Affinage

SF3A3

Splicing factor 3A subunit 3 · UniProt Q12874

Length
501 aa
Mass
58.8 kDa
Annotated
2026-06-10
23 papers in source corpus 20 papers cited in narrative 20 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 1990 High

    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

    PMID:2147224

    Open questions at the time
    • Did not define which domains mediate U2 binding
    • Mechanism of branch-site activation not resolved
  2. 1990 High

    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

    PMID:2118103

    Open questions at the time
    • Did not establish the binding partners contacted by the zinc fingers
    • No structural model of the motif
  3. 1992 Medium

    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

    PMID:1505518

    Open questions at the time
    • Direct physical contact not yet shown
    • Export phenotype mechanism unresolved
  4. 1993 High

    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

    PMID:8211112 PMID:8367487

    Open questions at the time
    • Stoichiometry and subunit contacts within SF3a not yet mapped in human
    • Branch-site recognition mechanism not directly demonstrated
  5. 1993 High

    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

    PMID:8211114 PMID:8330742

    Open questions at the time
    • Functional consequence of homodimerization unclear
    • Human counterpart contacts inferred not proven at this stage
  6. 1996 High

    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

    PMID:8718683 PMID:8969185

    Open questions at the time
    • Atomic basis of the conformational change not determined
    • How accessibility change promotes branch-site selection unresolved
  7. 1994 High

    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

    PMID:7816610

    Open questions at the time
    • Conservation of N-terminal recruitment function not tested here
    • Human-specific regulatory roles not addressed
  8. 2001 High

    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

    PMID:11533230

    Open questions at the time
    • Structural detail of the Sm protein contact not resolved
    • Dynamics of stepwise assembly in cells not addressed
  9. 2008 Medium

    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

    PMID:18713018

    Open questions at the time
    • Whether repression involves SF3A3's splicing activity is unknown
    • Physiological relevance in CAR target gene regulation not established
  10. 2014 Medium

    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

    PMID:24651488

    Open questions at the time
    • Branch-site mechanism in trypanosomes not probed
    • Functional contribution of SAP130 interaction unclear
  11. 2021 Medium

    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

    PMID:33662273

    Open questions at the time
    • Specific spliced targets driving phenotype not exhaustively defined
    • Direct SF3A3 binding to these pre-mRNAs not shown
  12. 2022 Medium

    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

    PMID:35248043 PMID:35365208

    Open questions at the time
    • Whether degradation alters splicing output directly is untested
    • Generality of these regulatory mechanisms across tissues unknown
  13. 2025 Medium

    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

    PMID:40598817

    Open questions at the time
    • Binding site of PEITC on SF3A3 not mapped
    • Breadth of SF3A3-regulated alternative splicing program not defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • 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.
  • 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

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 2 GO:0140110 transcription regulator activity 1
Localization
GO:0005634 nucleus 2
Pathway
R-HSA-8953854 Metabolism of RNA 3
Partners
CARCIRCSCAPPRP11PRP21SF3A1SF3A2
Complex memberships
17S U2 snRNPPrp9-Prp11-Prp21 complexSF3a heterotrimer

Evidence

Reading pass · 20 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1993 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. Biochemical reconstitution, protein fractionation, and immunological characterization of 17S U2 snRNP Science High 8211112
1990 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. In vitro splicing and spliceosome assembly in prp9 mutant yeast extracts; RNA immunoprecipitation Molecular and cellular biology High 2147224
1990 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. DNA sequencing and site-directed mutagenesis with functional complementation assay The EMBO journal High 2118103
1993 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. Genetic epistasis (synthetic lethal analysis), protein-protein interaction assays in yeast; identification of mammalian counterpart complex Science High 8211114
1993 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. Antibody inhibition of HeLa nuclear splicing extracts; functional reconstitution with purified 17S vs 12S U2 snRNP Proceedings of the National Academy of Sciences of the United States of America High 8367487
1993 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. In vivo protein-protein interaction assay (yeast two-hybrid), deletion mutagenesis, dominant-negative phenotype analysis Genes & development Medium 8330742
1993 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. In vitro spliceosome assembly assays, genetic analysis, biochemical complementation experiments Genes & development High 8405998
1994 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. cDNA cloning, sequence analysis, chimeric protein construction, in vivo complementation of yeast ts mutant Nucleic acids research High 7816610
1996 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. Recombinant protein expression in E. coli, metal-affinity purification, in vitro splicing assays, oligonucleotide-directed RNaseH cleavage assay The Journal of biological chemistry High 8969185
2001 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. Recombinant protein expression in insect cells, in vitro binding assays, 17S U2 snRNP assembly assays, prespliceosome formation assays, domain deletion/mutagenesis analysis Molecular and cellular biology High 11533230
1996 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. Site-directed mutagenesis, genetic epistasis, deletion analysis, protein-protein interaction assays RNA Medium 8718683
1992 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. Genetic suppressor screen, gene cloning and sequencing, in vivo depletion analysis, splicing and nuclear export assays The EMBO journal Medium 1505518
2008 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. Yeast two-hybrid screening, co-immunoprecipitation, GST pull-down, reporter gene assay, siRNA knockdown Biological chemistry Medium 18713018
2021 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. Translational regulation assays, stem-loop reporter constructs, eIF3D knockdown, splicing analysis, in vivo xenograft models Molecular cell Medium 33662273
2022 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. Biotin-labeled RNA pulldown, RNA immunoprecipitation (RIP), co-immunoprecipitation, immunoblotting, luciferase reporter assay, in vitro and in vivo rescue experiments Journal of experimental & clinical cancer research Medium 35365208
2022 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. Co-immunoprecipitation (E2F6-KDM5C interaction), chromatin immunoprecipitation (ChIP), luciferase reporter assay, methylation analysis Cancer cell international Medium 35248043
2014 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. Epitope tagging and localization, RNAi depletion, yeast two-hybrid screening, tandem affinity purification, mass spectrometry PloS one Medium 24651488
2023 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. siRNA knockdown, cell proliferation assays, cell cycle analysis Archives of biochemistry and biophysics Low 37356608
2025 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. Alternative splicing analysis, knockdown/overexpression, surface plasmon resonance, mass spectrometry, in vitro and in vivo functional assays Advanced science Medium 40598817
2025 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. Co-immunoprecipitation (STIL-FOXM1), ChIP-qPCR, RT-qPCR, xenograft rescue experiments Cell division Low 39825314

Source papers

Stage 0 corpus · 23 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1993 Interaction of mammalian splicing factor SF3a with U2 snRNP and relation of its 60-kD subunit to yeast PRP9. Science (New York, N.Y.) 139 8211112
1993 Four yeast spliceosomal proteins (PRP5, PRP9, PRP11, and PRP21) interact to promote U2 snRNP binding to pre-mRNA. Genes & development 125 8405998
1990 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. Molecular and cellular biology 103 2147224
1990 The molecular characterization of PRP6 and PRP9 yeast genes reveals a new cysteine/histidine motif common to several splicing factors. The EMBO journal 77 2118103
1993 Interaction between PRP11 and SPP91 yeast splicing factors and characterization of a PRP9-PRP11-SPP91 complex. Science (New York, N.Y.) 67 8211114
1993 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. Proceedings of the National Academy of Sciences of the United States of America 54 8367487
2021 Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer. Molecular cell 52 33662273
2001 Domains in human splicing factors SF3a60 and SF3a66 required for binding to SF3a120, assembly of the 17S U2 snRNP, and prespliceosome formation. Molecular and cellular biology 49 11533230
1993 Interactions between PRP9 and SPP91 splicing factors identify a protein complex required in prespliceosome assembly. Genes & development 47 8330742
1992 A novel gene, spp91-1, suppresses the splicing defect and the pre-mRNA nuclear export in the prp9-1 mutant. The EMBO journal 42 1505518
1994 Splicing factor SF3a60 is the mammalian homologue of PRP9 of S.cerevisiae: the conserved zinc finger-like motif is functionally exchangeable in vivo. Nucleic acids research 37 7816610
1996 In vitro studies of the Prp9.Prp11.Prp21 complex indicate a pathway for U2 small nuclear ribonucleoprotein activation. The Journal of biological chemistry 36 8969185
2022 CircSCAP interacts with SF3A3 to inhibit the malignance of non-small cell lung cancer by activating p53 signaling. Journal of experimental & clinical cancer research : CR 32 35365208
2022 E2F6/KDM5C promotes SF3A3 expression and bladder cancer progression through a specific hypomethylated DNA promoter. Cancer cell international 14 35248043
1996 Essential domains of the PRP21 splicing factor are implicated in the binding to PRP9 and PRP11 proteins and are conserved through evolution. RNA (New York, N.Y.) 13 8718683
1991 Cloning of the two essential yeast genes, PRP6 and PRP9, and their rapid mapping, disruption and partial sequencing using a linker insertion strategy. Molecular & general genetics : MGG 13 1848649
2022 Integrated In Silico Analyses Identify PUF60 and SF3A3 as New Spliceosome-Related Breast Cancer RNA-Binding Proteins. Biology 8 35453681
2008 Specific inhibition of transcriptional activity of the constitutive androstane receptor (CAR) by the splicing factor SF3a3. Biological chemistry 5 18713018
2025 SF3A3 Drives Tumorigenesis in Endometrial Cancer by Enhancing c-FOS Expression and Represents a Potential Therapeutic Target. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 4 40598817
2014 Proteins associated with SF3a60 in T. brucei. PloS one 3 24651488
2023 Inhibition of splicing factors SF3A3 and SRSF5 contributes to As3+/Se4+ combination-mediated proliferation suppression and apoptosis induction in acute promyelocytic leukemia cells. Archives of biochemistry and biophysics 2 37356608
1997 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. Yeast (Chichester, England) 2 9046088
2025 Interaction of STIL with FOXM1 regulates SF3A3 transcription in the hepatocellular carcinoma development. Cell division 1 39825314

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