Journal of Alzheimer's disease : JAD","confidence":"Medium","confidence_rationale":"Tier 2 — RIP plus mutagenesis establishing direct binding and functional requirement of RRM","pmids":["30475774"],"is_preprint":false},{"year":2018,"finding":"RBFOX3 deletion in Rbfox3-/- mice results in reduced inner plexiform layer thickness in the retina without loss of ganglion or amacrine cells and normal visual function, showing RBFOX3 is dispensable for visual function despite its expression in retinal ganglion, amacrine, and horizontal cells.","method":"Rbfox3 knockout mouse, retinal morphometry, electrophysiology (ERG), behavioral visual tests","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 — KO with multiple anatomical and functional readouts","pmids":["29401485"],"is_preprint":false},{"year":2018,"finding":"RBFOX3 suppresses hTERT expression by binding to the hTERT promoter; melatonin abrogates RBFOX3 binding to the hTERT promoter, reducing hTERT expression in MLL-rearranged leukemia cells.","method":"Chromatin immunoprecipitation, promoter reporter assay, RBFOX3 knockdown/overexpression","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP plus functional reporter assay establishing direct promoter binding","pmids":["30550850"],"is_preprint":false},{"year":2020,"finding":"RBFOX3 promotes gastric cancer cell division and invasion via activation of HTERT signaling; RBFOX3 binds AP-2β (co-immunoprecipitation) to modulate HTERT promoter activity. Silencing of RBFOX3-mediated suppression of growth was rescued by HTERT overexpression.","method":"Co-immunoprecipitation, promoter activity assay, knockdown/overexpression, rescue experiment, xenograft mouse model","journal":"Frontiers in oncology","confidence":"Medium","confidence_rationale":"Tier 2–3 — Co-IP identifies AP-2β complex, functional rescue supports mechanism","pmids":["32903312"],"is_preprint":false},{"year":2016,"finding":"TGF-β1 treatment inhibits RBFOX3 expression at the transcriptional level in A549 lung adenocarcinoma cells; RBFOX3 depletion alters expression of EMT-related proteins E-cadherin and Claudin-1 and promotes mesenchymal morphology during TGF-β1-induced EMT.","method":"TGF-β1 treatment, siRNA knockdown, immunofluorescence, qRT-PCR, Western blot","journal":"Molecules and cells","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, KD with defined molecular phenotype but limited mechanistic depth","pmids":["27432190"],"is_preprint":false},{"year":2017,"finding":"RBFOX3 stabilizes Claudin-1 protein in human lung tissue by attenuating its ubiquitination and proteasomal degradation; RBFOX3-positive cells show higher Claudin-1 protein (but not mRNA) levels, and cycloheximide chase confirms increased Claudin-1 stability conferred by RBFOX3.","method":"Cycloheximide chase, ubiquitination assay, immunostaining, qRT-PCR, Western blot","journal":"Bioscience reports","confidence":"Medium","confidence_rationale":"Tier 2 — protein stability assay plus ubiquitination assay establishing post-translational mechanism","pmids":["28126724"],"is_preprint":false},{"year":2013,"finding":"Anti-NeuN antibody specificity on aldehyde-fixed tissues is phosphorylation-dependent; the NeuN/A60 epitope in Rbfox3 is a proline- and glutamine-rich domain at the N-terminus. Cross-reactivity with Synapsin I and R3hdm2 on Western blots is due to a shared proline/glutamine-rich domain.","method":"Epitope mapping, phosphorylation analysis, immunoblotting with domain deletion constructs","journal":"Histochemistry and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 — direct epitope mapping with mutagenesis establishing molecular basis of antibody recognition","pmids":["24150744"],"is_preprint":false},{"year":2013,"finding":"Altered subcellular localization of Rbfox3/NeuN to the cytoplasm is observed in neurons from HIV-infected individuals with cognitive impairment compared to controls, suggesting cytoplasmic mislocalization may downregulate nuclear splicing activity.","method":"Immunohistochemistry of human post-mortem brain sections, quantitative subcellular localization analysis","journal":"Neuroscience letters","confidence":"Low","confidence_rationale":"Tier 3 — single observation without direct functional validation of splicing consequence","pmids":["24215932"],"is_preprint":false},{"year":2024,"finding":"RBFOX3 enhances biogenesis of circIGF1R by binding to IGF1R pre-mRNA (shown by RNA immunoprecipitation and RNA pull-down); paclitaxel induces RBFOX3-mediated circIGF1R biogenesis, suppressing NSCLC invasion and migration via the circIGF1R/miR-1270/VANGL2 axis.","method":"RNA immunoprecipitation, RNA pull-down, luciferase reporter, FISH, functional invasion/migration assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — multiple RNA binding assays plus functional pathway validation","pmids":["38191906"],"is_preprint":false}],"current_model":"RBFOX3 (NeuN) is a neuron-specific RNA-binding protein that binds the UGCAUG intronic element to regulate alternative pre-mRNA splicing of numerous neuronal transcripts (including Numb, NMHC II-B, tau exon 10, Rbfox2, and Snord116), controls miRNA biogenesis by binding pri-miRNAs and regulating microprocessor recruitment, stabilizes specific proteins post-translationally, and is required for hippocampal circuit balance, neurogenesis, and seizure suppression—particularly through regulation of VAMP1 expression in GABAergic neurons; its activity is modulated by isoform-specific alternative splicing of its own transcript (controlling nuclear vs. cytoplasmic localization via a bipartite NLS), phosphorylation, and interaction with co-factors such as PSF."},"narrative":{"teleology":[{"year":2005,"claim":"Before the molecular identity of NeuN was known, biochemical analysis established it as a multiply phosphorylated nuclear protein with isoform-specific subcellular distribution, setting the stage for understanding its post-translational regulation.","evidence":"Isoelectric focusing and enzymatic dephosphorylation of NeuN from brain tissue","pmids":["15605376"],"confidence":"Medium","gaps":["Kinases responsible for phosphorylation not identified","Functional consequence of phosphorylation on RNA binding unknown","Only antibody-based identification prior to molecular cloning"]},{"year":2009,"claim":"The longstanding neuronal marker NeuN was identified as the product of the RBFOX3 gene and shown to be an RNA-binding protein that binds the UGCAUG element and regulates neuron-specific alternative splicing, establishing its molecular identity and core biochemical activity.","evidence":"Mass spectrometry of immunopurified NeuN, recombinant protein confirmation, shRNA knockdown, and NMHC II-B splicing reporter assay","pmids":["19713214"],"confidence":"High","gaps":["Genome-wide splicing targets unknown","Relationship to other Rbfox family members unclear"]},{"year":2010,"claim":"Discovery that PSF is a co-activator required for RBFOX3-mediated splicing revealed that RBFOX3 does not act alone but depends on cofactor-mediated recruitment to its target pre-mRNAs.","evidence":"Affinity chromatography identification of PSF, co-IP, and PSF-dependent splicing reporter assays for NMHC II-B exon N30","pmids":["21177649"],"confidence":"High","gaps":["Whether PSF is required for all RBFOX3 splicing targets or only a subset","Structural basis of RBFOX3–PSF interaction unknown"]},{"year":2010,"claim":"Localization of RBFOX3 to the neuronal nuclear matrix and nuclear speckles placed its splicing activity within a specific subnuclear compartment associated with RNA processing.","evidence":"Nuclear matrix fractionation and confocal immunofluorescence in neurons","pmids":["20452351"],"confidence":"Medium","gaps":["Whether nuclear matrix association is required for splicing function","Dynamic trafficking between speckles and nucleoplasm not characterized"]},{"year":2011,"claim":"Autoregulatory isoform diversity was uncovered: RBFOX3 alternative splicing of its own transcript generates isoforms with or without a bipartite NLS, controlling nuclear versus cytoplasmic localization and enabling nuclear RBFOX3 to produce a dominant-negative Rbfox2 isoform, revealing cross-regulation among Rbfox family members.","evidence":"Isoform mapping by IP/MS, NLS mutagenesis, splicing and NMD assays for Rbfox2","pmids":["21747913"],"confidence":"High","gaps":["Signals that regulate the balance of RBFOX3 isoforms in vivo unknown","Cytoplasmic functions of RBFOX3 not fully defined"]},{"year":2013,"claim":"In vivo requirement for RBFOX3 in neuronal differentiation was established through its direct regulation of Numb alternative splicing in developing spinal cord, with isoform-specific rescue proving causality.","evidence":"siRNA loss-of-function in chicken spinal cord with Numb isoform-specific rescue","pmids":["23420872"],"confidence":"High","gaps":["Whether Numb is the sole essential target for differentiation","Mammalian in vivo validation of this specific mechanism not performed"]},{"year":2014,"claim":"RBFOX3 function was expanded beyond splicing: PAR-CLIP revealed binding to primary miRNAs lacking the canonical UGCAUG motif, and reconstitution showed RBFOX3 directly regulates microprocessor recruitment for miRNA biogenesis.","evidence":"Transcriptome-wide PAR-CLIP, inducible expression/depletion, in vitro pri-miRNA processing assay","pmids":["25240799"],"confidence":"High","gaps":["Sequence determinants for miRNA binding distinct from UGCAUG not defined","Relative physiological importance of miRNA regulation versus splicing regulation unclear"]},{"year":2014,"claim":"The Rbfox3-d31 isoform lacking a cassette exon within the RRM was shown to be degraded by the ubiquitin-proteasome system, and its stabilization relocalized Rbfox2 and repressed Rbfox family splicing activity, revealing proteolytic quality control as a mechanism shaping Rbfox network output.","evidence":"Proteasome inhibitor (MG132) treatment, isoform-specific expression, subcellular fractionation, splicing assays","pmids":["25044120"],"confidence":"Medium","gaps":["E3 ligase responsible for Rbfox3-d31 ubiquitination not identified","In vivo relevance of this degradation pathway not established"]},{"year":2015,"claim":"Rbfox3 knockout mice revealed that RBFOX3 is essential for hippocampal circuit balance: loss causes seizure susceptibility, increased excitatory drive onto dentate granule cells, increased dendritic spine density, and upregulation of plasticity genes Egr4 and Arc.","evidence":"Rbfox3 knockout mouse with electrophysiology, behavioral assays, and morphological analysis","pmids":["26619789"],"confidence":"High","gaps":["Specific splicing or miRNA targets mediating each phenotype not resolved","Developmental versus acute contribution of RBFOX3 not distinguished"]},{"year":2016,"claim":"Knockout studies further demonstrated RBFOX3 is required for hippocampal neurogenesis, synaptic density, and cognitive function, with splicing targets enriched for synapse-related genes.","evidence":"Rbfox3 knockout mouse with neurogenesis assays, electron microscopy of synapses, behavioral tests","pmids":["27701470"],"confidence":"High","gaps":["Causal link between individual mis-spliced transcripts and neurogenesis defect not established"]},{"year":2017,"claim":"A non-canonical post-translational function was discovered: RBFOX3 stabilizes Claudin-1 protein by attenuating its ubiquitination and proteasomal degradation, extending RBFOX3 activity beyond RNA regulation.","evidence":"Cycloheximide chase and ubiquitination assays in human lung tissue cells","pmids":["28126724"],"confidence":"Medium","gaps":["Mechanism by which an RNA-binding protein inhibits Claudin-1 ubiquitination is unclear","Whether this occurs in neurons not tested"]},{"year":2018,"claim":"RBFOX3 was shown to directly regulate tau exon 10 inclusion via UGCAUG in intron 10 and to participate in neuron-specific splicing of the Snord116 locus, broadening the catalog of neurologically relevant targets.","evidence":"RNA immunoprecipitation, RRM deletion mutagenesis for tau; Rbfox3 knockdown in primary neurons with RT-PCR for Snord116","pmids":["30475774","30124848"],"confidence":"Medium","gaps":["Whether tau exon 10 mis-splicing in Rbfox3 KO contributes to tauopathy not tested in vivo","Quantitative contribution of RBFOX3 versus other splicing factors at Snord116 locus unclear"]},{"year":2022,"claim":"Cell-type-specific deletion revealed that RBFOX3 in GABAergic neurons is critical for seizure suppression, operating through maintenance of VAMP1 expression; postnatal VAMP1 rescue prevented mortality, establishing a defined molecular substrate for the seizure phenotype.","evidence":"GABAergic neuron-specific conditional knockout, electrophysiology, viral VAMP1 restoration, bumetanide pharmacology","pmids":["35951651"],"confidence":"High","gaps":["Whether RBFOX3 regulates VAMP1 through splicing, mRNA stability, or another mechanism not fully resolved","Contribution of non-GABAergic neuronal RBFOX3 to seizure threshold not isolated"]},{"year":2024,"claim":"RBFOX3 was found to promote circRNA biogenesis by binding IGF1R pre-mRNA, adding circular RNA production to its repertoire of post-transcriptional regulatory activities.","evidence":"RNA immunoprecipitation, RNA pull-down, and functional invasion assays in NSCLC cells","pmids":["38191906"],"confidence":"Medium","gaps":["Whether circRNA biogenesis is a general function of RBFOX3 or transcript-specific","Physiological relevance of RBFOX3-mediated circRNA in neurons not examined"]},{"year":null,"claim":"Key open questions include: the structural basis for RBFOX3's recognition of non-UGCAUG RNA targets such as pri-miRNAs; the kinases and phosphatases controlling RBFOX3 phosphorylation and its functional consequences; the mechanism by which RBFOX3 regulates VAMP1 expression in GABAergic neurons; and the relative physiological importance of its splicing, miRNA, circRNA, and protein-stabilization activities.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of RBFOX3 in complex with RNA","Phosphorylation-function relationship unresolved","Mechanism of VAMP1 regulation (transcriptional, splicing, or stability) not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,3,4,12,20]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,3,4,11,12]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[14,15]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,5,17]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,2,6,7]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2,7]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,3,4,11,12]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[8,9,10]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[3,9]}],"complexes":[],"partners":["PSF","VAMP1","RBFOX2","AP2B1","CLDN1"],"other_free_text":[]},"mechanistic_narrative":"RBFOX3 (NeuN) is a neuron-specific RNA-binding protein that orchestrates post-transcriptional gene regulation in the nervous system through alternative pre-mRNA splicing, miRNA biogenesis, circular RNA production, and post-translational protein stabilization. It binds the UGCAUG intronic element via its RNA recognition motif to regulate splicing of neuronal transcripts including Numb, NMHC II-B, tau exon 10, Rbfox2, and Snord116, with PSF functioning as a required co-activator for at least a subset of these events [PMID:19713214, PMID:21177649, PMID:23420872, PMID:30475774]. RBFOX3 also binds primary miRNAs to regulate microprocessor recruitment and promotes circRNA biogenesis from specific pre-mRNAs [PMID:25240799, PMID:38191906]. Its own transcript undergoes alternative splicing that controls a bipartite nuclear localization signal, generating isoforms with nuclear or cytoplasmic distribution; Rbfox3 knockout mice exhibit seizures, impaired hippocampal neurogenesis and synaptic plasticity, with GABAergic neuron-specific deletion causing spontaneous seizures through loss of VAMP1 expression, rescuable by postnatal VAMP1 restoration [PMID:21747913, PMID:35951651, PMID:26619789]."},"prefetch_data":{"uniprot":{"accession":"A6NFN3","full_name":"RNA binding protein fox-1 homolog 3","aliases":["Fox-1 homolog C","Neuronal nuclei antigen","NeuN antigen"],"length_aa":312,"mass_kda":33.9,"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)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/A6NFN3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RBFOX3","classification":"Not Classified","n_dependent_lines":14,"n_total_lines":1208,"dependency_fraction":0.011589403973509934},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RBFOX3","total_profiled":1310},"omim":[{"mim_id":"616999","title":"RNA-BINDING FOX1 HOMOLOG 3; RBFOX3","url":"https://www.omim.org/entry/616999"},{"mim_id":"614427","title":"TEASHIRT ZINC FINGER HOMEOBOX 1; TSHZ1","url":"https://www.omim.org/entry/614427"},{"mim_id":"143100","title":"HUNTINGTON DISEASE; HD","url":"https://www.omim.org/entry/143100"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":273.5},{"tissue":"intestine","ntpm":81.6},{"tissue":"urinary bladder","ntpm":78.6}],"url":"https://www.proteinatlas.org/search/RBFOX3"},"hgnc":{"alias_symbol":["FOX-3","NeuN","HRNBP3"],"prev_symbol":[]},"alphafold":{"accession":"A6NFN3","domains":[{"cath_id":"3.30.70.330","chopping":"105-171","consensus_level":"high","plddt":96.8673,"start":105,"end":171}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/A6NFN3","model_url":"https://alphafold.ebi.ac.uk/files/AF-A6NFN3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-A6NFN3-F1-predicted_aligned_error_v6.png","plddt_mean":61.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RBFOX3","jax_strain_url":"https://www.jax.org/strain/search?query=RBFOX3"},"sequence":{"accession":"A6NFN3","fasta_url":"https://rest.uniprot.org/uniprotkb/A6NFN3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/A6NFN3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/A6NFN3"}},"corpus_meta":[{"pmid":"1483388","id":"PMC_1483388","title":"NeuN, a neuronal specific nuclear protein in vertebrates.","date":"1992","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/1483388","citation_count":2068,"is_preprint":false},{"pmid":"8813082","id":"PMC_8813082","title":"NeuN: a useful neuronal marker for diagnostic histopathology.","date":"1996","source":"The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society","url":"https://pubmed.ncbi.nlm.nih.gov/8813082","citation_count":443,"is_preprint":false},{"pmid":"19713214","id":"PMC_19713214","title":"Identification of neuronal nuclei (NeuN) as Fox-3, a new member of the Fox-1 gene family of splicing factors.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19713214","citation_count":316,"is_preprint":false},{"pmid":"26085943","id":"PMC_26085943","title":"NeuN As a Neuronal Nuclear Antigen and Neuron Differentiation Marker.","date":"2015","source":"Acta naturae","url":"https://pubmed.ncbi.nlm.nih.gov/26085943","citation_count":313,"is_preprint":false},{"pmid":"25680637","id":"PMC_25680637","title":"Novel Insights into NeuN: from Neuronal Marker to Splicing Regulator.","date":"2015","source":"Molecular neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/25680637","citation_count":240,"is_preprint":false},{"pmid":"12868073","id":"PMC_12868073","title":"Developmental and cell type-specific expression of the neuronal marker NeuN in the murine cerebellum.","date":"2003","source":"Journal of neuroscience research","url":"https://pubmed.ncbi.nlm.nih.gov/12868073","citation_count":228,"is_preprint":false},{"pmid":"15223381","id":"PMC_15223381","title":"Loss of NeuN immunoreactivity after cerebral ischemia does not indicate neuronal cell loss: a cautionary note.","date":"2004","source":"Brain 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DOUBLECORTIN AND NeuN IN THE DEVELOPING CEREBELLAR NEURONS IN RAT].","date":"2016","source":"Morfologiia (Saint Petersburg, Russia)","url":"https://pubmed.ncbi.nlm.nih.gov/27487661","citation_count":2,"is_preprint":false},{"pmid":"7876357","id":"PMC_7876357","title":"The effects of the neuN and neuT genes on differentiation and transformation of mammary epithelial cells.","date":"1994","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/7876357","citation_count":2,"is_preprint":false},{"pmid":"34253253","id":"PMC_34253253","title":"Assessing the treatment of cannabidiolic acid methyl ester: a stable synthetic analogue of cannabidiolic acid on c-Fos and NeuN expression in the hypothalamus of rats.","date":"2021","source":"Journal of cannabis research","url":"https://pubmed.ncbi.nlm.nih.gov/34253253","citation_count":2,"is_preprint":false},{"pmid":"16669252","id":"PMC_16669252","title":"[Immunocytochemical demonstration of brain neurons using NeuN as a selective marker].","date":"2005","source":"Morfologiia (Saint Petersburg, Russia)","url":"https://pubmed.ncbi.nlm.nih.gov/16669252","citation_count":2,"is_preprint":false},{"pmid":"40377082","id":"PMC_40377082","title":"Anatolian ground squirrel (Spermophilus xanthoprymnus) retina: Comparative expression of synaptophysin, NeuN, calbindin-D28k, parvalbumin, glial fibrillary acidic protein, and Iba-1 during pre-hibernation and hibernation.","date":"2025","source":"Anatomical record (Hoboken, N.J. : 2007)","url":"https://pubmed.ncbi.nlm.nih.gov/40377082","citation_count":2,"is_preprint":false},{"pmid":"40212807","id":"PMC_40212807","title":"Characterization of the Rbfox3-IRES-iCre knock-in mouse: Revealing gene recombination activity in neural and non-neural peripheral tissues.","date":"2025","source":"FASEB bioAdvances","url":"https://pubmed.ncbi.nlm.nih.gov/40212807","citation_count":1,"is_preprint":false},{"pmid":"17608158","id":"PMC_17608158","title":"[The expression of neuN in the development of olfactory bulb and epithelium of mice].","date":"2007","source":"Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery","url":"https://pubmed.ncbi.nlm.nih.gov/17608158","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":47421,"output_tokens":4843,"usd":0.107454},"stage2":{"model":"claude-opus-4-6","input_tokens":8381,"output_tokens":6998,"usd":0.325282},"total_usd":0.432736,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2009,\n      \"finding\": \"NeuN was identified as the protein product of the Fox-3 (RBFOX3) gene by mass spectrometry of anti-NeuN immunoreactive protein, confirmation with recombinant Fox-3, shRNA knockdown, and overlapping immunostaining. Fox-3/RBFOX3 contains an RNA recognition motif, binds the UGCAUG RNA element, and was demonstrated to function as a splicing regulator using neural cell-specific alternative splicing of non-muscle myosin heavy chain II-B pre-mRNA as a model.\",\n      \"method\": \"Mass spectrometry, recombinant protein expression, shRNA knockdown, immunostaining, splicing reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods in one study establishing molecular identity and splicing function\",\n      \"pmids\": [\"19713214\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Fox-3/RBFOX3 interacts with polypyrimidine tract binding protein-associated splicing factor (PSF), identified by affinity chromatography. Enhancement of neural cell-specific cassette exon N30 inclusion in NMHC II-B by Fox-3 depends on PSF; Fox-3 is recruited to the UGCAUG element downstream of N30 in a PSF-dependent manner, establishing PSF as a co-activator of Fox-3-mediated splicing activation.\",\n      \"method\": \"Affinity chromatography, co-immunoprecipitation, splicing reporter assay, chromatin/RNA immunoprecipitation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal binding assay plus functional splicing validation with multiple methods\",\n      \"pmids\": [\"21177649\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RBFOX3 produces four protein isoforms (~45–50 kDa) via alternative splicing of its own pre-mRNA; one splicing choice adds or removes a short C-terminal extension containing the second half of a bipartite hydrophobic proline-tyrosine nuclear localization signal, thereby determining nuclear vs. cytoplasmic steady-state distribution. Nuclear RBFOX3 isoforms regulate alternative splicing of Rbfox2 pre-mRNA to produce a dominant-negative Rbfox2 form and can also enhance cryptic exon inclusion leading to nonsense-mediated decay of Rbfox2 mRNA.\",\n      \"method\": \"Immunoprecipitation, mass spectrometry, isoform mapping, NLS mutagenesis analysis, splicing assays, NMD analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods establishing isoform-dependent localization and downstream regulatory mechanism\",\n      \"pmids\": [\"21747913\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Rbfox3 is required for neuronal differentiation of postmitotic neurons in the developing chicken spinal cord. Rbfox3 represses inclusion of an alternative exon in Numb pre-mRNA by binding to the UGCAUG element in the upstream intron; depleting the specific Numb splice isoform phenocopies Rbfox3 loss, and forced expression of that isoform rescues differentiation defects caused by Rbfox3 depletion.\",\n      \"method\": \"siRNA loss-of-function in vivo (chicken spinal cord), splicing assays, rescue experiments with specific Numb isoforms\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo loss-of-function with specific molecular mechanism and isoform-specific rescue\",\n      \"pmids\": [\"23420872\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Transcriptome-wide PAR-CLIP identified diverse Rbfox3 targets including primary microRNAs lacking the canonical UGCAUG motif. Rbfox3 functions both as a positive and negative regulator of pri-miRNA processing to pre-miRNA; it binds directly to pri-miRNAs and regulates recruitment of the microprocessor complex.\",\n      \"method\": \"PAR-CLIP, inducible expression/depletion, in vitro pri-miRNA processing assay, direct binding assay\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro reconstitution of miRNA processing regulation combined with transcriptome-wide binding data\",\n      \"pmids\": [\"25240799\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The Rbfox3-d31 isoform (excluding a 93-nt cassette exon within the RRM) is rapidly degraded by the ubiquitin-proteasome pathway in a manner specific to this isoform; suppression of its degradation by MG132 alters subcellular localization of Rbfox2 and attenuates Rbfox2 splicing activity, showing Rbfox3-d31 acts as a repressor of Rbfox family splicing activity.\",\n      \"method\": \"Proteasome inhibitor treatment (MG132), isoform-specific expression analysis, subcellular fractionation, splicing assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — single lab with orthogonal pharmacological and molecular methods\",\n      \"pmids\": [\"25044120\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"NeuN/Fox-3 (RBFOX3) is an intrinsic component of the neuronal nuclear matrix and a marker of nuclear speckles in neurons, as determined by nuclear matrix extraction and immunofluorescence.\",\n      \"method\": \"Nuclear matrix fractionation, immunofluorescence/confocal microscopy\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct biochemical fractionation with functional implication for nuclear compartmentalization\",\n      \"pmids\": [\"20452351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"NeuN (RBFOX3) is a phosphoprotein; enzymatic dephosphorylation abolishes anti-NeuN immunoreactivity, and both the 46- and 48-kDa isoforms separate into multiple spots by isoelectric focusing, indicating multiple phosphorylated forms. The 48-kDa isoform is preferentially cytoplasmic whereas both isoforms are nuclear, and NeuN is excluded from densely packed chromatin regions.\",\n      \"method\": \"Isoelectric focusing, enzymatic dephosphorylation, biochemical fractionation, immunohistochemistry\",\n      \"journal\": \"Journal of neuroscience research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical characterization with multiple methods in one study\",\n      \"pmids\": [\"15605376\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Rbfox3 knockout mice display increased seizure susceptibility, decreased anxiety, defective synaptic transmission and plasticity in the perforant pathway, increased frequency of excitatory synaptic events in dentate granule cells associated with increased neurotransmitter release probability and dendritic spine density, and increased expression of plasticity genes Egr4 and Arc.\",\n      \"method\": \"Rbfox3 knockout mouse, electrophysiology, behavioral assays, morphological analysis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with multiple defined cellular and circuit-level phenotypes\",\n      \"pmids\": [\"26619789\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Rbfox3 homozygous knockout mice exhibit deficits in hippocampal neurogenesis, impaired cognitive abilities, altered synaptic plasticity and density in the hippocampal dentate gyrus. RBFOX3 regulates exons of genes with synapse-related function.\",\n      \"method\": \"Rbfox3 knockout mouse, neurogenesis assays, synaptic plasticity electrophysiology, electron microscopy of synapses, behavioral tests\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO model with multiple orthogonal phenotypic readouts\",\n      \"pmids\": [\"27701470\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Deletion of Rbfox3 specifically in GABAergic neurons causes spontaneous seizures and high premature mortality via increased presynaptic release, enhanced excitatory GABA action, and reduced VAMP1 (a GABAergic-specific presynaptic protein) expression in hippocampal dentate gyrus. Postnatal restoration of VAMP1 rescued premature mortality. Deletion of Rbfox3 in NPY-expressing GABAergic neurons lowered intrinsic excitability and increased seizure susceptibility.\",\n      \"method\": \"Cell-type-specific conditional knockout, electrophysiology, viral VAMP1 rescue, bumetanide pharmacology, immunohistochemistry\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — cell-type-specific KO with defined molecular substrate (VAMP1) and rescue experiment\",\n      \"pmids\": [\"35951651\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Rbfox3/NeuN regulates alternative splicing of SNORD116 (Snord116) primary transcript in neurons; knockdown of Rbfox3 in Snord116+/- neurons reduced splicing of a Snord116 transgene, demonstrating neuron-specific splicing of this locus requires Rbfox3.\",\n      \"method\": \"Rbfox3 knockdown in primary neurons, RT-PCR splicing assay, RNA FISH\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct knockdown with defined splicing readout in neurons\",\n      \"pmids\": [\"30124848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Rbfox3/NeuN regulates alternative splicing of tau exon 10 via binding to UGCAUG in tau intron 10; deletion mutants of the RNA recognition motif (RRM) or its three RNA-binding sites abolished exon 10 inclusion enhancement. Intron 10 of tau pre-mRNA co-immunoprecipitated with Rbfox3/NeuN.\",\n      \"method\": \"RNA immunoprecipitation, splicing minigene assay, RRM deletion mutagenesis\",\n      \"journal\": \"Journal of Alzheimer's disease : JAD\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RIP plus mutagenesis establishing direct binding and functional requirement of RRM\",\n      \"pmids\": [\"30475774\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RBFOX3 deletion in Rbfox3-/- mice results in reduced inner plexiform layer thickness in the retina without loss of ganglion or amacrine cells and normal visual function, showing RBFOX3 is dispensable for visual function despite its expression in retinal ganglion, amacrine, and horizontal cells.\",\n      \"method\": \"Rbfox3 knockout mouse, retinal morphometry, electrophysiology (ERG), behavioral visual tests\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO with multiple anatomical and functional readouts\",\n      \"pmids\": [\"29401485\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RBFOX3 suppresses hTERT expression by binding to the hTERT promoter; melatonin abrogates RBFOX3 binding to the hTERT promoter, reducing hTERT expression in MLL-rearranged leukemia cells.\",\n      \"method\": \"Chromatin immunoprecipitation, promoter reporter assay, RBFOX3 knockdown/overexpression\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP plus functional reporter assay establishing direct promoter binding\",\n      \"pmids\": [\"30550850\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RBFOX3 promotes gastric cancer cell division and invasion via activation of HTERT signaling; RBFOX3 binds AP-2β (co-immunoprecipitation) to modulate HTERT promoter activity. Silencing of RBFOX3-mediated suppression of growth was rescued by HTERT overexpression.\",\n      \"method\": \"Co-immunoprecipitation, promoter activity assay, knockdown/overexpression, rescue experiment, xenograft mouse model\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — Co-IP identifies AP-2β complex, functional rescue supports mechanism\",\n      \"pmids\": [\"32903312\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"TGF-β1 treatment inhibits RBFOX3 expression at the transcriptional level in A549 lung adenocarcinoma cells; RBFOX3 depletion alters expression of EMT-related proteins E-cadherin and Claudin-1 and promotes mesenchymal morphology during TGF-β1-induced EMT.\",\n      \"method\": \"TGF-β1 treatment, siRNA knockdown, immunofluorescence, qRT-PCR, Western blot\",\n      \"journal\": \"Molecules and cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, KD with defined molecular phenotype but limited mechanistic depth\",\n      \"pmids\": [\"27432190\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RBFOX3 stabilizes Claudin-1 protein in human lung tissue by attenuating its ubiquitination and proteasomal degradation; RBFOX3-positive cells show higher Claudin-1 protein (but not mRNA) levels, and cycloheximide chase confirms increased Claudin-1 stability conferred by RBFOX3.\",\n      \"method\": \"Cycloheximide chase, ubiquitination assay, immunostaining, qRT-PCR, Western blot\",\n      \"journal\": \"Bioscience reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — protein stability assay plus ubiquitination assay establishing post-translational mechanism\",\n      \"pmids\": [\"28126724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Anti-NeuN antibody specificity on aldehyde-fixed tissues is phosphorylation-dependent; the NeuN/A60 epitope in Rbfox3 is a proline- and glutamine-rich domain at the N-terminus. Cross-reactivity with Synapsin I and R3hdm2 on Western blots is due to a shared proline/glutamine-rich domain.\",\n      \"method\": \"Epitope mapping, phosphorylation analysis, immunoblotting with domain deletion constructs\",\n      \"journal\": \"Histochemistry and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct epitope mapping with mutagenesis establishing molecular basis of antibody recognition\",\n      \"pmids\": [\"24150744\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Altered subcellular localization of Rbfox3/NeuN to the cytoplasm is observed in neurons from HIV-infected individuals with cognitive impairment compared to controls, suggesting cytoplasmic mislocalization may downregulate nuclear splicing activity.\",\n      \"method\": \"Immunohistochemistry of human post-mortem brain sections, quantitative subcellular localization analysis\",\n      \"journal\": \"Neuroscience letters\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single observation without direct functional validation of splicing consequence\",\n      \"pmids\": [\"24215932\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RBFOX3 enhances biogenesis of circIGF1R by binding to IGF1R pre-mRNA (shown by RNA immunoprecipitation and RNA pull-down); paclitaxel induces RBFOX3-mediated circIGF1R biogenesis, suppressing NSCLC invasion and migration via the circIGF1R/miR-1270/VANGL2 axis.\",\n      \"method\": \"RNA immunoprecipitation, RNA pull-down, luciferase reporter, FISH, functional invasion/migration assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple RNA binding assays plus functional pathway validation\",\n      \"pmids\": [\"38191906\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RBFOX3 (NeuN) is a neuron-specific RNA-binding protein that binds the UGCAUG intronic element to regulate alternative pre-mRNA splicing of numerous neuronal transcripts (including Numb, NMHC II-B, tau exon 10, Rbfox2, and Snord116), controls miRNA biogenesis by binding pri-miRNAs and regulating microprocessor recruitment, stabilizes specific proteins post-translationally, and is required for hippocampal circuit balance, neurogenesis, and seizure suppression—particularly through regulation of VAMP1 expression in GABAergic neurons; its activity is modulated by isoform-specific alternative splicing of its own transcript (controlling nuclear vs. cytoplasmic localization via a bipartite NLS), phosphorylation, and interaction with co-factors such as PSF.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RBFOX3 (NeuN) is a neuron-specific RNA-binding protein that orchestrates post-transcriptional gene regulation in the nervous system through alternative pre-mRNA splicing, miRNA biogenesis, circular RNA production, and post-translational protein stabilization. It binds the UGCAUG intronic element via its RNA recognition motif to regulate splicing of neuronal transcripts including Numb, NMHC II-B, tau exon 10, Rbfox2, and Snord116, with PSF functioning as a required co-activator for at least a subset of these events [PMID:19713214, PMID:21177649, PMID:23420872, PMID:30475774]. RBFOX3 also binds primary miRNAs to regulate microprocessor recruitment and promotes circRNA biogenesis from specific pre-mRNAs [PMID:25240799, PMID:38191906]. Its own transcript undergoes alternative splicing that controls a bipartite nuclear localization signal, generating isoforms with nuclear or cytoplasmic distribution; Rbfox3 knockout mice exhibit seizures, impaired hippocampal neurogenesis and synaptic plasticity, with GABAergic neuron-specific deletion causing spontaneous seizures through loss of VAMP1 expression, rescuable by postnatal VAMP1 restoration [PMID:21747913, PMID:35951651, PMID:26619789].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Before the molecular identity of NeuN was known, biochemical analysis established it as a multiply phosphorylated nuclear protein with isoform-specific subcellular distribution, setting the stage for understanding its post-translational regulation.\",\n      \"evidence\": \"Isoelectric focusing and enzymatic dephosphorylation of NeuN from brain tissue\",\n      \"pmids\": [\"15605376\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinases responsible for phosphorylation not identified\", \"Functional consequence of phosphorylation on RNA binding unknown\", \"Only antibody-based identification prior to molecular cloning\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"The longstanding neuronal marker NeuN was identified as the product of the RBFOX3 gene and shown to be an RNA-binding protein that binds the UGCAUG element and regulates neuron-specific alternative splicing, establishing its molecular identity and core biochemical activity.\",\n      \"evidence\": \"Mass spectrometry of immunopurified NeuN, recombinant protein confirmation, shRNA knockdown, and NMHC II-B splicing reporter assay\",\n      \"pmids\": [\"19713214\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genome-wide splicing targets unknown\", \"Relationship to other Rbfox family members unclear\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Discovery that PSF is a co-activator required for RBFOX3-mediated splicing revealed that RBFOX3 does not act alone but depends on cofactor-mediated recruitment to its target pre-mRNAs.\",\n      \"evidence\": \"Affinity chromatography identification of PSF, co-IP, and PSF-dependent splicing reporter assays for NMHC II-B exon N30\",\n      \"pmids\": [\"21177649\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether PSF is required for all RBFOX3 splicing targets or only a subset\", \"Structural basis of RBFOX3–PSF interaction unknown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Localization of RBFOX3 to the neuronal nuclear matrix and nuclear speckles placed its splicing activity within a specific subnuclear compartment associated with RNA processing.\",\n      \"evidence\": \"Nuclear matrix fractionation and confocal immunofluorescence in neurons\",\n      \"pmids\": [\"20452351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether nuclear matrix association is required for splicing function\", \"Dynamic trafficking between speckles and nucleoplasm not characterized\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Autoregulatory isoform diversity was uncovered: RBFOX3 alternative splicing of its own transcript generates isoforms with or without a bipartite NLS, controlling nuclear versus cytoplasmic localization and enabling nuclear RBFOX3 to produce a dominant-negative Rbfox2 isoform, revealing cross-regulation among Rbfox family members.\",\n      \"evidence\": \"Isoform mapping by IP/MS, NLS mutagenesis, splicing and NMD assays for Rbfox2\",\n      \"pmids\": [\"21747913\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signals that regulate the balance of RBFOX3 isoforms in vivo unknown\", \"Cytoplasmic functions of RBFOX3 not fully defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"In vivo requirement for RBFOX3 in neuronal differentiation was established through its direct regulation of Numb alternative splicing in developing spinal cord, with isoform-specific rescue proving causality.\",\n      \"evidence\": \"siRNA loss-of-function in chicken spinal cord with Numb isoform-specific rescue\",\n      \"pmids\": [\"23420872\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Numb is the sole essential target for differentiation\", \"Mammalian in vivo validation of this specific mechanism not performed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"RBFOX3 function was expanded beyond splicing: PAR-CLIP revealed binding to primary miRNAs lacking the canonical UGCAUG motif, and reconstitution showed RBFOX3 directly regulates microprocessor recruitment for miRNA biogenesis.\",\n      \"evidence\": \"Transcriptome-wide PAR-CLIP, inducible expression/depletion, in vitro pri-miRNA processing assay\",\n      \"pmids\": [\"25240799\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sequence determinants for miRNA binding distinct from UGCAUG not defined\", \"Relative physiological importance of miRNA regulation versus splicing regulation unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The Rbfox3-d31 isoform lacking a cassette exon within the RRM was shown to be degraded by the ubiquitin-proteasome system, and its stabilization relocalized Rbfox2 and repressed Rbfox family splicing activity, revealing proteolytic quality control as a mechanism shaping Rbfox network output.\",\n      \"evidence\": \"Proteasome inhibitor (MG132) treatment, isoform-specific expression, subcellular fractionation, splicing assays\",\n      \"pmids\": [\"25044120\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase responsible for Rbfox3-d31 ubiquitination not identified\", \"In vivo relevance of this degradation pathway not established\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Rbfox3 knockout mice revealed that RBFOX3 is essential for hippocampal circuit balance: loss causes seizure susceptibility, increased excitatory drive onto dentate granule cells, increased dendritic spine density, and upregulation of plasticity genes Egr4 and Arc.\",\n      \"evidence\": \"Rbfox3 knockout mouse with electrophysiology, behavioral assays, and morphological analysis\",\n      \"pmids\": [\"26619789\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific splicing or miRNA targets mediating each phenotype not resolved\", \"Developmental versus acute contribution of RBFOX3 not distinguished\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Knockout studies further demonstrated RBFOX3 is required for hippocampal neurogenesis, synaptic density, and cognitive function, with splicing targets enriched for synapse-related genes.\",\n      \"evidence\": \"Rbfox3 knockout mouse with neurogenesis assays, electron microscopy of synapses, behavioral tests\",\n      \"pmids\": [\"27701470\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Causal link between individual mis-spliced transcripts and neurogenesis defect not established\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"A non-canonical post-translational function was discovered: RBFOX3 stabilizes Claudin-1 protein by attenuating its ubiquitination and proteasomal degradation, extending RBFOX3 activity beyond RNA regulation.\",\n      \"evidence\": \"Cycloheximide chase and ubiquitination assays in human lung tissue cells\",\n      \"pmids\": [\"28126724\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which an RNA-binding protein inhibits Claudin-1 ubiquitination is unclear\", \"Whether this occurs in neurons not tested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"RBFOX3 was shown to directly regulate tau exon 10 inclusion via UGCAUG in intron 10 and to participate in neuron-specific splicing of the Snord116 locus, broadening the catalog of neurologically relevant targets.\",\n      \"evidence\": \"RNA immunoprecipitation, RRM deletion mutagenesis for tau; Rbfox3 knockdown in primary neurons with RT-PCR for Snord116\",\n      \"pmids\": [\"30475774\", \"30124848\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether tau exon 10 mis-splicing in Rbfox3 KO contributes to tauopathy not tested in vivo\", \"Quantitative contribution of RBFOX3 versus other splicing factors at Snord116 locus unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Cell-type-specific deletion revealed that RBFOX3 in GABAergic neurons is critical for seizure suppression, operating through maintenance of VAMP1 expression; postnatal VAMP1 rescue prevented mortality, establishing a defined molecular substrate for the seizure phenotype.\",\n      \"evidence\": \"GABAergic neuron-specific conditional knockout, electrophysiology, viral VAMP1 restoration, bumetanide pharmacology\",\n      \"pmids\": [\"35951651\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RBFOX3 regulates VAMP1 through splicing, mRNA stability, or another mechanism not fully resolved\", \"Contribution of non-GABAergic neuronal RBFOX3 to seizure threshold not isolated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"RBFOX3 was found to promote circRNA biogenesis by binding IGF1R pre-mRNA, adding circular RNA production to its repertoire of post-transcriptional regulatory activities.\",\n      \"evidence\": \"RNA immunoprecipitation, RNA pull-down, and functional invasion assays in NSCLC cells\",\n      \"pmids\": [\"38191906\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether circRNA biogenesis is a general function of RBFOX3 or transcript-specific\", \"Physiological relevance of RBFOX3-mediated circRNA in neurons not examined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include: the structural basis for RBFOX3's recognition of non-UGCAUG RNA targets such as pri-miRNAs; the kinases and phosphatases controlling RBFOX3 phosphorylation and its functional consequences; the mechanism by which RBFOX3 regulates VAMP1 expression in GABAergic neurons; and the relative physiological importance of its splicing, miRNA, circRNA, and protein-stabilization activities.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of RBFOX3 in complex with RNA\", \"Phosphorylation-function relationship unresolved\", \"Mechanism of VAMP1 regulation (transcriptional, splicing, or stability) not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 3, 4, 12, 20]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 3, 4, 11, 12]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [14, 15]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 5, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2, 6, 7]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2, 7]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008953854\", \"supporting_discovery_ids\": [0, 3, 4, 11, 12]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 3, 4, 11, 12]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [8, 9, 10]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [3, 9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PSF\",\n      \"VAMP1\",\n      \"RBFOX2\",\n      \"AP2B1\",\n      \"CLDN1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\nWait, I made an error in the pathway section — I included an invalid term_id \"GO:0008953854\". Let me correct:\n\n```json\n{\n  \"mechanistic_narrative\": \"RBFOX3 (NeuN) is a neuron-specific RNA-binding protein that orchestrates post-transcriptional gene regulation in the nervous system through alternative pre-mRNA splicing, miRNA biogenesis, circular RNA production, and post-translational protein stabilization. It binds the UGCAUG intronic element via its RNA recognition motif to regulate splicing of neuronal transcripts including Numb, NMHC II-B, tau exon 10, Rbfox2, and Snord116, with PSF functioning as a required co-activator for at least a subset of these events [PMID:19713214, PMID:21177649, PMID:23420872, PMID:30475774]. RBFOX3 also binds primary miRNAs to regulate microprocessor recruitment and promotes circRNA biogenesis from specific pre-mRNAs [PMID:25240799, PMID:38191906]. Its own transcript undergoes alternative splicing that controls a bipartite nuclear localization signal, generating isoforms with nuclear or cytoplasmic distribution; Rbfox3 knockout mice exhibit seizures, impaired hippocampal neurogenesis and synaptic plasticity, with GABAergic neuron-specific deletion causing spontaneous seizures through loss of VAMP1 expression, rescuable by postnatal VAMP1 restoration [PMID:21747913, PMID:35951651, PMID:26619789].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Before the molecular identity of NeuN was known, biochemical analysis established it as a multiply phosphorylated nuclear protein with isoform-specific subcellular distribution, setting the stage for understanding its post-translational regulation.\",\n      \"evidence\": \"Isoelectric focusing and enzymatic dephosphorylation of NeuN from brain tissue\",\n      \"pmids\": [\"15605376\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinases responsible for phosphorylation not identified\", \"Functional consequence of phosphorylation on RNA binding unknown\", \"Only antibody-based identification prior to molecular cloning\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"The longstanding neuronal marker NeuN was identified as the product of the RBFOX3 gene and shown to be an RNA-binding protein that binds the UGCAUG element and regulates neuron-specific alternative splicing, establishing its molecular identity and core biochemical activity.\",\n      \"evidence\": \"Mass spectrometry of immunopurified NeuN, recombinant protein confirmation, shRNA knockdown, and NMHC II-B splicing reporter assay\",\n      \"pmids\": [\"19713214\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genome-wide splicing targets unknown\", \"Relationship to other Rbfox family members unclear\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Discovery that PSF is a co-activator required for RBFOX3-mediated splicing revealed that RBFOX3 does not act alone but depends on cofactor-mediated recruitment to its target pre-mRNAs.\",\n      \"evidence\": \"Affinity chromatography identification of PSF, co-IP, and PSF-dependent splicing reporter assays for NMHC II-B exon N30\",\n      \"pmids\": [\"21177649\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether PSF is required for all RBFOX3 splicing targets or only a subset\", \"Structural basis of RBFOX3–PSF interaction unknown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Localization of RBFOX3 to the neuronal nuclear matrix and nuclear speckles placed its splicing activity within a specific subnuclear compartment associated with RNA processing.\",\n      \"evidence\": \"Nuclear matrix fractionation and confocal immunofluorescence in neurons\",\n      \"pmids\": [\"20452351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether nuclear matrix association is required for splicing function\", \"Dynamic trafficking between speckles and nucleoplasm not characterized\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Autoregulatory isoform diversity was uncovered: RBFOX3 alternative splicing of its own transcript generates isoforms with or without a bipartite NLS, controlling nuclear versus cytoplasmic localization and enabling nuclear RBFOX3 to produce a dominant-negative Rbfox2 isoform, revealing cross-regulation among Rbfox family members.\",\n      \"evidence\": \"Isoform mapping by IP/MS, NLS mutagenesis, splicing and NMD assays for Rbfox2\",\n      \"pmids\": [\"21747913\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signals that regulate the balance of RBFOX3 isoforms in vivo unknown\", \"Cytoplasmic functions of RBFOX3 not fully defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"In vivo requirement for RBFOX3 in neuronal differentiation was established through its direct regulation of Numb alternative splicing in developing spinal cord, with isoform-specific rescue proving causality.\",\n      \"evidence\": \"siRNA loss-of-function in chicken spinal cord with Numb isoform-specific rescue\",\n      \"pmids\": [\"23420872\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Numb is the sole essential target for differentiation\", \"Mammalian in vivo validation of this specific mechanism not performed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"RBFOX3 function was expanded beyond splicing: PAR-CLIP revealed binding to primary miRNAs lacking the canonical UGCAUG motif, and reconstitution showed RBFOX3 directly regulates microprocessor recruitment for miRNA biogenesis.\",\n      \"evidence\": \"Transcriptome-wide PAR-CLIP, inducible expression/depletion, in vitro pri-miRNA processing assay\",\n      \"pmids\": [\"25240799\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sequence determinants for miRNA binding distinct from UGCAUG not defined\", \"Relative physiological importance of miRNA regulation versus splicing regulation unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The Rbfox3-d31 isoform lacking a cassette exon within the RRM was shown to be degraded by the ubiquitin-proteasome system, and its stabilization relocalized Rbfox2 and repressed Rbfox family splicing activity, revealing proteolytic quality control as a mechanism shaping Rbfox network output.\",\n      \"evidence\": \"Proteasome inhibitor (MG132) treatment, isoform-specific expression, subcellular fractionation, splicing assays\",\n      \"pmids\": [\"25044120\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase responsible for Rbfox3-d31 ubiquitination not identified\", \"In vivo relevance of this degradation pathway not established\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Rbfox3 knockout mice revealed that RBFOX3 is essential for hippocampal circuit balance: loss causes seizure susceptibility, increased excitatory drive onto dentate granule cells, increased dendritic spine density, and upregulation of plasticity genes Egr4 and Arc.\",\n      \"evidence\": \"Rbfox3 knockout mouse with electrophysiology, behavioral assays, and morphological analysis\",\n      \"pmids\": [\"26619789\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific splicing or miRNA targets mediating each phenotype not resolved\", \"Developmental versus acute contribution of RBFOX3 not distinguished\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Knockout studies further demonstrated RBFOX3 is required for hippocampal neurogenesis, synaptic density, and cognitive function, with splicing targets enriched for synapse-related genes.\",\n      \"evidence\": \"Rbfox3 knockout mouse with neurogenesis assays, electron microscopy of synapses, behavioral tests\",\n      \"pmids\": [\"27701470\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Causal link between individual mis-spliced transcripts and neurogenesis defect not established\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"A non-canonical post-translational function was discovered: RBFOX3 stabilizes Claudin-1 protein by attenuating its ubiquitination and proteasomal degradation, extending RBFOX3 activity beyond RNA regulation.\",\n      \"evidence\": \"Cycloheximide chase and ubiquitination assays in human lung tissue cells\",\n      \"pmids\": [\"28126724\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which an RNA-binding protein inhibits Claudin-1 ubiquitination is unclear\", \"Whether this occurs in neurons not tested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"RBFOX3 was shown to directly regulate tau exon 10 inclusion via UGCAUG in intron 10 and to participate in neuron-specific splicing of the Snord116 locus, broadening the catalog of neurologically relevant targets.\",\n      \"evidence\": \"RNA immunoprecipitation, RRM deletion mutagenesis for tau; Rbfox3 knockdown in primary neurons with RT-PCR for Snord116\",\n      \"pmids\": [\"30475774\", \"30124848\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether tau exon 10 mis-splicing in Rbfox3 KO contributes to tauopathy not tested in vivo\", \"Quantitative contribution of RBFOX3 versus other splicing factors at Snord116 locus unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Cell-type-specific deletion revealed that RBFOX3 in GABAergic neurons is critical for seizure suppression, operating through maintenance of VAMP1 expression; postnatal VAMP1 rescue prevented mortality, establishing a defined molecular substrate for the seizure phenotype.\",\n      \"evidence\": \"GABAergic neuron-specific conditional knockout, electrophysiology, viral VAMP1 restoration, bumetanide pharmacology\",\n      \"pmids\": [\"35951651\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RBFOX3 regulates VAMP1 through splicing, mRNA stability, or another mechanism not fully resolved\", \"Contribution of non-GABAergic neuronal RBFOX3 to seizure threshold not isolated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"RBFOX3 was found to promote circRNA biogenesis by binding IGF1R pre-mRNA, adding circular RNA production to its repertoire of post-transcriptional regulatory activities.\",\n      \"evidence\": \"RNA immunoprecipitation, RNA pull-down, and functional invasion assays in NSCLC cells\",\n      \"pmids\": [\"38191906\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether circRNA biogenesis is a general function of RBFOX3 or transcript-specific\", \"Physiological relevance of RBFOX3-mediated circRNA in neurons not examined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include: the structural basis for RBFOX3's recognition of non-UGCAUG RNA targets such as pri-miRNAs; the kinases and phosphatases controlling RBFOX3 phosphorylation and its functional consequences; the mechanism by which RBFOX3 regulates VAMP1 expression in GABAergic neurons; and the relative physiological importance of its splicing, miRNA, circRNA, and protein-stabilization activities.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of RBFOX3 in complex with RNA\", \"Phosphorylation-function relationship unresolved\", \"Mechanism of VAMP1 regulation (transcriptional, splicing, or stability) not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 3, 4, 12, 20]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 3, 4, 11, 12]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [14, 15]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 5, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2, 6, 7]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2, 7]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 3, 4, 11, 12]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [8, 9, 10]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [3, 9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PSF\",\n      \"VAMP1\",\n      \"RBFOX2\",\n      \"TFAP2B\",\n      \"CLDN1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}