{"gene":"CWF19L2","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2024,"finding":"CWF19L2 interacts with multiple spliceosome proteins to participate in proper assembly and stability of the spliceosome, and directly binds and regulates splicing of spermatogenesis-related genes (Znhit1, Btrc, Fbxw7) and RNA splicing regulators (Rbfox1, Celf1, Rbm10), as demonstrated by LACE-seq and RNA-seq integration in germline conditional Cwf19l2 knockout mice.","method":"Germline conditional knockout mouse (loss-of-function), RNA-seq, LACE-seq (direct RNA binding), co-immunoprecipitation with spliceosome proteins","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, direct RNA-binding by LACE-seq, KO mouse phenotype, and multiple orthogonal methods in one study","pmids":["38889293"],"is_preprint":false},{"year":2024,"finding":"CWF19L2 indirectly amplifies splicing regulation by modulating RBFOX1 activity, thereby controlling a broader splicing factor network during early spermatogenesis.","method":"RNA-seq analysis of Cwf19l2 conditional knockout mice combined with LACE-seq binding data","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, indirect effect inferred from KO transcriptomics and binding data without direct reconstitution of the RBFOX1 regulatory axis","pmids":["38889293"],"is_preprint":false},{"year":2025,"finding":"CWF19L2 was identified as a novel NVL2-interacting nuclear protein and is required for debranching of intron-derived lariat RNAs, functioning as potently as the canonical debranching enzyme DBR1; it also interacts with ILS spliceosomal components and the MTR4-RNA exosome complex.","method":"Co-immunoprecipitation (CWF19L2 with NVL2, ILS components, DBR1, MTR4-RNA exosome), RNA debranching assay using pre-mRNA splicing reporter minigene, endogenous lariat RNA detection by RT-PCR, cryo-EM structural indication of CWF19L2 loading into ILS, super-resolution immunofluorescence","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — cryo-EM structural evidence, Co-IP binding, functional debranching assay, and localization imaging, all orthogonal methods in one study","pmids":["41422678"],"is_preprint":false},{"year":2025,"finding":"Super-resolution immunofluorescence imaging showed that CWF19L2 localizes to distinct but closely associated nuclear foci relative to DBR1 and CWF19L1, suggesting compartmentalized participation in lariat RNA processing.","method":"Super-resolution immunofluorescence imaging","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization by super-resolution imaging in a single study, associated with functional debranching phenotype","pmids":["41422678"],"is_preprint":false}],"current_model":"CWF19L2 is a nuclear spliceosomal protein that associates with the intron lariat spliceosome (ILS) and multiple spliceosome/splicing-factor proteins, directly binds pre-mRNA substrates to regulate alternative splicing, and is required for debranching of intron-derived lariat RNAs in concert with DBR1 and the MTR4-RNA exosome; in the germline it orchestrates a splicing factor network (including indirect regulation via RBFOX1) to ensure accurate pre-mRNA splicing during early spermatogenesis."},"narrative":{"mechanistic_narrative":"CWF19L2 is a nuclear spliceosomal protein that functions in pre-mRNA splicing and the downstream processing of intron-derived lariat RNAs [PMID:38889293, PMID:41422678]. It associates with multiple spliceosome proteins and the intron lariat spliceosome (ILS), with cryo-EM evidence indicating loading of CWF19L2 into the ILS, and participates in proper spliceosome assembly and stability [PMID:38889293, PMID:41422678]. CWF19L2 directly binds pre-mRNA substrates to regulate alternative splicing, controlling spermatogenesis-related genes (Znhit1, Btrc, Fbxw7) and splicing regulators (Rbfox1, Celf1, Rbm10); germline conditional knockout disrupts these splicing programs during early spermatogenesis [PMID:38889293]. Beyond splicing assembly, CWF19L2 is an NVL2-interacting protein required for debranching of intron-derived lariat RNAs, functioning as potently as the canonical debranching enzyme DBR1 and acting in concert with ILS components and the MTR4-RNA exosome complex [PMID:41422678]. It localizes to distinct but closely associated nuclear foci relative to DBR1 and CWF19L1, consistent with compartmentalized lariat RNA processing [PMID:41422678].","teleology":[{"year":2024,"claim":"Established that CWF19L2 is a spliceosome-associated factor that directly binds pre-mRNA and is required for accurate splicing of a defined germline gene program, defining its role in spermatogenesis.","evidence":"Germline conditional knockout mouse with RNA-seq, LACE-seq direct RNA-binding, and reciprocal Co-IP with spliceosome proteins","pmids":["38889293"],"confidence":"High","gaps":["Mechanism of CWF19L2 recruitment into the spliceosome not resolved","No structural detail of its spliceosome contacts in this study","Whether splicing role is germline-specific or general is untested"]},{"year":2024,"claim":"Extended the model to show CWF19L2 amplifies splicing control indirectly by modulating RBFOX1, implicating it in a broader splicing factor network.","evidence":"Integration of conditional knockout RNA-seq with LACE-seq binding data","pmids":["38889293"],"confidence":"Medium","gaps":["Indirect effect inferred from KO transcriptomics without reconstitution of the RBFOX1 axis","Direct biochemical link between CWF19L2 and RBFOX1 regulation not demonstrated"]},{"year":2025,"claim":"Defined a distinct biochemical activity by showing CWF19L2 is required for lariat RNA debranching, working with DBR1 and the MTR4-RNA exosome, connecting its spliceosome association to intron RNA turnover.","evidence":"Co-IP with NVL2/ILS components/DBR1/MTR4-RNA exosome, RNA debranching assay using a splicing reporter minigene, endogenous lariat RT-PCR, and cryo-EM indication of ILS loading","pmids":["41422678"],"confidence":"High","gaps":["Whether CWF19L2 itself is catalytic or an accessory factor in debranching is unresolved","Functional relationship between its splicing and debranching roles not integrated","Structure of the CWF19L2-DBR1-exosome assembly not determined"]},{"year":2025,"claim":"Resolved the spatial organization of CWF19L2 relative to debranching machinery, suggesting compartmentalized nuclear processing of lariat RNA.","evidence":"Super-resolution immunofluorescence imaging comparing CWF19L2, DBR1, and CWF19L1 foci","pmids":["41422678"],"confidence":"Medium","gaps":["Functional meaning of the distinct foci not established","Single-study localization without orthogonal confirmation","Identity and composition of the CWF19L2 foci unknown"]},{"year":null,"claim":"It remains unknown whether CWF19L2 contributes catalytically to lariat debranching or solely as a scaffolding/recruitment factor, and how its spliceosome-assembly role mechanistically integrates with intron RNA turnover.","evidence":"","pmids":[],"confidence":"Low","gaps":["No defined catalytic mechanism for CWF19L2","No structural model of its action within the ILS at substrate resolution","Generality of its functions beyond the germline untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,3]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,2]}],"complexes":["intron lariat spliceosome (ILS)","MTR4-RNA exosome"],"partners":["DBR1","NVL2","RBFOX1","CWF19L1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q2TBE0","full_name":"CWF19-like protein 2","aliases":[],"length_aa":894,"mass_kda":103.8,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q2TBE0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CWF19L2","classification":"Common Essential","n_dependent_lines":875,"n_total_lines":1208,"dependency_fraction":0.7243377483443708},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"COMMD2","stoichiometry":10.0},{"gene":"COMMD6","stoichiometry":10.0},{"gene":"AAMP","stoichiometry":0.2},{"gene":"CDKN2A","stoichiometry":0.2},{"gene":"COMMD1","stoichiometry":0.2},{"gene":"COMMD4","stoichiometry":0.2},{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"DDB1","stoichiometry":0.2},{"gene":"DDX21","stoichiometry":0.2},{"gene":"DHX9","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CWF19L2","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nuclear speckles","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CWF19L2"},"hgnc":{"alias_symbol":["FLJ32343"],"prev_symbol":[]},"alphafold":{"accession":"Q2TBE0","domains":[{"cath_id":"-","chopping":"593-626_634-649","consensus_level":"medium","plddt":72.6532,"start":593,"end":649},{"cath_id":"3.30.428.10","chopping":"686-891","consensus_level":"high","plddt":89.0104,"start":686,"end":891},{"cath_id":"1.20.5","chopping":"650-677","consensus_level":"medium","plddt":81.3743,"start":650,"end":677}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q2TBE0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q2TBE0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q2TBE0-F1-predicted_aligned_error_v6.png","plddt_mean":66.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CWF19L2","jax_strain_url":"https://www.jax.org/strain/search?query=CWF19L2"},"sequence":{"accession":"Q2TBE0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q2TBE0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q2TBE0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q2TBE0"}},"corpus_meta":[{"pmid":"18398821","id":"PMC_18398821","title":"Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients.","date":"2008","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/18398821","citation_count":82,"is_preprint":false},{"pmid":"38889293","id":"PMC_38889293","title":"CWF19L2 is Essential for Male Fertility and Spermatogenesis by Regulating Alternative Splicing.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/38889293","citation_count":22,"is_preprint":false},{"pmid":"39526184","id":"PMC_39526184","title":"Systematic identification of therapeutic targets for coronary artery calcification: an integrated transcriptomic and proteomic Mendelian randomization.","date":"2024","source":"Frontiers in cardiovascular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39526184","citation_count":2,"is_preprint":false},{"pmid":"41422678","id":"PMC_41422678","title":"NVL2-interacting protein CWF19L2 is required for debranching of intron-derived lariat RNAs.","date":"2025","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/41422678","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4139,"output_tokens":1117,"usd":0.014586,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7679,"output_tokens":2028,"usd":0.044547,"stage2_stop_reason":"end_turn"},"total_usd":0.059133,"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\": 2024,\n      \"finding\": \"CWF19L2 interacts with multiple spliceosome proteins to participate in proper assembly and stability of the spliceosome, and directly binds and regulates splicing of spermatogenesis-related genes (Znhit1, Btrc, Fbxw7) and RNA splicing regulators (Rbfox1, Celf1, Rbm10), as demonstrated by LACE-seq and RNA-seq integration in germline conditional Cwf19l2 knockout mice.\",\n      \"method\": \"Germline conditional knockout mouse (loss-of-function), RNA-seq, LACE-seq (direct RNA binding), co-immunoprecipitation with spliceosome proteins\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, direct RNA-binding by LACE-seq, KO mouse phenotype, and multiple orthogonal methods in one study\",\n      \"pmids\": [\"38889293\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CWF19L2 indirectly amplifies splicing regulation by modulating RBFOX1 activity, thereby controlling a broader splicing factor network during early spermatogenesis.\",\n      \"method\": \"RNA-seq analysis of Cwf19l2 conditional knockout mice combined with LACE-seq binding data\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, indirect effect inferred from KO transcriptomics and binding data without direct reconstitution of the RBFOX1 regulatory axis\",\n      \"pmids\": [\"38889293\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CWF19L2 was identified as a novel NVL2-interacting nuclear protein and is required for debranching of intron-derived lariat RNAs, functioning as potently as the canonical debranching enzyme DBR1; it also interacts with ILS spliceosomal components and the MTR4-RNA exosome complex.\",\n      \"method\": \"Co-immunoprecipitation (CWF19L2 with NVL2, ILS components, DBR1, MTR4-RNA exosome), RNA debranching assay using pre-mRNA splicing reporter minigene, endogenous lariat RNA detection by RT-PCR, cryo-EM structural indication of CWF19L2 loading into ILS, super-resolution immunofluorescence\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — cryo-EM structural evidence, Co-IP binding, functional debranching assay, and localization imaging, all orthogonal methods in one study\",\n      \"pmids\": [\"41422678\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Super-resolution immunofluorescence imaging showed that CWF19L2 localizes to distinct but closely associated nuclear foci relative to DBR1 and CWF19L1, suggesting compartmentalized participation in lariat RNA processing.\",\n      \"method\": \"Super-resolution immunofluorescence imaging\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization by super-resolution imaging in a single study, associated with functional debranching phenotype\",\n      \"pmids\": [\"41422678\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CWF19L2 is a nuclear spliceosomal protein that associates with the intron lariat spliceosome (ILS) and multiple spliceosome/splicing-factor proteins, directly binds pre-mRNA substrates to regulate alternative splicing, and is required for debranching of intron-derived lariat RNAs in concert with DBR1 and the MTR4-RNA exosome; in the germline it orchestrates a splicing factor network (including indirect regulation via RBFOX1) to ensure accurate pre-mRNA splicing during early spermatogenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CWF19L2 is a nuclear spliceosomal protein that functions in pre-mRNA splicing and the downstream processing of intron-derived lariat RNAs [#0, #2]. It associates with multiple spliceosome proteins and the intron lariat spliceosome (ILS), with cryo-EM evidence indicating loading of CWF19L2 into the ILS, and participates in proper spliceosome assembly and stability [#0, #2]. CWF19L2 directly binds pre-mRNA substrates to regulate alternative splicing, controlling spermatogenesis-related genes (Znhit1, Btrc, Fbxw7) and splicing regulators (Rbfox1, Celf1, Rbm10); germline conditional knockout disrupts these splicing programs during early spermatogenesis [#0]. Beyond splicing assembly, CWF19L2 is an NVL2-interacting protein required for debranching of intron-derived lariat RNAs, functioning as potently as the canonical debranching enzyme DBR1 and acting in concert with ILS components and the MTR4-RNA exosome complex [#2]. It localizes to distinct but closely associated nuclear foci relative to DBR1 and CWF19L1, consistent with compartmentalized lariat RNA processing [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2024,\n      \"claim\": \"Established that CWF19L2 is a spliceosome-associated factor that directly binds pre-mRNA and is required for accurate splicing of a defined germline gene program, defining its role in spermatogenesis.\",\n      \"evidence\": \"Germline conditional knockout mouse with RNA-seq, LACE-seq direct RNA-binding, and reciprocal Co-IP with spliceosome proteins\",\n      \"pmids\": [\"38889293\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Mechanism of CWF19L2 recruitment into the spliceosome not resolved\",\n        \"No structural detail of its spliceosome contacts in this study\",\n        \"Whether splicing role is germline-specific or general is untested\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the model to show CWF19L2 amplifies splicing control indirectly by modulating RBFOX1, implicating it in a broader splicing factor network.\",\n      \"evidence\": \"Integration of conditional knockout RNA-seq with LACE-seq binding data\",\n      \"pmids\": [\"38889293\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Indirect effect inferred from KO transcriptomics without reconstitution of the RBFOX1 axis\",\n        \"Direct biochemical link between CWF19L2 and RBFOX1 regulation not demonstrated\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined a distinct biochemical activity by showing CWF19L2 is required for lariat RNA debranching, working with DBR1 and the MTR4-RNA exosome, connecting its spliceosome association to intron RNA turnover.\",\n      \"evidence\": \"Co-IP with NVL2/ILS components/DBR1/MTR4-RNA exosome, RNA debranching assay using a splicing reporter minigene, endogenous lariat RT-PCR, and cryo-EM indication of ILS loading\",\n      \"pmids\": [\"41422678\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether CWF19L2 itself is catalytic or an accessory factor in debranching is unresolved\",\n        \"Functional relationship between its splicing and debranching roles not integrated\",\n        \"Structure of the CWF19L2-DBR1-exosome assembly not determined\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolved the spatial organization of CWF19L2 relative to debranching machinery, suggesting compartmentalized nuclear processing of lariat RNA.\",\n      \"evidence\": \"Super-resolution immunofluorescence imaging comparing CWF19L2, DBR1, and CWF19L1 foci\",\n      \"pmids\": [\"41422678\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional meaning of the distinct foci not established\",\n        \"Single-study localization without orthogonal confirmation\",\n        \"Identity and composition of the CWF19L2 foci unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether CWF19L2 contributes catalytically to lariat debranching or solely as a scaffolding/recruitment factor, and how its spliceosome-assembly role mechanistically integrates with intron RNA turnover.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No defined catalytic mechanism for CWF19L2\",\n        \"No structural model of its action within the ILS at substrate resolution\",\n        \"Generality of its functions beyond the germline untested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"complexes\": [\n      \"intron lariat spliceosome (ILS)\",\n      \"MTR4-RNA exosome\"\n    ],\n    \"partners\": [\n      \"DBR1\",\n      \"NVL2\",\n      \"RBFOX1\",\n      \"CWF19L1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":5,"faith_pct":100.0}}