CWC27 (NY-CO-10/SDCCAG10) is a nuclear spliceosomal pseudoenzyme with an N-terminal cyclophilin-like domain and a long C-terminal interaction region. It participates in major and minor pre-mRNA splicing as a transient component of activated spliceosomes, contacting the endonuclease-like domain of PRP8 and leaving during spliceosome activation. Its C-terminal region binds the splicing factor CWC22 and stabilizes a CWC22–EIF4A3 assembly associated with exon junction complex recruitment. Human-cell association studies also connect CWC27 to assembled EJC components, within a recruitment network that can engage EIF4A3 before spliceosome activation. CWC27 depletion disrupts splicing in human retinal pigment epithelial cells. The full-length 472-residue product binds CWC22; the 390-residue splice product lacks most of the C-terminal interaction region. Biallelic disruptive variants cause retinal degeneration with or without additional developmental anomalies.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0071013 catalytic step 2 spliceosome | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: On-path PAINT inference is retained as contextual step-2 membership, with directly inspected target evidence and unresolved stage dependence. Reason: The 1,072-node PTHR45625 tree places the exact 472-residue target MSA sequence below PTN000116297, where the current GO:0071013 IBD cites Q13356, Q6UX04, Q9H2H8 and Q9Y3C6. The target appearing among these descendant sources is legitimate experimental grounding. PMID:11991638 Table 1 identifies CWC27 under its verified secondary accession O60529, with five unique peptides in a post-first-step C-complex-enriched preparation and none in H complex. Later human structures place CWC27 mainly in Bact and show its loss during activation, so this state-dependent membership remains non-core rather than a universal description. The old positive preparation is not demonstrated contamination, and neither donor count nor self evidence invalidates the node placement. The separate on-path IRD for NOT PPIase activity concerns a different term. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000116297 SUPPORTS TRANSFER Exact GO:0071013 IBD lies on the target path; target and PPIL1/PPIL3 IDA PMID:11991638 records provide experimental descendants. Current PPIL2 term records are inferred, a snapshot distinction that does not erase the historical IBD. UniProtKB:Q6UX04 SUPPORTS TRANSFER Table 1 of PMID:11991638 verifies target-positive C-complex membership through secondary accession O60529. Later structural timing remains context-dependent. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Nuclear localization is supported by human imaging and spliceosomal experiments, despite a current ARBA snapshot difference. Reason: The literal combined-method sources include mouse Cwc27 Q3TKY6, ENSMUSP00000022228, UniProt SL-0191 and ARBA00026330. Mouse Q3TKY6 has an experimental nuclear annotation, while human HPA staining and human nuclear spliceosome work independently support the location. The present ARBA rule has 1,293 branches but none matches the captured CWC27 domain/subfamily facts; this is a current-rule versus historical-source discrepancy, not a reason to deny the independently established nucleus annotation. Nucleoplasm is reviewed separately. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}. |
| GO:0006457 protein folding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: The conserved-site mapping overextends the demonstrated CWC27 activity to protein folding. Reason: IPR020892 maps the cyclophilin PPIase conserved-site signature to protein folding. Its family description also mentions noncatalytic chaperone functions, so the mapping is not exclusively a claim of PPIase catalysis. However, the CWC27-specific NMR experiments in PMID:20676357 show peptide binding without acceleration of the tested isomerizations, and the CWC22 binding/stabilization experiments in PMID:32329775 do not measure folding of a polypeptide or complex into its correct tertiary structure. This family-level process inference therefore exceeds the demonstrated target function and is marked over-annotated. This judgment does not refute every possible noncatalytic folding role; that remains an experimental question. UNDECIDED can cover unresolved evidence even when accessible, but the demonstrated source-to-target overextension warrants the more informative action here. |
| GO:0000398 mRNA splicing, via spliceosome | NAS PMID:29360106 Structure of the human activated spliceosome in three confor... | ACCEPT | Summary: Human activated-spliceosome structures and functional splicing evidence support involvement in spliceosomal mRNA splicing. Reason: PMID:29360106 resolves CWC27/NY-CO-10 in early human major Bact, weaker in the mature class and absent late, with contact to the endonuclease-like domain of PRP8. These structures establish a contribution to the spliceosomal machinery without assigning RNA cleavage chemistry to CWC27. Human-cell depletion and recombinant CWC22-complex experiments in PMID:32329775 support the splicing role. PMID:42635127 additionally supports a CWC27–CWC22 module associated with EIF4A3 and EJC components: association persists during inhibition before pre-B assembly. Its recruitment model is positive corroboration, while the data permit several routes and do not establish direct CWC27–EIF4A3 binding. |
| GO:0000398 mRNA splicing, via spliceosome | NAS PMID:33509932 Structure of the activated human minor spliceosome. | ACCEPT | Summary: CWC27 is a structural component of the experimentally trapped human minor Bact spliceosome. Reason: The original PMID:33509932 explicitly includes CWC27/NY-CO-10 in its 45-protein model derived from HeLa nuclear extract. MINX-U12 was truncated 18 nucleotides beyond the branch-point sequence to prevent PRP2 remodeling and accumulate a pre-branching Bact complex. This directly supports structural participation in minor spliceosomal splicing, while neither CWC27 RNA catalysis nor step-2 occupancy follows from that structure. Supporting Evidence: |
| GO:0005681 spliceosomal complex | IPI PMID:39068178 Molecular basis for the activation of human spliceosome. | ACCEPT | Summary: CWC27 is directly resolved in a human spliceosome activation intermediate. Reason: PMID:39068178 places CWC27 in Bact-I and reports its dissociation in the transition to Bact-II. The protein is not present throughout every state enumerated in that paper. The broad spliceosomal-complex assertion is directly supported; RNA-contact and remodeling functions described for RNF113A, CWC22 or PRP2 are not transferred to CWC27. Supporting Evidence: PMID:39068178 only transiently appears in Bact-I and is dissociated in Bact-II. |
| GO:0071018 U12-type catalytic step 2 spliceosome | IPI PMID:33509932 Structure of the activated human minor spliceosome. | MODIFY | Summary: The source establishes minor Bact membership before branching, rather than the post-first-cleavage state in the existing term. Reason: GO:0071018 explicitly describes the minor spliceosome after the first splicing cleavage. The actual PMID:33509932 substrate and structural preparation are instead trapped before branching by truncating the RNA beyond the branch-point sequence, and CWC27 is explicitly included in that structure. GO:0005689 covers U12-type spliceosomal complexes at any assembly stage and preserves the positive source-supported membership with the appropriate specificity. The term correction does not dispute minor-spliceosome participation or imply CWC27 catalyzes a splicing reaction. Proposed replacements: U12-type spliceosomal complex Supporting Evidence: PMID:33509932 Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | ACCEPT | Summary: Human Protein Atlas immunofluorescence supports nucleoplasmic localization. Reason: The saved HPA ENSG00000153015 record reports nucleoplasm with several antibodies in human A-431, U-251 MG, U2OS or MCF7 cells, including enhanced-reliability assays and U2OS siRNA validation for HPA020344. A separate antibody reports microtubules in U2OS as well as nucleoplasm; this does not negate the nuclear signal and is not promoted to an additional annotation. Mouse NIH3T3 imaging is kept distinct. This assessment uses the assay record, not a claim to have inspected image pixels. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt |
| GO:0000398 mRNA splicing, via spliceosome | IC PMID:29360106 Structure of the human activated spliceosome in three confor... | ACCEPT | Summary: The structural CWC27 component supports the splicing inference, while the cited GO:0071005 premise is too stage-specific for this paper. Reason: Human CWC27 is observed in the major Bact spliceosome in PMID:29360106. The literal IC source GO:0071005 defines a precatalytic complex with all five snRNPs, whereas this three-snRNP Bact preparation is activated but not yet competent to branch. Correcting that component term to general U2-type spliceosomal complex leaves the positive inference of involvement in spliceosomal mRNA splicing intact. The source accession and original IC tuple are preserved. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: GO:0071005 SOURCE BAD The current all-five-snRNP definition does not describe the actual Bact structure. Positive U2-spliceosome membership and the inferred splicing process remain supported. Supporting Evidence: |
| GO:0071005 U2-type precatalytic spliceosome | IDA PMID:29360106 Structure of the human activated spliceosome in three confor... | MODIFY | Summary: The actual major Bact structure supports U2-type spliceosomal complex, without the all-five-snRNP restriction of the existing term. Reason: The current GO:0071005 definition requires the U1/U2/U4/U5/U6 precatalytic complex. PMID:29360106 resolves a U2/U5/U6 Bact preparation with CWC27, before branching, and distinguishes early, mature and late conformations. GO:0005684 covers any complex formed during U2-type splicing and is therefore the appropriate broader component term. Neither the informal word activated nor a pre-branching state justifies substituting the catalytic-step-1 term. Later PMID:39068178 places the target in Bact-I, with a distinct state series that should not be collapsed into universal timing. Proposed replacements: U2-type spliceosomal complex Supporting Evidence: PMID:29360106 the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) |
| GO:0003755 peptidyl-prolyl cis-trans isomerase activity | IDA NOT PMID:20676357 Structural and biochemical characterization of the human cyc... | ACCEPT | Summary: The NOT annotation is supported by direct tetrapeptide isomerase assays of the human CWC27 cyclophilin domain. Reason: PMID:20676357 tests standard AAPF, AFPF and AGPF substrates by NMR and finds no detectable SDCCAG-10/CWC27-catalyzed cis–trans exchange under the stated conditions. It also finds no cyclosporin binding, while positive suc-AGPF-pNA chemical shifts demonstrate peptide binding without exchange acceleration. The report supports the existing NOT PPIase annotation at its assay scope. The active-site comparison and a PPIA mutant are not a CWC27 rescue experiment, and inactivity is not used to assert that all CWC27 products lack every possible noncatalytic folding function. Supporting Evidence: PMID:20676357 PPIL2 and SDCCAG-10 are not active under the experimental conditions tested. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-9770131 | ACCEPT | Summary: The B* formation event places the CWC27 participant in the nucleoplasm, including its released form. Reason: Actual Reactome R-HSA-9770131 has CWC27 in the input Bact complex and as a released output. Both paths reach human Q6UX04 residues 2–472, entity 8867885, in the nucleoplasm. This is positive location evidence, not evidence that CWC27 remains a constituent of the completed B* product or performs the catalytic activity attached to the larger complex. The event’s 2020 EJC-ordering narrative is a model qualified by the later 2026 association study. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-9770145 | ACCEPT | Summary: The Bact assembly model includes human CWC27 in the nucleoplasm. Reason: Reactome R-HSA-9770145 includes CWC27 as an input and within output Bact complex 9769560; both target paths resolve to entity 8867885, human Q6UX04 residues 2–472, nucleoplasm. The activity of the assembly machinery is not assigned to CWC27 itself. Human HPA and independent structural work corroborate the location. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt Reactome:R-HSA-9770145 |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-9921507 | ACCEPT | Summary: The NS5 interaction model places the CWC27-containing spliceosomal assembly in the nucleoplasm. Reason: Both target paths in Reactome R-HSA-9921507 reach CWC27 entity 8867885 through spliceosomal assembly 72074, including the output NS5-containing complex. This supports the location annotation. The model describes NS5 contacts with CD2BP2 and DDX23; it does not establish direct NS5–CWC27 binding or a distinct antiviral role for CWC27. The assembly’s legacy C/Bact label is not used to settle target-specific catalytic-stage occupancy. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt Reactome:R-HSA-9921507 |
| GO:0000398 mRNA splicing, via spliceosome | IC PMID:11991638 Purification and characterization of native spliceosomes sui... | ACCEPT | Summary: Direct target detection in a post-first-step spliceosomal preparation supports involvement in splicing. Reason: PMID:11991638 Table 1 identifies NY-CO-10/O60529, a verified secondary accession of human CWC27, by five unique peptides in C complex and none in H complex. The substrate arrests after the first splicing step, and earlier complexes are depleted by RNase H. This grounds the literal GO:0071013 IC premise in the experimental context. Independent Bact structures and human-cell splicing perturbations reinforce the broad process without requiring identical target occupancy in every preparation. |
| GO:0071013 catalytic step 2 spliceosome | IDA PMID:11991638 Purification and characterization of native spliceosomes sui... | KEEP AS NON CORE | Summary: Target-positive mass spectrometry supports contextual membership in a C-complex-enriched preparation, despite later structural-stage differences. Reason: The original Table 1 reports five unique peptides for NY-CO-10/O60529 in C complex and none in H complex; the current official CWC27 record resolves that secondary accession. The HeLa preparation uses an AG-to-GG 3′ splice-site mutation to arrest after the first step and RNase H to remove earlier complexes. Affinity eluates contain 75–85% intermediate RNA; the separate later gradient peak reaches 96%, and the target MS result is not specifically assigned to that gradient peak. Later stage-resolved structures generally place CWC27 in Bact and document release during activation, but do not demonstrate contamination of this earlier positive experiment. Retain the experimentally supported association as non-core and leave the context-dependent discrepancy unresolved; neither a universal step-2 role nor an official isoform assignment is claimed. Supporting Evidence: PMID:11991638 These spliceosomes consist largely of C complex containing splicing intermediates |
| GO:1990935 splicing factor binding | IPI Q6UX04-1 PMID:32329775 Structural and functional insights into CWC27/CWC22 heterodi... | NEW | Summary: Purified full-length human CWC27 directly binds the splicing factor CWC22. Reason: PMID:32329775 Figure 3 and its recombinant-protein Methods establish reciprocal retention of bacterially expressed full-length human CWC27 (Q6UX04, residues 1–472) and CWC22-S (residues 100–665). Binding persists without EIF4A3. CWC27 residues 354–472 also bind CWC22, and the minimal-complex structure places a CWC27 C-terminal helix against the CWC22 MIF4G domain. GO:1990935 describes binding to a splicing protein and accurately classifies this measured binary interaction; no existing source row records a binding MF. This new molecular-function assertion does not depend on a status warning or a missing process annotation. It is scoped to the tested full-length product; the explicitly tested Q6UX04-2 product fails CWC22 retention. Neither direct EIF4A3 binding nor equal activity of both products is asserted. Supporting Evidence: PMID:32329775 CBP-CWC22-S co-retains PTS-CWC27 |
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Download this section (compressed HTML)Q: Does the cyclophilin domain perform a noncatalytic folding or chaperone function distinct from its demonstrated peptide binding and absence of activity on the tested tetrapeptides?
Q: What preparation or stage dependence accounts for the target-positive post-first-step C-complex mass spectrometry versus the loss of CWC27 during Bact activation in later structures?
Q: Which EJC recruitment events require CWC27 itself, and how do the early CWC27-independent associations and the CWC27–CWC22 pathway contribute in different transcript contexts?
Q: What endogenous functions and expression contexts belong to the 390-residue splice product that fails recombinant CWC22 retention?
Q: Should GO distinguish pre-branching major and minor activated Bact complexes beneath GO:0005684 and GO:0005689 from the catalytically active or post-first-cleavage states? The source preparations resolve this distinction, but the word activated is already used in synonyms for existing catalytic terms.
Experiment: Compare endogenous CWC27 occupancy across matched major and minor spliceosomal preparations with RNA-stage measurements and isoform-resolving peptides, separating enrichment purity from protein stoichiometry.
Experiment: Use matched depletion/rescue of the official full-length and 390-residue products, CWC22-binding mutants and cyclophilin-domain mutants to distinguish splicing, protein-stabilization and EJC-deposition effects.
Experiment: Test purified CWC27 domains in noncatalytic folding or anti-aggregation assays with defined substrates and controls, separately from the established tetrapeptide isomerase assays.
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