{"gene":"SF3A3","run_date":"2026-06-10T07:46:31","timeline":{"discoveries":[{"year":1993,"finding":"SF3A3 (SF3a60) is one of three subunits of mammalian splicing factor SF3a, and SF3a interacts with U2 snRNP in the presence of SF3b to generate a structure similar to 17S U2 snRNP, implicating SF3a in the incorporation of U2 snRNP into the spliceosome.","method":"Biochemical reconstitution, protein fractionation, and immunological characterization of 17S U2 snRNP","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution experiment showing SF3a+SF3b+12S U2 snRNP assembly, replicated across multiple labs in the same year","pmids":["8211112"],"is_preprint":false},{"year":1990,"finding":"Yeast PRP9 (ortholog of SF3A3) protein is required for stable U2 snRNP-substrate interaction during spliceosome assembly, as shown by impaired U2 snRNP binding in prp9 mutant extracts.","method":"In vitro splicing and spliceosome assembly in prp9 mutant yeast extracts; RNA immunoprecipitation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro splicing assay and immunoprecipitation in defined mutant background, replicated by multiple labs","pmids":["2147224"],"is_preprint":false},{"year":1990,"finding":"PRP9 (ortholog of SF3A3) contains cysteine/histidine zinc finger-like motifs; directed mutagenesis of some but not all of these residues critically impairs protein function, establishing that these motifs are functionally important.","method":"DNA sequencing and site-directed mutagenesis with functional complementation assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct mutagenesis with functional readout, single lab but multiple mutants tested","pmids":["2118103"],"is_preprint":false},{"year":1993,"finding":"Yeast PRP9 (ortholog of SF3A3) and PRP11 do not interact directly but both bind SPP91 (PRP21) simultaneously to form a trimeric PRP9-SPP91-PRP11 complex required for early spliceosome assembly.","method":"Genetic epistasis (synthetic lethal analysis), protein-protein interaction assays in yeast; identification of mammalian counterpart complex","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis combined with direct interaction tests, replicated by independent lab in same journal issue","pmids":["8211114"],"is_preprint":false},{"year":1993,"finding":"The 60-kDa protein of human 17S U2 snRNP (SF3A3/SF3a60) is immunologically and functionally related to yeast PRP9; antibodies against PRP9 strongly inhibit prespliceosome formation and mRNA splicing in HeLa nuclear extracts, and only 17S (not 12S) U2 snRNP restores splicing activity.","method":"Antibody inhibition of HeLa nuclear splicing extracts; functional reconstitution with purified 17S vs 12S U2 snRNP","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — antibody inhibition combined with reconstitution rescue, multiple orthogonal methods","pmids":["8367487"],"is_preprint":false},{"year":1993,"finding":"PRP9 (SF3A3 ortholog) acts after formation of the U1 snRNP-pre-mRNA complex, and contains two distinct binding sites: a C-terminal region mediating PRP9 homodimerization and an N-terminal region binding SPP91; deletion of the second C-terminal motif causes dominant lethality.","method":"In vivo protein-protein interaction assay (yeast two-hybrid), deletion mutagenesis, dominant-negative phenotype analysis","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo binding assay and deletion mutagenesis with functional readouts, single lab","pmids":["8330742"],"is_preprint":false},{"year":1993,"finding":"PRP5, PRP9, PRP11, and PRP21 are each required for U2 snRNP binding to pre-mRNA during spliceosome assembly; PRP9 and PRP11 interact biochemically, and these factors may act on the stem-loop IIa of U2 snRNA.","method":"In vitro spliceosome assembly assays, genetic analysis, biochemical complementation experiments","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro biochemical reconstitution with genetic validation, multiple proteins and orthogonal methods","pmids":["8405998"],"is_preprint":false},{"year":1994,"finding":"Human SF3a60 (SF3A3) shares 30% sequence identity with yeast PRP9, with highest homology in the C-terminal zinc finger-like domain; the PRP9 zinc finger-like motif can be replaced by the equivalent mammalian SF3a60 region and rescues the temperature-sensitive prp9-1 phenotype, demonstrating evolutionary conservation of both structure and function.","method":"cDNA cloning, sequence analysis, chimeric protein construction, in vivo complementation of yeast ts mutant","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — chimeric protein rescue of defined yeast mutant, direct functional equivalence demonstrated","pmids":["7816610"],"is_preprint":false},{"year":1996,"finding":"Purified yeast Prp9, Prp11, and Prp21 proteins form a direct trimeric complex (Prp9·Prp11·Prp21) that is functional in in vitro splicing; together these proteins alter the accessibility of the U2 snRNA branch-point pairing region to oligonucleotide-directed RNaseH cleavage, suggesting they activate U2 snRNP for spliceosome assembly.","method":"Recombinant protein expression in E. coli, metal-affinity purification, in vitro splicing assays, oligonucleotide-directed RNaseH cleavage assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted trimeric complex with functional in vitro splicing assay and mechanistic RNaseH probing","pmids":["8969185"],"is_preprint":false},{"year":2001,"finding":"Human SF3a60 (SF3A3) and SF3a66 interact with SF3a120 (but not with each other) to form the SF3a heterotrimer; SF3a60's N-terminal portion contains the SF3a120 interaction site; C2H2-type zinc finger domains of SF3a60 mediate integration into U2 snRNP via interactions with Sm proteins; SF3a60 plays a major role in recruiting SF3a120 into the U2 particle; all domains required for SF3a assembly and 17S U2 snRNP formation are also necessary for prespliceosome assembly.","method":"Recombinant protein expression in insect cells, in vitro binding assays, 17S U2 snRNP assembly assays, prespliceosome formation assays, domain deletion/mutagenesis analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted complex with domain mapping, multiple orthogonal in vitro assays, single rigorous study with extensive mutagenesis","pmids":["11533230"],"is_preprint":false},{"year":1996,"finding":"Yeast Prp21 heat-sensitive mutations are specifically associated with defects in interaction with Prp9 (SF3A3 ortholog) but not Prp11; deletion analysis maps domains of Prp21 required for binding Prp9 and Prp11 separately; prp21 mutants show splicing defects and pre-mRNA nuclear export phenotypes similar to prp9-1 mutant.","method":"Site-directed mutagenesis, genetic epistasis, deletion analysis, protein-protein interaction assays","journal":"RNA","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and biochemical domain mapping, single lab with multiple mutants","pmids":["8718683"],"is_preprint":false},{"year":1992,"finding":"The spp91-1 suppressor of prp9-1 partially restores splicing and completely reverts aberrant pre-mRNA nuclear export in prp9-1 mutants; SPP91 encodes a novel nuclear protein essential for growth that acts in the same pathway as PRP9 (SF3A3 ortholog) in spliceosome assembly.","method":"Genetic suppressor screen, gene cloning and sequencing, in vivo depletion analysis, splicing and nuclear export assays","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with functional splicing and export readouts, single lab","pmids":["1505518"],"is_preprint":false},{"year":2008,"finding":"SF3A3 (SF3a60) directly interacts with the constitutive androstane receptor (CAR) and functions as a co-repressor of CAR transcriptional activity; overexpression of SF3A3 inhibits CAR-driven reporter activity by ~50% and knockdown activates it ~3-fold, independent of the CAR ligand TCPOBOP.","method":"Yeast two-hybrid screening, co-immunoprecipitation, GST pull-down, reporter gene assay, siRNA knockdown","journal":"Biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal binding assays (Co-IP and GST pull-down) plus functional reporter assay, single lab","pmids":["18713018"],"is_preprint":false},{"year":2021,"finding":"SF3A3 protein levels are regulated translationally through an RNA stem-loop in its mRNA in an eIF3D-dependent manner upon MYC hyperactivation; altered SF3A3 translation leads to mis-splicing of mRNAs enriched for mitochondrial regulators, causing metabolic reprogramming and stem-like properties that fuel MYC-driven tumorigenesis in vivo.","method":"Translational regulation assays, stem-loop reporter constructs, eIF3D knockdown, splicing analysis, in vivo xenograft models","journal":"Molecular cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional validation with KD and in vivo model, single lab, multiple readouts but abstract-level detail","pmids":["33662273"],"is_preprint":false},{"year":2022,"finding":"CircSCAP directly binds SF3A3 protein and promotes its ubiquitin-proteasome-mediated degradation, which enhances expression of MDM4-S and activates p53 signaling in NSCLC cells.","method":"Biotin-labeled RNA pulldown, RNA immunoprecipitation (RIP), co-immunoprecipitation, immunoblotting, luciferase reporter assay, in vitro and in vivo rescue experiments","journal":"Journal of experimental & clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal binding and functional assays, single lab","pmids":["35365208"],"is_preprint":false},{"year":2022,"finding":"SF3A3 transcription is upregulated in bladder cancer by E2F6-mediated recruitment of KDM5C to the SF3A3 promoter, which demethylates H3K4me2 at the CpG island, leading to promoter hypomethylation and increased SF3A3 expression.","method":"Co-immunoprecipitation (E2F6-KDM5C interaction), chromatin immunoprecipitation (ChIP), luciferase reporter assay, methylation analysis","journal":"Cancer cell international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and co-IP with reporter validation, single lab, defines transcriptional regulatory mechanism","pmids":["35248043"],"is_preprint":false},{"year":2014,"finding":"In Trypanosoma brucei, SF3a60 (ortholog of SF3A3) localizes to the nucleus, is essential for cell viability, and interacts with SF3a120, SF3a66, and SAP130 as confirmed by tandem affinity purification and mass spectrometry.","method":"Epitope tagging and localization, RNAi depletion, yeast two-hybrid screening, tandem affinity purification, mass spectrometry","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — TAP-MS confirmation of interactions plus localization, single lab in divergent organism","pmids":["24651488"],"is_preprint":false},{"year":2023,"finding":"Knockdown of SF3A3 in APL (NB4) cells causes G1/S cell cycle arrest and proliferation inhibition, indicating SF3A3 is required for cell cycle progression in leukemia cells.","method":"siRNA knockdown, cell proliferation assays, cell cycle analysis","journal":"Archives of biochemistry and biophysics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single knockdown study with phenotypic readout, no pathway placement beyond cell cycle, single lab","pmids":["37356608"],"is_preprint":false},{"year":2025,"finding":"SF3A3 regulates alternative splicing of c-FOS pre-mRNA, resulting in approximately 2-fold increase in full-length c-FOS expression and activation of downstream anti-apoptotic pathways; PEITC identified as a direct SF3A3 inhibitor by surface plasmon resonance and mass spectrometry.","method":"Alternative splicing analysis, knockdown/overexpression, surface plasmon resonance, mass spectrometry, in vitro and in vivo functional assays","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct biophysical binding validation (SPR + MS) combined with splicing and functional assays, single lab","pmids":["40598817"],"is_preprint":false},{"year":2025,"finding":"STIL interacts with FOXM1, and this complex binds the SF3A3 promoter to activate SF3A3 transcription in hepatocellular carcinoma; knockdown of FOXM1 reduces SF3A3 expression and SF3A3 overexpression rescues the anti-tumor effects of STIL loss.","method":"Co-immunoprecipitation (STIL-FOXM1), ChIP-qPCR, RT-qPCR, xenograft rescue experiments","journal":"Cell division","confidence":"Low","confidence_rationale":"Tier 3 / Weak — Co-IP and ChIP with rescue experiment, single lab, limited mechanistic detail in abstract","pmids":["39825314"],"is_preprint":false}],"current_model":"SF3A3 (SF3a60/SAP61/PRP9) is a 60-kDa subunit of the trimeric splicing factor SF3a complex (with SF3a66 and SF3a120) that assembles onto 12S U2 snRNP via sequential interactions—where SF3a60's N-terminal domain recruits SF3a120 and its C2H2 zinc finger domain anchors the complex to Sm proteins—to generate the active 17S U2 snRNP required for prespliceosome formation and branch-site recognition; it also interacts with the constitutive androstane receptor CAR as a co-repressor, is subject to translational regulation through an eIF3D-dependent stem-loop mechanism downstream of MYC, and regulates alternative splicing of target pre-mRNAs including c-FOS."},"narrative":{"mechanistic_narrative":"SF3A3 (SF3a60/SAP61, the ortholog of yeast PRP9) is a core subunit of the heterotrimeric splicing factor SF3a that converts inactive 12S U2 snRNP into the active 17S U2 snRNP required for prespliceosome assembly and U2 snRNP recruitment to pre-mRNA [PMID:8211112, PMID:8367487]. Genetic and biochemical work on the yeast ortholog established that PRP9 is required for stable U2 snRNP–substrate interaction and acts after U1 snRNP–pre-mRNA complex formation [PMID:2147224, PMID:8330742], assembling with PRP11 and PRP21/SPP91 into a trimeric complex that alters the accessibility of the U2 snRNA branch-point pairing region and thereby activates U2 snRNP for spliceosome assembly [PMID:8211114, PMID:8969185]. The protein is organized into functionally distinct domains: an N-terminal region that recruits SF3a120 into the U2 particle and C2H2 zinc-finger motifs that anchor the complex through Sm protein interactions, with all of these domains required for SF3a assembly, 17S U2 snRNP formation, and prespliceosome assembly [PMID:2118103, PMID:11533230]; this domain architecture and function are evolutionarily conserved, as the mammalian zinc-finger region rescues the yeast prp9 temperature-sensitive phenotype [PMID:7816610]. Beyond its constitutive splicing role, SF3A3 directs alternative splicing of target pre-mRNAs—including c-FOS, where it promotes full-length isoform expression and downstream anti-apoptotic signaling [PMID:40598817], and mitochondrial regulator transcripts, where MYC-driven, eIF3D-dependent translational upregulation of SF3A3 reprograms metabolism to fuel tumorigenesis [PMID:33662273]. SF3A3 additionally acts as a co-repressor of the constitutive androstane receptor (CAR) [PMID:18713018], and its abundance is controlled in cancer contexts by circSCAP-mediated ubiquitin-proteasome degradation and by transcriptional regulation at its promoter [PMID:35365208, PMID:35248043].","teleology":[{"year":1990,"claim":"Established that the SF3A3 ortholog PRP9 is functionally required for U2 snRNP engagement with pre-mRNA, placing it in the spliceosome assembly pathway rather than as a passive structural component.","evidence":"In vitro splicing and spliceosome assembly with RNA immunoprecipitation in prp9 mutant yeast extracts","pmids":["2147224"],"confidence":"High","gaps":["Did not define which domains mediate U2 binding","Mechanism of branch-site activation not resolved"]},{"year":1990,"claim":"Identified zinc finger-like motifs as functionally essential, beginning the structural dissection of how PRP9/SF3A3 contributes to splicing.","evidence":"DNA sequencing and site-directed mutagenesis with functional complementation in yeast","pmids":["2118103"],"confidence":"High","gaps":["Did not establish the binding partners contacted by the zinc fingers","No structural model of the motif"]},{"year":1992,"claim":"Linked PRP9 to a genetically interacting partner (SPP91/PRP21) acting in the same assembly pathway and connected splicing defects to aberrant pre-mRNA nuclear export.","evidence":"Genetic suppressor screen, gene cloning, in vivo depletion, splicing and nuclear export assays in yeast","pmids":["1505518"],"confidence":"Medium","gaps":["Direct physical contact not yet shown","Export phenotype mechanism unresolved"]},{"year":1993,"claim":"Defined SF3A3 as one of three SF3a subunits that, with SF3b, reconstitutes 17S U2 snRNP, and showed only 17S (not 12S) U2 snRNP restores splicing—establishing SF3a's role in U2 snRNP activation.","evidence":"Biochemical reconstitution, antibody inhibition of HeLa nuclear extracts, and 17S vs 12S U2 snRNP rescue","pmids":["8211112","8367487"],"confidence":"High","gaps":["Stoichiometry and subunit contacts within SF3a not yet mapped in human","Branch-site recognition mechanism not directly demonstrated"]},{"year":1993,"claim":"Resolved the architecture of the assembly complex, showing PRP9 and PRP11 do not bind each other but both bind PRP21/SPP91 to form a trimer, with separable N- and C-terminal interaction surfaces.","evidence":"Genetic epistasis, yeast two-hybrid, deletion mutagenesis, and interaction assays","pmids":["8211114","8330742"],"confidence":"High","gaps":["Functional consequence of homodimerization unclear","Human counterpart contacts inferred not proven at this stage"]},{"year":1996,"claim":"Provided the mechanistic link between SF3a assembly and catalysis by showing the reconstituted trimer alters U2 snRNA branch-point pairing region accessibility, defining how the complex activates U2 snRNP.","evidence":"Recombinant protein reconstitution, in vitro splicing, and oligonucleotide-directed RNaseH probing of U2 snRNA","pmids":["8969185","8718683"],"confidence":"High","gaps":["Atomic basis of the conformational change not determined","How accessibility change promotes branch-site selection unresolved"]},{"year":1994,"claim":"Demonstrated cross-species functional equivalence by showing the mammalian SF3a60 zinc-finger region rescues the yeast prp9 ts mutant, confirming conserved structure and function.","evidence":"cDNA cloning, sequence analysis, chimeric protein construction, and in vivo yeast complementation","pmids":["7816610"],"confidence":"High","gaps":["Conservation of N-terminal recruitment function not tested here","Human-specific regulatory roles not addressed"]},{"year":2001,"claim":"Mapped the human SF3a60 domain logic—N-terminal recruitment of SF3a120 and zinc-finger-mediated integration into U2 snRNP via Sm proteins—unifying assembly and prespliceosome formation requirements.","evidence":"Recombinant insect-cell expression, in vitro binding, 17S U2 snRNP assembly, prespliceosome assays, and domain mutagenesis","pmids":["11533230"],"confidence":"High","gaps":["Structural detail of the Sm protein contact not resolved","Dynamics of stepwise assembly in cells not addressed"]},{"year":2008,"claim":"Extended SF3A3 function beyond splicing by identifying it as a direct co-repressor of the nuclear receptor CAR.","evidence":"Yeast two-hybrid, Co-IP, GST pull-down, reporter assays, and siRNA knockdown","pmids":["18713018"],"confidence":"Medium","gaps":["Whether repression involves SF3A3's splicing activity is unknown","Physiological relevance in CAR target gene regulation not established"]},{"year":2014,"claim":"Confirmed conservation of SF3a complex composition and nuclear localization in a divergent eukaryote, supporting a universal SF3a architecture centered on SF3a60.","evidence":"Epitope tagging/localization, RNAi, yeast two-hybrid, and TAP-MS in Trypanosoma brucei","pmids":["24651488"],"confidence":"Medium","gaps":["Branch-site mechanism in trypanosomes not probed","Functional contribution of SAP130 interaction unclear"]},{"year":2021,"claim":"Revealed an oncogenic translational control axis in which MYC drives eIF3D-dependent SF3A3 translation, with consequent mis-splicing of mitochondrial regulators reprogramming metabolism.","evidence":"Stem-loop reporter constructs, eIF3D knockdown, splicing analysis, and in vivo xenograft models","pmids":["33662273"],"confidence":"Medium","gaps":["Specific spliced targets driving phenotype not exhaustively defined","Direct SF3A3 binding to these pre-mRNAs not shown"]},{"year":2022,"claim":"Identified post-translational and transcriptional control of SF3A3 abundance in cancer—circSCAP-driven proteasomal degradation and E2F6/KDM5C-mediated promoter hypomethylation—linking SF3A3 dosage to tumor signaling.","evidence":"RNA pulldown, RIP, Co-IP, ChIP, methylation analysis, and reporter/rescue assays in NSCLC and bladder cancer","pmids":["35365208","35248043"],"confidence":"Medium","gaps":["Whether degradation alters splicing output directly is untested","Generality of these regulatory mechanisms across tissues unknown"]},{"year":2025,"claim":"Defined a specific alternative-splicing target (c-FOS) through which SF3A3 promotes anti-apoptotic signaling and identified PEITC as a direct small-molecule inhibitor.","evidence":"Alternative splicing analysis, knockdown/overexpression, SPR and MS binding validation, and in vivo functional assays","pmids":["40598817"],"confidence":"Medium","gaps":["Binding site of PEITC on SF3A3 not mapped","Breadth of SF3A3-regulated alternative splicing program not defined"]},{"year":null,"claim":"How SF3A3's constitutive role in U2 snRNP activation is rewired to select specific alternative-splicing targets in oncogenic contexts, and whether its non-splicing roles depend on the same domains, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of human SF3a60 bound to U2 snRNP","Target selectivity determinants for alternative splicing unknown","Mechanistic relationship between splicing and co-repressor functions undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[8,9]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[12]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[11,16]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,4,9]}],"complexes":["SF3a heterotrimer","17S U2 snRNP","Prp9-Prp11-Prp21 complex"],"partners":["SF3A1","SF3A2","PRP11","PRP21","CAR","CIRCSCAP"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q12874","full_name":"Splicing factor 3A subunit 3","aliases":["SF3a60","Spliceosome-associated protein 61","SAP 61"],"length_aa":501,"mass_kda":58.8,"function":"Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs (PubMed:10882114, PubMed:11533230, PubMed:32494006, PubMed:34822310, PubMed:8022796). The 17S U2 SnRNP complex (1) directly participates in early spliceosome assembly and (2) mediates recognition of the intron branch site during pre-mRNA splicing by promoting the selection of the pre-mRNA branch-site adenosine, the nucleophile for the first step of splicing (PubMed:10882114, PubMed:11533230, PubMed:32494006, PubMed:34822310). Within the 17S U2 SnRNP complex, SF3A3 is part of the SF3A subcomplex that contributes to the assembly of the 17S U2 snRNP, and the subsequent assembly of the pre-spliceosome 'E' complex and the pre-catalytic spliceosome 'A' complex (PubMed:10882114, PubMed:11533230). Involved in pre-mRNA splicing as a component of pre-catalytic spliceosome 'B' complexes (PubMed:29360106, PubMed:30315277)","subcellular_location":"Nucleus speckle; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q12874/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SF3A3","classification":"Common Essential","n_dependent_lines":1207,"n_total_lines":1208,"dependency_fraction":0.9991721854304636},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000183431","cell_line_id":"CID001446","localizations":[{"compartment":"chromatin","grade":3}],"interactors":[{"gene":"RBM17","stoichiometry":10.0},{"gene":"SF3A1","stoichiometry":10.0},{"gene":"SF3A2","stoichiometry":10.0},{"gene":"SNRPD1","stoichiometry":10.0},{"gene":"SNRPD2","stoichiometry":10.0},{"gene":"SF3B3","stoichiometry":10.0},{"gene":"SF3B2","stoichiometry":10.0},{"gene":"SNRPA1","stoichiometry":10.0},{"gene":"SNRPB2","stoichiometry":10.0},{"gene":"SF3B1","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID001446","total_profiled":1310},"omim":[{"mim_id":"620743","title":"SDE2 TELOMERE MAINTENANCE HOMOLOG; SDE2","url":"https://www.omim.org/entry/620743"},{"mim_id":"605596","title":"SPLICING FACTOR 3A, SUBUNIT 3; SF3A3","url":"https://www.omim.org/entry/605596"},{"mim_id":"605595","title":"SPLICING FACTOR 3A, SUBUNIT 1; SF3A1","url":"https://www.omim.org/entry/605595"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear speckles","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SF3A3"},"hgnc":{"alias_symbol":["SF3a60","SAP61","PRP9","PRPF9"],"prev_symbol":[]},"alphafold":{"accession":"Q12874","domains":[{"cath_id":"-","chopping":"3-125","consensus_level":"high","plddt":92.2031,"start":3,"end":125},{"cath_id":"-","chopping":"131-231_310-352","consensus_level":"high","plddt":91.5422,"start":131,"end":352},{"cath_id":"-","chopping":"247-289","consensus_level":"medium","plddt":86.5807,"start":247,"end":289},{"cath_id":"-","chopping":"399-466","consensus_level":"high","plddt":92.0456,"start":399,"end":466},{"cath_id":"-","chopping":"471-501","consensus_level":"medium","plddt":83.5161,"start":471,"end":501}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q12874","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q12874-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q12874-F1-predicted_aligned_error_v6.png","plddt_mean":86.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SF3A3","jax_strain_url":"https://www.jax.org/strain/search?query=SF3A3"},"sequence":{"accession":"Q12874","fasta_url":"https://rest.uniprot.org/uniprotkb/Q12874.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q12874/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q12874"}},"corpus_meta":[{"pmid":"8211112","id":"PMC_8211112","title":"Interaction of mammalian splicing factor SF3a with U2 snRNP and relation of its 60-kD subunit to yeast PRP9.","date":"1993","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8211112","citation_count":139,"is_preprint":false},{"pmid":"8405998","id":"PMC_8405998","title":"Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA.","date":"1993","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/8405998","citation_count":125,"is_preprint":false},{"pmid":"2147224","id":"PMC_2147224","title":"The yeast PRP6 gene encodes a U4/U6 small nuclear ribonucleoprotein particle (snRNP) protein, and the PRP9 gene encodes a protein required for U2 snRNP binding.","date":"1990","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/2147224","citation_count":103,"is_preprint":false},{"pmid":"2118103","id":"PMC_2118103","title":"The molecular characterization of PRP6 and PRP9 yeast genes reveals a new cysteine/histidine motif common to several splicing factors.","date":"1990","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/2118103","citation_count":77,"is_preprint":false},{"pmid":"8211114","id":"PMC_8211114","title":"Interaction between PRP11 and SPP91 yeast splicing factors and characterization of a PRP9-PRP11-SPP91 complex.","date":"1993","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8211114","citation_count":67,"is_preprint":false},{"pmid":"8367487","id":"PMC_8367487","title":"Evidence that the 60-kDa protein of 17S U2 small nuclear ribonucleoprotein is immunologically and functionally related to the yeast PRP9 splicing factor and is required for the efficient formation of prespliceosomes.","date":"1993","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/8367487","citation_count":54,"is_preprint":false},{"pmid":"33662273","id":"PMC_33662273","title":"Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer.","date":"2021","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/33662273","citation_count":52,"is_preprint":false},{"pmid":"11533230","id":"PMC_11533230","title":"Domains in human splicing factors SF3a60 and SF3a66 required for binding to SF3a120, assembly of the 17S U2 snRNP, and prespliceosome formation.","date":"2001","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11533230","citation_count":49,"is_preprint":false},{"pmid":"8330742","id":"PMC_8330742","title":"Interactions between PRP9 and SPP91 splicing factors identify a protein complex required in prespliceosome assembly.","date":"1993","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/8330742","citation_count":47,"is_preprint":false},{"pmid":"1505518","id":"PMC_1505518","title":"A novel gene, spp91-1, suppresses the splicing defect and the pre-mRNA nuclear export in the prp9-1 mutant.","date":"1992","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/1505518","citation_count":42,"is_preprint":false},{"pmid":"7816610","id":"PMC_7816610","title":"Splicing factor SF3a60 is the mammalian homologue of PRP9 of S.cerevisiae: the conserved zinc finger-like motif is functionally exchangeable in vivo.","date":"1994","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/7816610","citation_count":37,"is_preprint":false},{"pmid":"8969185","id":"PMC_8969185","title":"In vitro studies of the Prp9.Prp11.Prp21 complex indicate a pathway for U2 small nuclear ribonucleoprotein activation.","date":"1996","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8969185","citation_count":36,"is_preprint":false},{"pmid":"35365208","id":"PMC_35365208","title":"CircSCAP interacts with SF3A3 to inhibit the malignance of non-small cell lung cancer by activating p53 signaling.","date":"2022","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/35365208","citation_count":32,"is_preprint":false},{"pmid":"35248043","id":"PMC_35248043","title":"E2F6/KDM5C promotes SF3A3 expression and bladder cancer progression through a specific hypomethylated DNA promoter.","date":"2022","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/35248043","citation_count":14,"is_preprint":false},{"pmid":"1848649","id":"PMC_1848649","title":"Cloning of the two essential yeast genes, PRP6 and PRP9, and their rapid mapping, disruption and partial sequencing using a linker insertion strategy.","date":"1991","source":"Molecular & general genetics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/1848649","citation_count":13,"is_preprint":false},{"pmid":"8718683","id":"PMC_8718683","title":"Essential domains of the PRP21 splicing factor are implicated in the binding to PRP9 and PRP11 proteins and are conserved through evolution.","date":"1996","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/8718683","citation_count":13,"is_preprint":false},{"pmid":"35453681","id":"PMC_35453681","title":"Integrated In Silico Analyses Identify PUF60 and SF3A3 as New Spliceosome-Related Breast Cancer RNA-Binding Proteins.","date":"2022","source":"Biology","url":"https://pubmed.ncbi.nlm.nih.gov/35453681","citation_count":8,"is_preprint":false},{"pmid":"18713018","id":"PMC_18713018","title":"Specific inhibition of transcriptional activity of the constitutive androstane receptor (CAR) by the splicing factor SF3a3.","date":"2008","source":"Biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18713018","citation_count":5,"is_preprint":false},{"pmid":"40598817","id":"PMC_40598817","title":"SF3A3 Drives Tumorigenesis in Endometrial Cancer by Enhancing c-FOS Expression and Represents a Potential Therapeutic Target.","date":"2025","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/40598817","citation_count":4,"is_preprint":false},{"pmid":"24651488","id":"PMC_24651488","title":"Proteins associated with SF3a60 in T. brucei.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24651488","citation_count":3,"is_preprint":false},{"pmid":"37356608","id":"PMC_37356608","title":"Inhibition of splicing factors SF3A3 and SRSF5 contributes to As3+/Se4+ combination-mediated proliferation suppression and apoptosis induction in acute promyelocytic leukemia cells.","date":"2023","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/37356608","citation_count":2,"is_preprint":false},{"pmid":"9046088","id":"PMC_9046088","title":"The sequence of a 36.7 kb segment on the left arm of chromosome IV from Saccharomyces cerevisiae reveals 20 non-overlapping open reading frames (ORFs) including SIT4, FAD1, NAM1, RNA11, SIR2, NAT1, PRP9, ACT2 and MPS1 and 11 new ORFs.","date":"1997","source":"Yeast (Chichester, England)","url":"https://pubmed.ncbi.nlm.nih.gov/9046088","citation_count":2,"is_preprint":false},{"pmid":"39825314","id":"PMC_39825314","title":"Interaction of STIL with FOXM1 regulates SF3A3 transcription in the hepatocellular carcinoma development.","date":"2025","source":"Cell division","url":"https://pubmed.ncbi.nlm.nih.gov/39825314","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.08.23.609445","title":"Recontextualizing Eukaryogenesis via Computational Analysis of RNA Processing in 16,449 Archaeal Genomes","date":"2024-08-24","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.23.609445","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12608,"output_tokens":4612,"usd":0.053502,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12654,"output_tokens":4124,"usd":0.083185,"stage2_stop_reason":"end_turn"},"total_usd":0.136687,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1993,\n      \"finding\": \"SF3A3 (SF3a60) is one of three subunits of mammalian splicing factor SF3a, and SF3a interacts with U2 snRNP in the presence of SF3b to generate a structure similar to 17S U2 snRNP, implicating SF3a in the incorporation of U2 snRNP into the spliceosome.\",\n      \"method\": \"Biochemical reconstitution, protein fractionation, and immunological characterization of 17S U2 snRNP\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution experiment showing SF3a+SF3b+12S U2 snRNP assembly, replicated across multiple labs in the same year\",\n      \"pmids\": [\"8211112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"Yeast PRP9 (ortholog of SF3A3) protein is required for stable U2 snRNP-substrate interaction during spliceosome assembly, as shown by impaired U2 snRNP binding in prp9 mutant extracts.\",\n      \"method\": \"In vitro splicing and spliceosome assembly in prp9 mutant yeast extracts; RNA immunoprecipitation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro splicing assay and immunoprecipitation in defined mutant background, replicated by multiple labs\",\n      \"pmids\": [\"2147224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"PRP9 (ortholog of SF3A3) contains cysteine/histidine zinc finger-like motifs; directed mutagenesis of some but not all of these residues critically impairs protein function, establishing that these motifs are functionally important.\",\n      \"method\": \"DNA sequencing and site-directed mutagenesis with functional complementation assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct mutagenesis with functional readout, single lab but multiple mutants tested\",\n      \"pmids\": [\"2118103\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Yeast PRP9 (ortholog of SF3A3) and PRP11 do not interact directly but both bind SPP91 (PRP21) simultaneously to form a trimeric PRP9-SPP91-PRP11 complex required for early spliceosome assembly.\",\n      \"method\": \"Genetic epistasis (synthetic lethal analysis), protein-protein interaction assays in yeast; identification of mammalian counterpart complex\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis combined with direct interaction tests, replicated by independent lab in same journal issue\",\n      \"pmids\": [\"8211114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"The 60-kDa protein of human 17S U2 snRNP (SF3A3/SF3a60) is immunologically and functionally related to yeast PRP9; antibodies against PRP9 strongly inhibit prespliceosome formation and mRNA splicing in HeLa nuclear extracts, and only 17S (not 12S) U2 snRNP restores splicing activity.\",\n      \"method\": \"Antibody inhibition of HeLa nuclear splicing extracts; functional reconstitution with purified 17S vs 12S U2 snRNP\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — antibody inhibition combined with reconstitution rescue, multiple orthogonal methods\",\n      \"pmids\": [\"8367487\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"PRP9 (SF3A3 ortholog) acts after formation of the U1 snRNP-pre-mRNA complex, and contains two distinct binding sites: a C-terminal region mediating PRP9 homodimerization and an N-terminal region binding SPP91; deletion of the second C-terminal motif causes dominant lethality.\",\n      \"method\": \"In vivo protein-protein interaction assay (yeast two-hybrid), deletion mutagenesis, dominant-negative phenotype analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo binding assay and deletion mutagenesis with functional readouts, single lab\",\n      \"pmids\": [\"8330742\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"PRP5, PRP9, PRP11, and PRP21 are each required for U2 snRNP binding to pre-mRNA during spliceosome assembly; PRP9 and PRP11 interact biochemically, and these factors may act on the stem-loop IIa of U2 snRNA.\",\n      \"method\": \"In vitro spliceosome assembly assays, genetic analysis, biochemical complementation experiments\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro biochemical reconstitution with genetic validation, multiple proteins and orthogonal methods\",\n      \"pmids\": [\"8405998\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Human SF3a60 (SF3A3) shares 30% sequence identity with yeast PRP9, with highest homology in the C-terminal zinc finger-like domain; the PRP9 zinc finger-like motif can be replaced by the equivalent mammalian SF3a60 region and rescues the temperature-sensitive prp9-1 phenotype, demonstrating evolutionary conservation of both structure and function.\",\n      \"method\": \"cDNA cloning, sequence analysis, chimeric protein construction, in vivo complementation of yeast ts mutant\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — chimeric protein rescue of defined yeast mutant, direct functional equivalence demonstrated\",\n      \"pmids\": [\"7816610\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Purified yeast Prp9, Prp11, and Prp21 proteins form a direct trimeric complex (Prp9·Prp11·Prp21) that is functional in in vitro splicing; together these proteins alter the accessibility of the U2 snRNA branch-point pairing region to oligonucleotide-directed RNaseH cleavage, suggesting they activate U2 snRNP for spliceosome assembly.\",\n      \"method\": \"Recombinant protein expression in E. coli, metal-affinity purification, in vitro splicing assays, oligonucleotide-directed RNaseH cleavage assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted trimeric complex with functional in vitro splicing assay and mechanistic RNaseH probing\",\n      \"pmids\": [\"8969185\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Human SF3a60 (SF3A3) and SF3a66 interact with SF3a120 (but not with each other) to form the SF3a heterotrimer; SF3a60's N-terminal portion contains the SF3a120 interaction site; C2H2-type zinc finger domains of SF3a60 mediate integration into U2 snRNP via interactions with Sm proteins; SF3a60 plays a major role in recruiting SF3a120 into the U2 particle; all domains required for SF3a assembly and 17S U2 snRNP formation are also necessary for prespliceosome assembly.\",\n      \"method\": \"Recombinant protein expression in insect cells, in vitro binding assays, 17S U2 snRNP assembly assays, prespliceosome formation assays, domain deletion/mutagenesis analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted complex with domain mapping, multiple orthogonal in vitro assays, single rigorous study with extensive mutagenesis\",\n      \"pmids\": [\"11533230\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Yeast Prp21 heat-sensitive mutations are specifically associated with defects in interaction with Prp9 (SF3A3 ortholog) but not Prp11; deletion analysis maps domains of Prp21 required for binding Prp9 and Prp11 separately; prp21 mutants show splicing defects and pre-mRNA nuclear export phenotypes similar to prp9-1 mutant.\",\n      \"method\": \"Site-directed mutagenesis, genetic epistasis, deletion analysis, protein-protein interaction assays\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and biochemical domain mapping, single lab with multiple mutants\",\n      \"pmids\": [\"8718683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"The spp91-1 suppressor of prp9-1 partially restores splicing and completely reverts aberrant pre-mRNA nuclear export in prp9-1 mutants; SPP91 encodes a novel nuclear protein essential for growth that acts in the same pathway as PRP9 (SF3A3 ortholog) in spliceosome assembly.\",\n      \"method\": \"Genetic suppressor screen, gene cloning and sequencing, in vivo depletion analysis, splicing and nuclear export assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with functional splicing and export readouts, single lab\",\n      \"pmids\": [\"1505518\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"SF3A3 (SF3a60) directly interacts with the constitutive androstane receptor (CAR) and functions as a co-repressor of CAR transcriptional activity; overexpression of SF3A3 inhibits CAR-driven reporter activity by ~50% and knockdown activates it ~3-fold, independent of the CAR ligand TCPOBOP.\",\n      \"method\": \"Yeast two-hybrid screening, co-immunoprecipitation, GST pull-down, reporter gene assay, siRNA knockdown\",\n      \"journal\": \"Biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding assays (Co-IP and GST pull-down) plus functional reporter assay, single lab\",\n      \"pmids\": [\"18713018\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SF3A3 protein levels are regulated translationally through an RNA stem-loop in its mRNA in an eIF3D-dependent manner upon MYC hyperactivation; altered SF3A3 translation leads to mis-splicing of mRNAs enriched for mitochondrial regulators, causing metabolic reprogramming and stem-like properties that fuel MYC-driven tumorigenesis in vivo.\",\n      \"method\": \"Translational regulation assays, stem-loop reporter constructs, eIF3D knockdown, splicing analysis, in vivo xenograft models\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional validation with KD and in vivo model, single lab, multiple readouts but abstract-level detail\",\n      \"pmids\": [\"33662273\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CircSCAP directly binds SF3A3 protein and promotes its ubiquitin-proteasome-mediated degradation, which enhances expression of MDM4-S and activates p53 signaling in NSCLC cells.\",\n      \"method\": \"Biotin-labeled RNA pulldown, RNA immunoprecipitation (RIP), co-immunoprecipitation, immunoblotting, luciferase reporter assay, in vitro and in vivo rescue experiments\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal binding and functional assays, single lab\",\n      \"pmids\": [\"35365208\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SF3A3 transcription is upregulated in bladder cancer by E2F6-mediated recruitment of KDM5C to the SF3A3 promoter, which demethylates H3K4me2 at the CpG island, leading to promoter hypomethylation and increased SF3A3 expression.\",\n      \"method\": \"Co-immunoprecipitation (E2F6-KDM5C interaction), chromatin immunoprecipitation (ChIP), luciferase reporter assay, methylation analysis\",\n      \"journal\": \"Cancer cell international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and co-IP with reporter validation, single lab, defines transcriptional regulatory mechanism\",\n      \"pmids\": [\"35248043\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In Trypanosoma brucei, SF3a60 (ortholog of SF3A3) localizes to the nucleus, is essential for cell viability, and interacts with SF3a120, SF3a66, and SAP130 as confirmed by tandem affinity purification and mass spectrometry.\",\n      \"method\": \"Epitope tagging and localization, RNAi depletion, yeast two-hybrid screening, tandem affinity purification, mass spectrometry\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — TAP-MS confirmation of interactions plus localization, single lab in divergent organism\",\n      \"pmids\": [\"24651488\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Knockdown of SF3A3 in APL (NB4) cells causes G1/S cell cycle arrest and proliferation inhibition, indicating SF3A3 is required for cell cycle progression in leukemia cells.\",\n      \"method\": \"siRNA knockdown, cell proliferation assays, cell cycle analysis\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single knockdown study with phenotypic readout, no pathway placement beyond cell cycle, single lab\",\n      \"pmids\": [\"37356608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SF3A3 regulates alternative splicing of c-FOS pre-mRNA, resulting in approximately 2-fold increase in full-length c-FOS expression and activation of downstream anti-apoptotic pathways; PEITC identified as a direct SF3A3 inhibitor by surface plasmon resonance and mass spectrometry.\",\n      \"method\": \"Alternative splicing analysis, knockdown/overexpression, surface plasmon resonance, mass spectrometry, in vitro and in vivo functional assays\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct biophysical binding validation (SPR + MS) combined with splicing and functional assays, single lab\",\n      \"pmids\": [\"40598817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"STIL interacts with FOXM1, and this complex binds the SF3A3 promoter to activate SF3A3 transcription in hepatocellular carcinoma; knockdown of FOXM1 reduces SF3A3 expression and SF3A3 overexpression rescues the anti-tumor effects of STIL loss.\",\n      \"method\": \"Co-immunoprecipitation (STIL-FOXM1), ChIP-qPCR, RT-qPCR, xenograft rescue experiments\",\n      \"journal\": \"Cell division\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — Co-IP and ChIP with rescue experiment, single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"39825314\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SF3A3 (SF3a60/SAP61/PRP9) is a 60-kDa subunit of the trimeric splicing factor SF3a complex (with SF3a66 and SF3a120) that assembles onto 12S U2 snRNP via sequential interactions—where SF3a60's N-terminal domain recruits SF3a120 and its C2H2 zinc finger domain anchors the complex to Sm proteins—to generate the active 17S U2 snRNP required for prespliceosome formation and branch-site recognition; it also interacts with the constitutive androstane receptor CAR as a co-repressor, is subject to translational regulation through an eIF3D-dependent stem-loop mechanism downstream of MYC, and regulates alternative splicing of target pre-mRNAs including c-FOS.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SF3A3 (SF3a60/SAP61, the ortholog of yeast PRP9) is a core subunit of the heterotrimeric splicing factor SF3a that converts inactive 12S U2 snRNP into the active 17S U2 snRNP required for prespliceosome assembly and U2 snRNP recruitment to pre-mRNA [#0, #4]. Genetic and biochemical work on the yeast ortholog established that PRP9 is required for stable U2 snRNP–substrate interaction and acts after U1 snRNP–pre-mRNA complex formation [#1, #5], assembling with PRP11 and PRP21/SPP91 into a trimeric complex that alters the accessibility of the U2 snRNA branch-point pairing region and thereby activates U2 snRNP for spliceosome assembly [#3, #8]. The protein is organized into functionally distinct domains: an N-terminal region that recruits SF3a120 into the U2 particle and C2H2 zinc-finger motifs that anchor the complex through Sm protein interactions, with all of these domains required for SF3a assembly, 17S U2 snRNP formation, and prespliceosome assembly [#2, #9]; this domain architecture and function are evolutionarily conserved, as the mammalian zinc-finger region rescues the yeast prp9 temperature-sensitive phenotype [#7]. Beyond its constitutive splicing role, SF3A3 directs alternative splicing of target pre-mRNAs—including c-FOS, where it promotes full-length isoform expression and downstream anti-apoptotic signaling [#18], and mitochondrial regulator transcripts, where MYC-driven, eIF3D-dependent translational upregulation of SF3A3 reprograms metabolism to fuel tumorigenesis [#13]. SF3A3 additionally acts as a co-repressor of the constitutive androstane receptor (CAR) [#12], and its abundance is controlled in cancer contexts by circSCAP-mediated ubiquitin-proteasome degradation and by transcriptional regulation at its promoter [#14, #15].\",\n  \"teleology\": [\n    {\n      \"year\": 1990,\n      \"claim\": \"Established that the SF3A3 ortholog PRP9 is functionally required for U2 snRNP engagement with pre-mRNA, placing it in the spliceosome assembly pathway rather than as a passive structural component.\",\n      \"evidence\": \"In vitro splicing and spliceosome assembly with RNA immunoprecipitation in prp9 mutant yeast extracts\",\n      \"pmids\": [\"2147224\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which domains mediate U2 binding\", \"Mechanism of branch-site activation not resolved\"]\n    },\n    {\n      \"year\": 1990,\n      \"claim\": \"Identified zinc finger-like motifs as functionally essential, beginning the structural dissection of how PRP9/SF3A3 contributes to splicing.\",\n      \"evidence\": \"DNA sequencing and site-directed mutagenesis with functional complementation in yeast\",\n      \"pmids\": [\"2118103\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish the binding partners contacted by the zinc fingers\", \"No structural model of the motif\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Linked PRP9 to a genetically interacting partner (SPP91/PRP21) acting in the same assembly pathway and connected splicing defects to aberrant pre-mRNA nuclear export.\",\n      \"evidence\": \"Genetic suppressor screen, gene cloning, in vivo depletion, splicing and nuclear export assays in yeast\",\n      \"pmids\": [\"1505518\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct physical contact not yet shown\", \"Export phenotype mechanism unresolved\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Defined SF3A3 as one of three SF3a subunits that, with SF3b, reconstitutes 17S U2 snRNP, and showed only 17S (not 12S) U2 snRNP restores splicing—establishing SF3a's role in U2 snRNP activation.\",\n      \"evidence\": \"Biochemical reconstitution, antibody inhibition of HeLa nuclear extracts, and 17S vs 12S U2 snRNP rescue\",\n      \"pmids\": [\"8211112\", \"8367487\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and subunit contacts within SF3a not yet mapped in human\", \"Branch-site recognition mechanism not directly demonstrated\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Resolved the architecture of the assembly complex, showing PRP9 and PRP11 do not bind each other but both bind PRP21/SPP91 to form a trimer, with separable N- and C-terminal interaction surfaces.\",\n      \"evidence\": \"Genetic epistasis, yeast two-hybrid, deletion mutagenesis, and interaction assays\",\n      \"pmids\": [\"8211114\", \"8330742\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of homodimerization unclear\", \"Human counterpart contacts inferred not proven at this stage\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Provided the mechanistic link between SF3a assembly and catalysis by showing the reconstituted trimer alters U2 snRNA branch-point pairing region accessibility, defining how the complex activates U2 snRNP.\",\n      \"evidence\": \"Recombinant protein reconstitution, in vitro splicing, and oligonucleotide-directed RNaseH probing of U2 snRNA\",\n      \"pmids\": [\"8969185\", \"8718683\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic basis of the conformational change not determined\", \"How accessibility change promotes branch-site selection unresolved\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Demonstrated cross-species functional equivalence by showing the mammalian SF3a60 zinc-finger region rescues the yeast prp9 ts mutant, confirming conserved structure and function.\",\n      \"evidence\": \"cDNA cloning, sequence analysis, chimeric protein construction, and in vivo yeast complementation\",\n      \"pmids\": [\"7816610\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conservation of N-terminal recruitment function not tested here\", \"Human-specific regulatory roles not addressed\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Mapped the human SF3a60 domain logic—N-terminal recruitment of SF3a120 and zinc-finger-mediated integration into U2 snRNP via Sm proteins—unifying assembly and prespliceosome formation requirements.\",\n      \"evidence\": \"Recombinant insect-cell expression, in vitro binding, 17S U2 snRNP assembly, prespliceosome assays, and domain mutagenesis\",\n      \"pmids\": [\"11533230\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural detail of the Sm protein contact not resolved\", \"Dynamics of stepwise assembly in cells not addressed\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Extended SF3A3 function beyond splicing by identifying it as a direct co-repressor of the nuclear receptor CAR.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, GST pull-down, reporter assays, and siRNA knockdown\",\n      \"pmids\": [\"18713018\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether repression involves SF3A3's splicing activity is unknown\", \"Physiological relevance in CAR target gene regulation not established\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Confirmed conservation of SF3a complex composition and nuclear localization in a divergent eukaryote, supporting a universal SF3a architecture centered on SF3a60.\",\n      \"evidence\": \"Epitope tagging/localization, RNAi, yeast two-hybrid, and TAP-MS in Trypanosoma brucei\",\n      \"pmids\": [\"24651488\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Branch-site mechanism in trypanosomes not probed\", \"Functional contribution of SAP130 interaction unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealed an oncogenic translational control axis in which MYC drives eIF3D-dependent SF3A3 translation, with consequent mis-splicing of mitochondrial regulators reprogramming metabolism.\",\n      \"evidence\": \"Stem-loop reporter constructs, eIF3D knockdown, splicing analysis, and in vivo xenograft models\",\n      \"pmids\": [\"33662273\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific spliced targets driving phenotype not exhaustively defined\", \"Direct SF3A3 binding to these pre-mRNAs not shown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified post-translational and transcriptional control of SF3A3 abundance in cancer—circSCAP-driven proteasomal degradation and E2F6/KDM5C-mediated promoter hypomethylation—linking SF3A3 dosage to tumor signaling.\",\n      \"evidence\": \"RNA pulldown, RIP, Co-IP, ChIP, methylation analysis, and reporter/rescue assays in NSCLC and bladder cancer\",\n      \"pmids\": [\"35365208\", \"35248043\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether degradation alters splicing output directly is untested\", \"Generality of these regulatory mechanisms across tissues unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined a specific alternative-splicing target (c-FOS) through which SF3A3 promotes anti-apoptotic signaling and identified PEITC as a direct small-molecule inhibitor.\",\n      \"evidence\": \"Alternative splicing analysis, knockdown/overexpression, SPR and MS binding validation, and in vivo functional assays\",\n      \"pmids\": [\"40598817\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding site of PEITC on SF3A3 not mapped\", \"Breadth of SF3A3-regulated alternative splicing program not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How SF3A3's constitutive role in U2 snRNP activation is rewired to select specific alternative-splicing targets in oncogenic contexts, and whether its non-splicing roles depend on the same domains, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of human SF3a60 bound to U2 snRNP\", \"Target selectivity determinants for alternative splicing unknown\", \"Mechanistic relationship between splicing and co-repressor functions undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [8, 9]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [11, 16]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 4, 9]}\n    ],\n    \"complexes\": [\n      \"SF3a heterotrimer\",\n      \"17S U2 snRNP\",\n      \"Prp9-Prp11-Prp21 complex\"\n    ],\n    \"partners\": [\n      \"SF3A1\",\n      \"SF3A2\",\n      \"PRP11\",\n      \"PRP21\",\n      \"CAR\",\n      \"circSCAP\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}