{"gene":"CDC40","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":1998,"finding":"Human PRP17 (hPRP17/CDC40) is required for the second catalytic step of pre-mRNA splicing; immunodepletion of hPRP16 from splicing extracts specifically blocks step II, and both hPrp16 and hPrp17 associate with the spliceosome late in the splicing pathway. Mutations at the 3' splice site that block step II do not prevent hPrp16/hPrp17 spliceosome association, placing their function prior to 3' splice site recognition.","method":"Immunodepletion from splicing extracts, recombinant protein add-back, spliceosome association assays","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — immunodepletion with full activity rescue by recombinant protein; multiple orthogonal methods in one study","pmids":["9524131"],"is_preprint":false},{"year":1998,"finding":"A yeast-human chimera carrying the C-terminal two-thirds of hPRP17 (containing WD repeats) complements both the cell-cycle and splicing defects of a yeast prp17 mutant; yeast and chimeric Prp17 proteins co-precipitate the intron-exon 2 lariat intermediate and the intron lariat product, demonstrating spliceosome association and functional conservation.","method":"Complementation of yeast prp17 mutant, co-immunoprecipitation of splicing intermediates","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — complementation assay plus co-IP of splicing intermediates; replicated across two labs (also confirmed in PMID:9524131)","pmids":["9769104"],"is_preprint":false},{"year":2000,"finding":"PRP8 alleles suppress both the temperature-sensitive growth phenotype and the splicing defect caused by absence of Prp17/Cdc40, and other PRP8 alleles show synthetic lethality with prp17 deletion; PRP8 mutations also suppress specific 3' splice site mutations in an ACT1-CUP1 reporter, placing Prp17 and Prp8 as interacting partners during the second catalytic step of splicing, with PRP17/CDC40 acting in 3' splice site recognition.","method":"Genetic suppression/synthetic lethality analysis, ACT1-CUP1 splicing reporter assay","journal":"Genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — extensive epistasis mapping with multiple allele combinations and a quantitative splicing reporter; independently confirmed by PMID:11565750","pmids":["10628969"],"is_preprint":false},{"year":1996,"finding":"Missense mutations in three temperature-sensitive prp17 alleles map to the N-terminal non-conserved region; the N-terminal region (not the WD-repeat C-terminus) is the functional domain required for interactions with Prp16, Prp18, and U5 snRNA; a mutually allele-specific interaction between Prp17 and snr7 (U5 snRNA) was identified.","method":"In vitro mutagenesis of WD repeats, deletion analysis, genetic synthetic lethality, allele-specific interaction mapping","journal":"Genetics","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — systematic mutagenesis of 11 missense alleles plus deletion analysis and allele-specific genetic interactions; single lab but multiple orthogonal methods","pmids":["8722761"],"is_preprint":false},{"year":2001,"finding":"The SRPK family kinase Sky1p genetically interacts with PRP17/SLU4 in 3' splice site recognition; deletion of SKY1 is synthetically lethal with all prp17 mutants tested and suppresses 3' AG mutations in ACT1-CUP1 splicing reporters, indicating that phosphorylation by Sky1p regulates 3' splice site fidelity in a pathway involving Prp17.","method":"Synthetic lethality screen, ACT1-CUP1 splicing reporter assay","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with quantitative splicing reporter; single lab, two orthogonal genetic methods","pmids":["11565750"],"is_preprint":false},{"year":2004,"finding":"CDC40/PRP17 controls cell cycle progression specifically through splicing of the ANC1 gene; deletion of the ANC1 intron relieves the cell cycle arrest and temperature sensitivity of cdc40 mutants, and point mutations in specific residues of the ANC1 intron define sequences required for CDC40-dependent splicing.","method":"Intron deletion suppression of cdc40 phenotype, point mutation analysis of intron sequences","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — intron deletion rescues cdc40 cell cycle arrest; combined with point mutation identification of critical intron residues; multiple orthogonal genetic methods","pmids":["15133121"],"is_preprint":false},{"year":2004,"finding":"Genome-wide microarray analysis shows Prp17 is preferentially required for splicing of introns longer than 200 nt, and is dispensable when the distance between the branch point nucleotide and the 3' splice site is ≤13 nt; in vitro splicing with substrates of varying branch-point to 3' splice site distances confirmed differential Prp17 dependency.","method":"Splicing-sensitive DNA microarray, in vitro splicing assay with defined pre-mRNA substrates","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — genome-wide splicing array combined with in vitro splicing reconstitution; single lab but two orthogonal methods","pmids":["15452114"],"is_preprint":false},{"year":2003,"finding":"Prp17 (Cdc40) is required for efficient splicing of TUB1 and TUB3 (alpha-tubulin) pre-mRNAs; reduced alpha-tubulin protein levels underlie the benomyl sensitivity and G2/M arrest of prp17 mutants; genomic replacement with an intronless TUB1 gene relieves the benomyl sensitivity but not the temperature sensitivity, indicating multiple limiting targets for mitosis.","method":"In vitro splicing with TUB3 pre-mRNA in prp17 extracts, intronless gene replacement suppression, RT-PCR/transcript analysis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — in vitro splicing assay combined with intronless gene suppression and transcript analysis; multiple orthogonal methods in one study","pmids":["12711678"],"is_preprint":false},{"year":2008,"finding":"Prp17 interacts with U2, U5, and U6 snRNPs but is not a core component of any single snRNP; it joins the spliceosome at the pre-catalytic A1 complex (after U4 dissociation), prior to both catalytic steps, and remains associated in post-splicing complexes containing lariat intron; in prp17Δ extracts, stalled spliceosomes are compromised for the Prp16 helicase-triggered conformational switch required for the second step.","method":"Co-immunoprecipitation of snRNAs using epitope-tagged Prp17, in vitro spliceosome assembly and co-precipitation on actin pre-mRNA, in vitro splicing kinetics","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP of snRNAs, in vitro spliceosome assembly at defined steps, kinetic splicing assays; multiple orthogonal methods in single lab","pmids":["18691155"],"is_preprint":false},{"year":2010,"finding":"C. elegans PRP-17 (ortholog of PRP17/CDC40) functions downstream of GLP-1 Notch signaling to promote meiotic entry largely via the GLD-1 pathway, and functions in female germline sex determination; PRP-17 can rescue temperature-sensitive lethality of yeast PRP17, confirming functional conservation and demonstrating that splicing per se (not a novel function) underlies these developmental roles.","method":"Genetic epistasis (RNAi in sensitized backgrounds), yeast complementation rescue","journal":"Developmental dynamics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis in C. elegans combined with yeast complementation; single lab, two orthogonal methods","pmids":["20419786"],"is_preprint":false},{"year":2020,"finding":"Biallelic loss-of-function mutations in PRP17 cause pontocerebellar hypoplasia with microcephaly (PCHM) in humans; loss of PRP17 disrupts splicing integrity, predominantly affecting short and high GC-content introns and genes involved in brain disorders; PPIL1 and PRP17 form an active isomerase-substrate interaction, but isomerase activity per se is not critical for function.","method":"Patient mutation identification, mouse knockouts (embryonic lethal), knockin mouse neuronal apoptosis, RNA splicing analysis","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 2 / Strong — mouse knockout lethality, patient knockin showing neuron-specific apoptosis, genome-wide splicing analysis, and biochemical isomerase assay; multiple orthogonal methods replicated across families","pmids":["33220177"],"is_preprint":false},{"year":2025,"finding":"CDC40 knockdown in lung cancer cells induces intron retention in CDCA5 pre-mRNA (specifically retention of the first intron), leading to decreased CDCA5 protein expression; co-immunoprecipitation reveals spliceosome components as the main binding partners of CDC40; CDC40 knockdown causes cell cycle defects, growth inhibition, and apoptosis.","method":"siRNA knockdown, RNA-seq/splicing analysis, Western blot for CDCA5 protein, co-immunoprecipitation/mass spectrometry","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with defined splicing phenotype and protein consequence, plus co-IP/MS for binding partners; single lab, multiple orthogonal methods","pmids":["39747150"],"is_preprint":false},{"year":2006,"finding":"CDC40/PRP17 has a role in the G1/S transition: cdc40 mutants show delayed G1/S and hypersensitivity to HU/MMS; deletion of G1 cyclin CLN2 enhances temperature sensitivity and G1/S delay in cdc40 cells; overexpression of cDNAs encoding chaperones, translation initiation factors, and glycolytic enzymes (none intron-containing) can suppress HU/MMS sensitivity and G1/S delay, suggesting crosstalk between splicing, translation, and glycolysis at cell cycle entry.","method":"cDNA overexpression suppressor screen, arrest/release cell cycle analysis, double mutant construction","journal":"Current genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic suppressor screen combined with cell cycle synchronization; single lab, two orthogonal approaches","pmids":["17171376"],"is_preprint":false},{"year":1986,"finding":"Epistasis analysis shows that rad6-1 is epistatic to cdc40-1 for sensitivity to UV and MMS, and rad50-1 is epistatic to cdc40-1 for MMS sensitivity in G1 stationary cells, placing CDC40 in the RAD6 DNA-repair pathway; cdc40-1 mutants are defective in UV-induced mutagenesis at the restrictive temperature.","method":"Double mutant epistasis analysis, survival assays after DNA damage","journal":"Mutation research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with multiple allele combinations and damage types; single lab, classic yeast genetics","pmids":["3523226"],"is_preprint":false}],"current_model":"CDC40/PRP17 is a WD-repeat spliceosome component that associates with U2, U5, and U6 snRNPs from the pre-catalytic A1 complex onward, facilitates the Prp16-dependent conformational switch required for the second catalytic step of pre-mRNA splicing (particularly for introns >200 nt or with long branch-point to 3' splice site spacing), genetically and physically interacts with Prp8 and other second-step factors (Prp16, Prp18, Slu7) at the 3' splice site, controls cell cycle progression through selective splicing of specific intron-containing transcripts (ANC1, TUB1/TUB3, CDCA5), forms an isomerase-substrate interaction with PPIL1 (though isomerase activity is non-essential), and is required for neuronal survival in humans, where biallelic loss causes pontocerebellar hypoplasia with microcephaly."},"narrative":{"mechanistic_narrative":"CDC40/PRP17 is a WD-repeat spliceosomal protein that promotes the second catalytic step of pre-mRNA splicing and, through selective splicing of intron-containing transcripts, governs cell cycle progression [PMID:9524131, PMID:15133121]. It joins the spliceosome late, at the pre-catalytic A1 complex after U4 dissociation, associates with U2, U5, and U6 snRNPs without being a core subunit of any single snRNP, and remains bound through post-splicing lariat-containing complexes [PMID:18691155]; in its absence stalled spliceosomes fail to undergo the Prp16 helicase-triggered conformational switch required for the second step [PMID:18691155]. CDC40 acts at the 3' splice site, where it genetically and physically cooperates with Prp8 and the second-step machinery, and where its N-terminal non-conserved region mediates interactions with Prp16, Prp18, and U5 snRNA [PMID:10628969, PMID:8722761]. Its requirement is substrate-selective: it is preferentially needed for introns longer than 200 nt and is dispensable when the branch point lies within ~13 nt of the 3' splice site [PMID:15452114]. Through this selectivity CDC40 controls mitosis and cell cycle entry by ensuring splicing of specific transcripts including ANC1, the alpha-tubulins TUB1/TUB3, and CDCA5, loss of which causes G2/M and G1/S defects, growth arrest, and apoptosis [PMID:15133121, PMID:12711678, PMID:39747150]. In humans, biallelic loss-of-function mutations in PRP17 cause pontocerebellar hypoplasia with microcephaly, with neuron-specific apoptosis driven by disrupted splicing of short, high-GC introns, and the protein forms an isomerase-substrate interaction with PPIL1 whose catalytic activity is non-essential [PMID:33220177].","teleology":[{"year":1986,"claim":"Before its splicing role was known, CDC40 was placed genetically in a DNA-damage response, establishing an early functional handle on the gene's phenotype.","evidence":"Double-mutant epistasis and DNA-damage survival assays in yeast G1 stationary cells","pmids":["3523226"],"confidence":"Medium","gaps":["Cannot distinguish a direct repair role from an indirect consequence of defective splicing of repair-pathway transcripts","No molecular mechanism linking CDC40 to RAD6/RAD50 defined"]},{"year":1996,"claim":"Mapping ts alleles localized the functional core to the N-terminal non-conserved region rather than the WD repeats, redefining which part of the protein mediates second-step interactions.","evidence":"Mutagenesis of 11 missense alleles, deletion analysis, and allele-specific genetic interactions in yeast","pmids":["8722761"],"confidence":"High","gaps":["Structural basis of the N-terminal Prp16/Prp18/U5 interactions not resolved","Role of the WD repeats left undefined"]},{"year":1998,"claim":"Two studies established that the human ortholog acts specifically at step II of splicing and associates with the spliceosome late, demonstrating cross-species functional conservation.","evidence":"Immunodepletion/add-back of splicing extracts, spliceosome association assays, and yeast-human chimera complementation with co-IP of splicing intermediates","pmids":["9524131","9769104"],"confidence":"High","gaps":["Precise biochemical contribution to step II catalysis not mechanistically defined","Timing relative to other late factors not yet resolved"]},{"year":2000,"claim":"Genetic suppression and synthetic lethality with PRP8 alleles, plus suppression of 3' splice site mutations, positioned CDC40 as a Prp8-interacting 3' splice site recognition factor.","evidence":"Epistasis/synthetic-lethality analysis and ACT1-CUP1 splicing reporter in yeast","pmids":["10628969"],"confidence":"High","gaps":["Direct physical contact with Prp8 vs. allele-bridged genetic interaction not distinguished","Molecular nature of 3' splice site recognition by CDC40 unresolved"]},{"year":2001,"claim":"Linking the SRPK kinase Sky1p to CDC40 in 3' splice site fidelity introduced phosphoregulation into the second-step recognition pathway.","evidence":"Synthetic lethality screen and ACT1-CUP1 reporter assay in yeast","pmids":["11565750"],"confidence":"Medium","gaps":["Direct phosphorylation target of Sky1p in this pathway not identified","Whether CDC40 itself is phosphorylated not established"]},{"year":2003,"claim":"Identifying TUB1/TUB3 as splicing targets connected CDC40's splicing defect to a concrete mitotic phenotype via reduced alpha-tubulin.","evidence":"In vitro splicing of TUB3 pre-mRNA, intronless gene replacement suppression, and transcript analysis in yeast","pmids":["12711678"],"confidence":"High","gaps":["Multiple limiting targets implied since intronless TUB1 does not rescue temperature sensitivity","Other mitotic targets not enumerated"]},{"year":2004,"claim":"Two studies defined CDC40's substrate selectivity—an intron-length/branch-point dependence and a specific cell-cycle target (ANC1)—explaining why only certain transcripts require it.","evidence":"Splicing-sensitive microarrays with in vitro splicing of defined substrates, plus intron-deletion suppression and intron point-mutation analysis in yeast","pmids":["15452114","15133121"],"confidence":"High","gaps":["Mechanism by which intron length/branch-point distance sets CDC40 dependency not defined","Full set of length-dependent endogenous targets not catalogued"]},{"year":2006,"claim":"A G1/S role and cyclin/metabolic crosstalk broadened CDC40's cell-cycle function beyond mitosis.","evidence":"cDNA overexpression suppressor screen, cell cycle arrest/release, and double-mutant construction in yeast","pmids":["17171376"],"confidence":"Medium","gaps":["Suppressing cDNAs are intronless, so the mechanistic link between splicing and G1/S remains indirect","Whether glycolytic/translation suppression reflects a genuine pathway or bypass unclear"]},{"year":2008,"claim":"Defining the snRNP associations and assembly stage established that CDC40 enters at the A1 complex and is needed for the Prp16-triggered second-step conformational switch.","evidence":"Reciprocal co-IP of snRNAs with tagged Prp17, staged in vitro spliceosome assembly, and splicing kinetics in yeast","pmids":["18691155"],"confidence":"High","gaps":["Structural details of how CDC40 enables the Prp16 switch not resolved","Order of recruitment relative to other second-step factors not fully mapped"]},{"year":2010,"claim":"C. elegans work showed the developmental roles of the ortholog (meiotic entry, sex determination) derive from its conserved splicing function rather than a novel activity.","evidence":"Genetic epistasis by RNAi in sensitized backgrounds and yeast complementation rescue","pmids":["20419786"],"confidence":"Medium","gaps":["Specific spliced targets underlying germline phenotypes not identified","Direct vs. indirect action within GLD-1 pathway not dissected"]},{"year":2020,"claim":"Human genetics tied PRP17 to a Mendelian neurodevelopmental disease and revealed a PPIL1 isomerase-substrate interaction whose catalytic activity is dispensable.","evidence":"Patient mutation identification, embryonic-lethal mouse knockouts, knockin mice with neuronal apoptosis, genome-wide splicing analysis, and isomerase assay","pmids":["33220177"],"confidence":"High","gaps":["Why neurons are selectively vulnerable not mechanistically resolved","Functional role of the non-catalytic PPIL1 interaction unclear"]},{"year":2025,"claim":"In human cancer cells CDC40 was shown to control CDCA5 expression via intron retention, extending its substrate-selective cell-cycle control to mammalian transcripts.","evidence":"siRNA knockdown with RNA-seq splicing analysis, CDCA5 Western blot, and co-IP/mass spectrometry in lung cancer cells","pmids":["39747150"],"confidence":"Medium","gaps":["Whether CDCA5 retention fully accounts for the proliferation/apoptosis phenotype not established","Direct vs. indirect effect on the CDCA5 first intron not distinguished"]},{"year":null,"claim":"How CDC40's substrate selectivity (intron length, GC content, branch-point distance) is mechanistically encoded at the spliceosome, and how this selectivity drives tissue-specific outcomes such as neuronal survival, remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of CDC40 within the catalytic spliceosome","Mechanism translating splicing selectivity into cell-type-specific phenotypes unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,8]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[8,3]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[5,7,11]}],"complexes":["spliceosome"],"partners":["PRP8","PRP16","PRP18","SLU7","PPIL1","SKY1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O60508","full_name":"Pre-mRNA-processing factor 17","aliases":["Cell division cycle 40 homolog","EH-binding protein 3","Ehb3","PRP17 homolog","hPRP17"],"length_aa":579,"mass_kda":65.5,"function":"Required for pre-mRNA splicing as component of the activated spliceosome (PubMed:33220177). Plays an important role in embryonic brain development; this function does not require proline isomerization (PubMed:33220177)","subcellular_location":"Nucleus; Nucleus speckle","url":"https://www.uniprot.org/uniprotkb/O60508/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CDC40","classification":"Common Essential","n_dependent_lines":1067,"n_total_lines":1208,"dependency_fraction":0.8832781456953642},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2},{"gene":"CPSF6","stoichiometry":0.2},{"gene":"DDX39B","stoichiometry":0.2},{"gene":"RBM39","stoichiometry":0.2},{"gene":"RTCB","stoichiometry":0.2},{"gene":"SF3A1","stoichiometry":0.2},{"gene":"SF3A2","stoichiometry":0.2},{"gene":"SF3B1","stoichiometry":0.2},{"gene":"SNRPA","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CDC40","total_profiled":1310},"omim":[{"mim_id":"619302","title":"PONTOCEREBELLAR HYPOPLASIA, TYPE 15; PCH15","url":"https://www.omim.org/entry/619302"},{"mim_id":"618059","title":"WD REPEAT-CONTAINING PROTEIN 25; WDR25","url":"https://www.omim.org/entry/618059"},{"mim_id":"607596","title":"PONTOCEREBELLAR HYPOPLASIA, TYPE 1A; PCH1A","url":"https://www.omim.org/entry/607596"},{"mim_id":"605585","title":"CELL DIVISION CYCLE 40; CDC40","url":"https://www.omim.org/entry/605585"},{"mim_id":"601301","title":"PEPTIDYL-PROLYL ISOMERASE-LIKE 1; PPIL1","url":"https://www.omim.org/entry/601301"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CDC40"},"hgnc":{"alias_symbol":["PRP17","EHB3","PRPF17","FLJ10564"],"prev_symbol":[]},"alphafold":{"accession":"O60508","domains":[{"cath_id":"-","chopping":"121-161","consensus_level":"high","plddt":89.3034,"start":121,"end":161},{"cath_id":"2.130.10.10","chopping":"239-577","consensus_level":"medium","plddt":93.9001,"start":239,"end":577}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O60508","model_url":"https://alphafold.ebi.ac.uk/files/AF-O60508-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O60508-F1-predicted_aligned_error_v6.png","plddt_mean":85.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CDC40","jax_strain_url":"https://www.jax.org/strain/search?query=CDC40"},"sequence":{"accession":"O60508","fasta_url":"https://rest.uniprot.org/uniprotkb/O60508.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O60508/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O60508"}},"corpus_meta":[{"pmid":"9524131","id":"PMC_9524131","title":"Human homologs of yeast prp16 and prp17 reveal conservation of the mechanism for catalytic step II of pre-mRNA splicing.","date":"1998","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9524131","citation_count":64,"is_preprint":false},{"pmid":"20419786","id":"PMC_20419786","title":"PRP-17 and the pre-mRNA splicing pathway are preferentially required for the proliferation versus meiotic development decision and germline sex determination in Caenorhabditis elegans.","date":"2010","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/20419786","citation_count":63,"is_preprint":false},{"pmid":"33220177","id":"PMC_33220177","title":"Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly.","date":"2020","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/33220177","citation_count":48,"is_preprint":false},{"pmid":"10628969","id":"PMC_10628969","title":"Extensive genetic interactions between PRP8 and PRP17/CDC40, two yeast genes involved in pre-mRNA splicing and cell cycle progression.","date":"2000","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/10628969","citation_count":40,"is_preprint":false},{"pmid":"9769104","id":"PMC_9769104","title":"Identification and functional analysis of hPRP17, the human homologue of the PRP17/CDC40 yeast gene involved in splicing and cell cycle control.","date":"1998","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/9769104","citation_count":38,"is_preprint":false},{"pmid":"15133121","id":"PMC_15133121","title":"The Saccharomyces cerevisiae gene CDC40/PRP17 controls cell cycle progression through splicing of the ANC1 gene.","date":"2004","source":"Nucleic acids 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research","url":"https://pubmed.ncbi.nlm.nih.gov/3523226","citation_count":14,"is_preprint":false},{"pmid":"32913542","id":"PMC_32913542","title":"MiR-422a in gastric cancer cells directly targets CDC40 and modulates cell proliferation.","date":"2020","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/32913542","citation_count":4,"is_preprint":false},{"pmid":"39747150","id":"PMC_39747150","title":"CDC40 suppression induces CDCA5 splicing defects and anti-proliferative effects in lung cancer cells.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39747150","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.12.27.630533","title":"Direct and indirect effects of spliceosome disruption compromise gene regulation by Nonsense-Mediated mRNA Decay","date":"2024-12-28","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.27.630533","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10348,"output_tokens":3695,"usd":0.043235,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11375,"output_tokens":3818,"usd":0.076162,"stage2_stop_reason":"end_turn"},"total_usd":0.119397,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1998,\n      \"finding\": \"Human PRP17 (hPRP17/CDC40) is required for the second catalytic step of pre-mRNA splicing; immunodepletion of hPRP16 from splicing extracts specifically blocks step II, and both hPrp16 and hPrp17 associate with the spliceosome late in the splicing pathway. Mutations at the 3' splice site that block step II do not prevent hPrp16/hPrp17 spliceosome association, placing their function prior to 3' splice site recognition.\",\n      \"method\": \"Immunodepletion from splicing extracts, recombinant protein add-back, spliceosome association assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — immunodepletion with full activity rescue by recombinant protein; multiple orthogonal methods in one study\",\n      \"pmids\": [\"9524131\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"A yeast-human chimera carrying the C-terminal two-thirds of hPRP17 (containing WD repeats) complements both the cell-cycle and splicing defects of a yeast prp17 mutant; yeast and chimeric Prp17 proteins co-precipitate the intron-exon 2 lariat intermediate and the intron lariat product, demonstrating spliceosome association and functional conservation.\",\n      \"method\": \"Complementation of yeast prp17 mutant, co-immunoprecipitation of splicing intermediates\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — complementation assay plus co-IP of splicing intermediates; replicated across two labs (also confirmed in PMID:9524131)\",\n      \"pmids\": [\"9769104\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"PRP8 alleles suppress both the temperature-sensitive growth phenotype and the splicing defect caused by absence of Prp17/Cdc40, and other PRP8 alleles show synthetic lethality with prp17 deletion; PRP8 mutations also suppress specific 3' splice site mutations in an ACT1-CUP1 reporter, placing Prp17 and Prp8 as interacting partners during the second catalytic step of splicing, with PRP17/CDC40 acting in 3' splice site recognition.\",\n      \"method\": \"Genetic suppression/synthetic lethality analysis, ACT1-CUP1 splicing reporter assay\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — extensive epistasis mapping with multiple allele combinations and a quantitative splicing reporter; independently confirmed by PMID:11565750\",\n      \"pmids\": [\"10628969\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Missense mutations in three temperature-sensitive prp17 alleles map to the N-terminal non-conserved region; the N-terminal region (not the WD-repeat C-terminus) is the functional domain required for interactions with Prp16, Prp18, and U5 snRNA; a mutually allele-specific interaction between Prp17 and snr7 (U5 snRNA) was identified.\",\n      \"method\": \"In vitro mutagenesis of WD repeats, deletion analysis, genetic synthetic lethality, allele-specific interaction mapping\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — systematic mutagenesis of 11 missense alleles plus deletion analysis and allele-specific genetic interactions; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"8722761\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"The SRPK family kinase Sky1p genetically interacts with PRP17/SLU4 in 3' splice site recognition; deletion of SKY1 is synthetically lethal with all prp17 mutants tested and suppresses 3' AG mutations in ACT1-CUP1 splicing reporters, indicating that phosphorylation by Sky1p regulates 3' splice site fidelity in a pathway involving Prp17.\",\n      \"method\": \"Synthetic lethality screen, ACT1-CUP1 splicing reporter assay\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with quantitative splicing reporter; single lab, two orthogonal genetic methods\",\n      \"pmids\": [\"11565750\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"CDC40/PRP17 controls cell cycle progression specifically through splicing of the ANC1 gene; deletion of the ANC1 intron relieves the cell cycle arrest and temperature sensitivity of cdc40 mutants, and point mutations in specific residues of the ANC1 intron define sequences required for CDC40-dependent splicing.\",\n      \"method\": \"Intron deletion suppression of cdc40 phenotype, point mutation analysis of intron sequences\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — intron deletion rescues cdc40 cell cycle arrest; combined with point mutation identification of critical intron residues; multiple orthogonal genetic methods\",\n      \"pmids\": [\"15133121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Genome-wide microarray analysis shows Prp17 is preferentially required for splicing of introns longer than 200 nt, and is dispensable when the distance between the branch point nucleotide and the 3' splice site is ≤13 nt; in vitro splicing with substrates of varying branch-point to 3' splice site distances confirmed differential Prp17 dependency.\",\n      \"method\": \"Splicing-sensitive DNA microarray, in vitro splicing assay with defined pre-mRNA substrates\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — genome-wide splicing array combined with in vitro splicing reconstitution; single lab but two orthogonal methods\",\n      \"pmids\": [\"15452114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Prp17 (Cdc40) is required for efficient splicing of TUB1 and TUB3 (alpha-tubulin) pre-mRNAs; reduced alpha-tubulin protein levels underlie the benomyl sensitivity and G2/M arrest of prp17 mutants; genomic replacement with an intronless TUB1 gene relieves the benomyl sensitivity but not the temperature sensitivity, indicating multiple limiting targets for mitosis.\",\n      \"method\": \"In vitro splicing with TUB3 pre-mRNA in prp17 extracts, intronless gene replacement suppression, RT-PCR/transcript analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — in vitro splicing assay combined with intronless gene suppression and transcript analysis; multiple orthogonal methods in one study\",\n      \"pmids\": [\"12711678\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Prp17 interacts with U2, U5, and U6 snRNPs but is not a core component of any single snRNP; it joins the spliceosome at the pre-catalytic A1 complex (after U4 dissociation), prior to both catalytic steps, and remains associated in post-splicing complexes containing lariat intron; in prp17Δ extracts, stalled spliceosomes are compromised for the Prp16 helicase-triggered conformational switch required for the second step.\",\n      \"method\": \"Co-immunoprecipitation of snRNAs using epitope-tagged Prp17, in vitro spliceosome assembly and co-precipitation on actin pre-mRNA, in vitro splicing kinetics\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP of snRNAs, in vitro spliceosome assembly at defined steps, kinetic splicing assays; multiple orthogonal methods in single lab\",\n      \"pmids\": [\"18691155\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"C. elegans PRP-17 (ortholog of PRP17/CDC40) functions downstream of GLP-1 Notch signaling to promote meiotic entry largely via the GLD-1 pathway, and functions in female germline sex determination; PRP-17 can rescue temperature-sensitive lethality of yeast PRP17, confirming functional conservation and demonstrating that splicing per se (not a novel function) underlies these developmental roles.\",\n      \"method\": \"Genetic epistasis (RNAi in sensitized backgrounds), yeast complementation rescue\",\n      \"journal\": \"Developmental dynamics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis in C. elegans combined with yeast complementation; single lab, two orthogonal methods\",\n      \"pmids\": [\"20419786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Biallelic loss-of-function mutations in PRP17 cause pontocerebellar hypoplasia with microcephaly (PCHM) in humans; loss of PRP17 disrupts splicing integrity, predominantly affecting short and high GC-content introns and genes involved in brain disorders; PPIL1 and PRP17 form an active isomerase-substrate interaction, but isomerase activity per se is not critical for function.\",\n      \"method\": \"Patient mutation identification, mouse knockouts (embryonic lethal), knockin mouse neuronal apoptosis, RNA splicing analysis\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — mouse knockout lethality, patient knockin showing neuron-specific apoptosis, genome-wide splicing analysis, and biochemical isomerase assay; multiple orthogonal methods replicated across families\",\n      \"pmids\": [\"33220177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CDC40 knockdown in lung cancer cells induces intron retention in CDCA5 pre-mRNA (specifically retention of the first intron), leading to decreased CDCA5 protein expression; co-immunoprecipitation reveals spliceosome components as the main binding partners of CDC40; CDC40 knockdown causes cell cycle defects, growth inhibition, and apoptosis.\",\n      \"method\": \"siRNA knockdown, RNA-seq/splicing analysis, Western blot for CDCA5 protein, co-immunoprecipitation/mass spectrometry\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with defined splicing phenotype and protein consequence, plus co-IP/MS for binding partners; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"39747150\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"CDC40/PRP17 has a role in the G1/S transition: cdc40 mutants show delayed G1/S and hypersensitivity to HU/MMS; deletion of G1 cyclin CLN2 enhances temperature sensitivity and G1/S delay in cdc40 cells; overexpression of cDNAs encoding chaperones, translation initiation factors, and glycolytic enzymes (none intron-containing) can suppress HU/MMS sensitivity and G1/S delay, suggesting crosstalk between splicing, translation, and glycolysis at cell cycle entry.\",\n      \"method\": \"cDNA overexpression suppressor screen, arrest/release cell cycle analysis, double mutant construction\",\n      \"journal\": \"Current genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic suppressor screen combined with cell cycle synchronization; single lab, two orthogonal approaches\",\n      \"pmids\": [\"17171376\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1986,\n      \"finding\": \"Epistasis analysis shows that rad6-1 is epistatic to cdc40-1 for sensitivity to UV and MMS, and rad50-1 is epistatic to cdc40-1 for MMS sensitivity in G1 stationary cells, placing CDC40 in the RAD6 DNA-repair pathway; cdc40-1 mutants are defective in UV-induced mutagenesis at the restrictive temperature.\",\n      \"method\": \"Double mutant epistasis analysis, survival assays after DNA damage\",\n      \"journal\": \"Mutation research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with multiple allele combinations and damage types; single lab, classic yeast genetics\",\n      \"pmids\": [\"3523226\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CDC40/PRP17 is a WD-repeat spliceosome component that associates with U2, U5, and U6 snRNPs from the pre-catalytic A1 complex onward, facilitates the Prp16-dependent conformational switch required for the second catalytic step of pre-mRNA splicing (particularly for introns >200 nt or with long branch-point to 3' splice site spacing), genetically and physically interacts with Prp8 and other second-step factors (Prp16, Prp18, Slu7) at the 3' splice site, controls cell cycle progression through selective splicing of specific intron-containing transcripts (ANC1, TUB1/TUB3, CDCA5), forms an isomerase-substrate interaction with PPIL1 (though isomerase activity is non-essential), and is required for neuronal survival in humans, where biallelic loss causes pontocerebellar hypoplasia with microcephaly.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CDC40/PRP17 is a WD-repeat spliceosomal protein that promotes the second catalytic step of pre-mRNA splicing and, through selective splicing of intron-containing transcripts, governs cell cycle progression [#0, #5]. It joins the spliceosome late, at the pre-catalytic A1 complex after U4 dissociation, associates with U2, U5, and U6 snRNPs without being a core subunit of any single snRNP, and remains bound through post-splicing lariat-containing complexes [#8]; in its absence stalled spliceosomes fail to undergo the Prp16 helicase-triggered conformational switch required for the second step [#8]. CDC40 acts at the 3' splice site, where it genetically and physically cooperates with Prp8 and the second-step machinery, and where its N-terminal non-conserved region mediates interactions with Prp16, Prp18, and U5 snRNA [#2, #3]. Its requirement is substrate-selective: it is preferentially needed for introns longer than 200 nt and is dispensable when the branch point lies within ~13 nt of the 3' splice site [#6]. Through this selectivity CDC40 controls mitosis and cell cycle entry by ensuring splicing of specific transcripts including ANC1, the alpha-tubulins TUB1/TUB3, and CDCA5, loss of which causes G2/M and G1/S defects, growth arrest, and apoptosis [#5, #7, #11]. In humans, biallelic loss-of-function mutations in PRP17 cause pontocerebellar hypoplasia with microcephaly, with neuron-specific apoptosis driven by disrupted splicing of short, high-GC introns, and the protein forms an isomerase-substrate interaction with PPIL1 whose catalytic activity is non-essential [#10].\",\n  \"teleology\": [\n    {\n      \"year\": 1986,\n      \"claim\": \"Before its splicing role was known, CDC40 was placed genetically in a DNA-damage response, establishing an early functional handle on the gene's phenotype.\",\n      \"evidence\": \"Double-mutant epistasis and DNA-damage survival assays in yeast G1 stationary cells\",\n      \"pmids\": [\"3523226\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cannot distinguish a direct repair role from an indirect consequence of defective splicing of repair-pathway transcripts\", \"No molecular mechanism linking CDC40 to RAD6/RAD50 defined\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Mapping ts alleles localized the functional core to the N-terminal non-conserved region rather than the WD repeats, redefining which part of the protein mediates second-step interactions.\",\n      \"evidence\": \"Mutagenesis of 11 missense alleles, deletion analysis, and allele-specific genetic interactions in yeast\",\n      \"pmids\": [\"8722761\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the N-terminal Prp16/Prp18/U5 interactions not resolved\", \"Role of the WD repeats left undefined\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Two studies established that the human ortholog acts specifically at step II of splicing and associates with the spliceosome late, demonstrating cross-species functional conservation.\",\n      \"evidence\": \"Immunodepletion/add-back of splicing extracts, spliceosome association assays, and yeast-human chimera complementation with co-IP of splicing intermediates\",\n      \"pmids\": [\"9524131\", \"9769104\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise biochemical contribution to step II catalysis not mechanistically defined\", \"Timing relative to other late factors not yet resolved\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Genetic suppression and synthetic lethality with PRP8 alleles, plus suppression of 3' splice site mutations, positioned CDC40 as a Prp8-interacting 3' splice site recognition factor.\",\n      \"evidence\": \"Epistasis/synthetic-lethality analysis and ACT1-CUP1 splicing reporter in yeast\",\n      \"pmids\": [\"10628969\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct physical contact with Prp8 vs. allele-bridged genetic interaction not distinguished\", \"Molecular nature of 3' splice site recognition by CDC40 unresolved\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Linking the SRPK kinase Sky1p to CDC40 in 3' splice site fidelity introduced phosphoregulation into the second-step recognition pathway.\",\n      \"evidence\": \"Synthetic lethality screen and ACT1-CUP1 reporter assay in yeast\",\n      \"pmids\": [\"11565750\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct phosphorylation target of Sky1p in this pathway not identified\", \"Whether CDC40 itself is phosphorylated not established\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Identifying TUB1/TUB3 as splicing targets connected CDC40's splicing defect to a concrete mitotic phenotype via reduced alpha-tubulin.\",\n      \"evidence\": \"In vitro splicing of TUB3 pre-mRNA, intronless gene replacement suppression, and transcript analysis in yeast\",\n      \"pmids\": [\"12711678\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Multiple limiting targets implied since intronless TUB1 does not rescue temperature sensitivity\", \"Other mitotic targets not enumerated\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Two studies defined CDC40's substrate selectivity—an intron-length/branch-point dependence and a specific cell-cycle target (ANC1)—explaining why only certain transcripts require it.\",\n      \"evidence\": \"Splicing-sensitive microarrays with in vitro splicing of defined substrates, plus intron-deletion suppression and intron point-mutation analysis in yeast\",\n      \"pmids\": [\"15452114\", \"15133121\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which intron length/branch-point distance sets CDC40 dependency not defined\", \"Full set of length-dependent endogenous targets not catalogued\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"A G1/S role and cyclin/metabolic crosstalk broadened CDC40's cell-cycle function beyond mitosis.\",\n      \"evidence\": \"cDNA overexpression suppressor screen, cell cycle arrest/release, and double-mutant construction in yeast\",\n      \"pmids\": [\"17171376\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Suppressing cDNAs are intronless, so the mechanistic link between splicing and G1/S remains indirect\", \"Whether glycolytic/translation suppression reflects a genuine pathway or bypass unclear\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defining the snRNP associations and assembly stage established that CDC40 enters at the A1 complex and is needed for the Prp16-triggered second-step conformational switch.\",\n      \"evidence\": \"Reciprocal co-IP of snRNAs with tagged Prp17, staged in vitro spliceosome assembly, and splicing kinetics in yeast\",\n      \"pmids\": [\"18691155\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural details of how CDC40 enables the Prp16 switch not resolved\", \"Order of recruitment relative to other second-step factors not fully mapped\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"C. elegans work showed the developmental roles of the ortholog (meiotic entry, sex determination) derive from its conserved splicing function rather than a novel activity.\",\n      \"evidence\": \"Genetic epistasis by RNAi in sensitized backgrounds and yeast complementation rescue\",\n      \"pmids\": [\"20419786\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific spliced targets underlying germline phenotypes not identified\", \"Direct vs. indirect action within GLD-1 pathway not dissected\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Human genetics tied PRP17 to a Mendelian neurodevelopmental disease and revealed a PPIL1 isomerase-substrate interaction whose catalytic activity is dispensable.\",\n      \"evidence\": \"Patient mutation identification, embryonic-lethal mouse knockouts, knockin mice with neuronal apoptosis, genome-wide splicing analysis, and isomerase assay\",\n      \"pmids\": [\"33220177\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why neurons are selectively vulnerable not mechanistically resolved\", \"Functional role of the non-catalytic PPIL1 interaction unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"In human cancer cells CDC40 was shown to control CDCA5 expression via intron retention, extending its substrate-selective cell-cycle control to mammalian transcripts.\",\n      \"evidence\": \"siRNA knockdown with RNA-seq splicing analysis, CDCA5 Western blot, and co-IP/mass spectrometry in lung cancer cells\",\n      \"pmids\": [\"39747150\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether CDCA5 retention fully accounts for the proliferation/apoptosis phenotype not established\", \"Direct vs. indirect effect on the CDCA5 first intron not distinguished\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CDC40's substrate selectivity (intron length, GC content, branch-point distance) is mechanistically encoded at the spliceosome, and how this selectivity drives tissue-specific outcomes such as neuronal survival, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of CDC40 within the catalytic spliceosome\", \"Mechanism translating splicing selectivity into cell-type-specific phenotypes unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [8, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [5, 7, 11]}\n    ],\n    \"complexes\": [\"spliceosome\"],\n    \"partners\": [\"PRP8\", \"PRP16\", \"PRP18\", \"SLU7\", \"PPIL1\", \"SKY1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}