{"gene":"CLASRP","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2002,"finding":"CLASRP (Clasp/Clk4-associating SR-related protein) was identified as a binding partner of kinase-inactive Clk4 (K189R mutant) but not wild-type Clk4, established by two-hybrid screen and in vitro protein interaction assay. The long form (ClaspL) localizes as nuclear dots while the short form (ClaspS) shows a nucleoplasmic pattern. Overexpression of ClaspL promotes accumulation of Clk4 K189R in nuclear dots and induces exon EB inclusion from Clk1 pre-mRNA.","method":"Yeast two-hybrid screen, in vitro protein interaction assay, HA-tagged localization imaging, overexpression with alternative splicing reporter","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction confirmed by two-hybrid and in vitro assay, functional splice outcome measured, single lab with two orthogonal methods","pmids":["12169693"],"is_preprint":false},{"year":2023,"finding":"CLASRP promotes proliferation, migration, and invasion of colorectal cancer (CRC) cells in vitro and tumor growth in vivo. Clk inhibitors suppress these effects of CLASRP overexpression, reduce CLASRP gene and protein levels, and induce apoptosis via activation of caspase-3 and caspase-8 pathways, placing CLASRP functionally downstream of CDC-like kinase (Clk) family activity.","method":"Plasmid overexpression and shRNA knockdown in CRC cells; proliferation, migration, invasion assays; xenograft mouse model; western blotting for caspase-3/8 cleavage; Clk inhibitor treatment","journal":"Functional & integrative genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss- and gain-of-function with defined cellular phenotypes, in vivo validation, pathway placement via Clk inhibitors, single lab with multiple orthogonal methods","pmids":["37658940"],"is_preprint":false},{"year":2023,"finding":"LINC00482 recruits transcription factor E2F1 to the CLASRP promoter to enhance CLASRP expression in NSCLC cells, as demonstrated by dual-luciferase reporter, ChIP, and RIP assays. LINC00482 knockdown reduces CLASRP levels; re-expression of CLASRP rescues cisplatin sensitivity lost upon LINC00482 knockdown, placing CLASRP downstream of the LINC00482/E2F1 axis in drug resistance.","method":"Dual-luciferase reporter assay, ChIP assay, RIP assay, shRNA knockdown, ectopic overexpression, CCK-8 proliferation assay, flow cytometry apoptosis, xenograft mouse model","journal":"Functional & integrative genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — three orthogonal biochemical assays (luciferase, ChIP, RIP) establish E2F1-CLASRP transcriptional axis; rescue experiment confirms pathway placement; single lab","pmids":["37966662"],"is_preprint":false}],"current_model":"CLASRP (also known as CLASP/SFRS16/SWAP2) is an SR-rich-related splicing regulatory protein that physically associates with kinase-inactive Clk4 (but not active Clk4) and, upon overexpression, promotes nuclear dot formation and exon inclusion in Clk1 pre-mRNA; its expression is transcriptionally driven by the E2F1 transcription factor downstream of lncRNA LINC00482, and its elevated levels promote colorectal cancer cell proliferation, migration, and invasion through a Clk-dependent pathway that can be blocked by Clk inhibitors triggering caspase-3/8-mediated apoptosis."},"narrative":{"mechanistic_narrative":"CLASRP (Clk4-associating SR-related protein) is a nuclear SR-related splicing regulatory protein that links CDC-like kinase (Clk) activity to alternative splicing control [PMID:12169693]. It was identified as a partner that binds the kinase-inactive Clk4 K189R mutant but not the active wild-type kinase, and its long isoform localizes to nuclear dots where it sequesters Clk4 K189R and drives exon EB inclusion from Clk1 pre-mRNA [PMID:12169693]. Beyond this kinase association and splicing readout, CLASRP functions within a Clk-dependent pathway promoting cell proliferation, migration, and invasion: in colorectal cancer cells its pro-tumorigenic effects are abolished by Clk inhibitors, which lower CLASRP levels and trigger caspase-3/8-mediated apoptosis [PMID:37658940]. Its expression is transcriptionally driven through a LINC00482/E2F1 axis, with E2F1 recruited to the CLASRP promoter to enhance expression and confer cisplatin resistance in NSCLC cells [PMID:37966662]. The biochemical mechanism by which CLASRP itself recognizes RNA or remodels spliceosome assembly has not been characterized in the available corpus.","teleology":[{"year":2002,"claim":"Established CLASRP as a physical link between the Clk4 kinase and the splicing machinery, defining an isoform-specific nuclear regulator of alternative splicing.","evidence":"Yeast two-hybrid and in vitro interaction assays with Clk4 K189R, HA-tagged localization imaging, and Clk1 alternative splicing reporter in cells","pmids":["12169693"],"confidence":"Medium","gaps":["No structural or domain-level basis for preferential binding to kinase-inactive Clk4 identified","Direct RNA-binding activity of CLASRP and the spliceosomal step it acts on not defined","Whether CLASRP is a Clk substrate or a scaffold left unresolved"]},{"year":2023,"claim":"Placed CLASRP functionally downstream of Clk activity as a driver of tumor cell proliferation, migration, and invasion whose effects depend on Clk signaling.","evidence":"Gain- and loss-of-function in colorectal cancer cells, xenograft model, Clk inhibitor treatment, and caspase-3/8 cleavage western blotting","pmids":["37658940"],"confidence":"Medium","gaps":["Specific splicing targets mediating the pro-tumorigenic phenotype not identified","Whether Clk inhibitors act directly on CLASRP-Clk complexes or through broader Clk effects unclear"]},{"year":2023,"claim":"Defined the upstream transcriptional control of CLASRP, showing a LINC00482/E2F1 axis drives its expression and contributes to chemoresistance.","evidence":"Dual-luciferase reporter, ChIP, and RIP assays plus knockdown/rescue and xenograft in NSCLC cells with cisplatin sensitivity readout","pmids":["37966662"],"confidence":"Medium","gaps":["Mechanism by which CLASRP confers cisplatin resistance at the molecular level not established","Whether the splicing function of CLASRP underlies its drug-resistance role untested"]},{"year":null,"claim":"The intrinsic biochemical activity of CLASRP — how it binds RNA, which spliceosome components it engages, and the splice events it controls genome-wide — remains undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No genome-wide map of CLASRP-regulated splicing events","No reconstitution of CLASRP within a defined splicing reaction","Relationship between Clk binding, nuclear dot formation, and catalytic splicing outcome unresolved"]}],"mechanism_profile":{"molecular_activity":[],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0]}],"complexes":[],"partners":["CLK4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N2M8","full_name":"CLK4-associating serine/arginine rich protein","aliases":["Splicing factor, arginine/serine-rich 16","Suppressor of white-apricot homolog 2"],"length_aa":674,"mass_kda":77.2,"function":"Probably functions as an alternative splicing regulator. May regulate the mRNA splicing of genes such as CLK1. May act by regulating members of the CLK kinase family (By similarity)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8N2M8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CLASRP","classification":"Common Essential","n_dependent_lines":530,"n_total_lines":1208,"dependency_fraction":0.43874172185430466},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"RBBP4","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CLASRP","total_profiled":1310},"omim":[{"mim_id":"618532","title":"CLK4-ASSOCIATING SERINE/ARGININE-RICH PROTEIN; CLASRP","url":"https://www.omim.org/entry/618532"}],"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/CLASRP"},"hgnc":{"alias_symbol":["SWAP2","CLASP"],"prev_symbol":["SFRS16"]},"alphafold":{"accession":"Q8N2M8","domains":[{"cath_id":"-","chopping":"51-89","consensus_level":"medium","plddt":84.9741,"start":51,"end":89},{"cath_id":"-","chopping":"102-145_202-260","consensus_level":"medium","plddt":83.7969,"start":102,"end":260},{"cath_id":"1.20.5","chopping":"2-30","consensus_level":"high","plddt":89.7121,"start":2,"end":30}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N2M8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N2M8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N2M8-F1-predicted_aligned_error_v6.png","plddt_mean":58.72},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CLASRP","jax_strain_url":"https://www.jax.org/strain/search?query=CLASRP"},"sequence":{"accession":"Q8N2M8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N2M8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N2M8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N2M8"}},"corpus_meta":[{"pmid":"17543864","id":"PMC_17543864","title":"Asymmetric 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The long form (ClaspL) localizes as nuclear dots while the short form (ClaspS) shows a nucleoplasmic pattern. Overexpression of ClaspL promotes accumulation of Clk4 K189R in nuclear dots and induces exon EB inclusion from Clk1 pre-mRNA.\",\n      \"method\": \"Yeast two-hybrid screen, in vitro protein interaction assay, HA-tagged localization imaging, overexpression with alternative splicing reporter\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction confirmed by two-hybrid and in vitro assay, functional splice outcome measured, single lab with two orthogonal methods\",\n      \"pmids\": [\"12169693\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CLASRP promotes proliferation, migration, and invasion of colorectal cancer (CRC) cells in vitro and tumor growth in vivo. Clk inhibitors suppress these effects of CLASRP overexpression, reduce CLASRP gene and protein levels, and induce apoptosis via activation of caspase-3 and caspase-8 pathways, placing CLASRP functionally downstream of CDC-like kinase (Clk) family activity.\",\n      \"method\": \"Plasmid overexpression and shRNA knockdown in CRC cells; proliferation, migration, invasion assays; xenograft mouse model; western blotting for caspase-3/8 cleavage; Clk inhibitor treatment\",\n      \"journal\": \"Functional & integrative genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss- and gain-of-function with defined cellular phenotypes, in vivo validation, pathway placement via Clk inhibitors, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"37658940\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"LINC00482 recruits transcription factor E2F1 to the CLASRP promoter to enhance CLASRP expression in NSCLC cells, as demonstrated by dual-luciferase reporter, ChIP, and RIP assays. LINC00482 knockdown reduces CLASRP levels; re-expression of CLASRP rescues cisplatin sensitivity lost upon LINC00482 knockdown, placing CLASRP downstream of the LINC00482/E2F1 axis in drug resistance.\",\n      \"method\": \"Dual-luciferase reporter assay, ChIP assay, RIP assay, shRNA knockdown, ectopic overexpression, CCK-8 proliferation assay, flow cytometry apoptosis, xenograft mouse model\",\n      \"journal\": \"Functional & integrative genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — three orthogonal biochemical assays (luciferase, ChIP, RIP) establish E2F1-CLASRP transcriptional axis; rescue experiment confirms pathway placement; single lab\",\n      \"pmids\": [\"37966662\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CLASRP (also known as CLASP/SFRS16/SWAP2) is an SR-rich-related splicing regulatory protein that physically associates with kinase-inactive Clk4 (but not active Clk4) and, upon overexpression, promotes nuclear dot formation and exon inclusion in Clk1 pre-mRNA; its expression is transcriptionally driven by the E2F1 transcription factor downstream of lncRNA LINC00482, and its elevated levels promote colorectal cancer cell proliferation, migration, and invasion through a Clk-dependent pathway that can be blocked by Clk inhibitors triggering caspase-3/8-mediated apoptosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CLASRP (Clk4-associating SR-related protein) is a nuclear SR-related splicing regulatory protein that links CDC-like kinase (Clk) activity to alternative splicing control [#0]. It was identified as a partner that binds the kinase-inactive Clk4 K189R mutant but not the active wild-type kinase, and its long isoform localizes to nuclear dots where it sequesters Clk4 K189R and drives exon EB inclusion from Clk1 pre-mRNA [#0]. Beyond this kinase association and splicing readout, CLASRP functions within a Clk-dependent pathway promoting cell proliferation, migration, and invasion: in colorectal cancer cells its pro-tumorigenic effects are abolished by Clk inhibitors, which lower CLASRP levels and trigger caspase-3/8-mediated apoptosis [#1]. Its expression is transcriptionally driven through a LINC00482/E2F1 axis, with E2F1 recruited to the CLASRP promoter to enhance expression and confer cisplatin resistance in NSCLC cells [#2]. The biochemical mechanism by which CLASRP itself recognizes RNA or remodels spliceosome assembly has not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established CLASRP as a physical link between the Clk4 kinase and the splicing machinery, defining an isoform-specific nuclear regulator of alternative splicing.\",\n      \"evidence\": \"Yeast two-hybrid and in vitro interaction assays with Clk4 K189R, HA-tagged localization imaging, and Clk1 alternative splicing reporter in cells\",\n      \"pmids\": [\"12169693\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural or domain-level basis for preferential binding to kinase-inactive Clk4 identified\",\n        \"Direct RNA-binding activity of CLASRP and the spliceosomal step it acts on not defined\",\n        \"Whether CLASRP is a Clk substrate or a scaffold left unresolved\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed CLASRP functionally downstream of Clk activity as a driver of tumor cell proliferation, migration, and invasion whose effects depend on Clk signaling.\",\n      \"evidence\": \"Gain- and loss-of-function in colorectal cancer cells, xenograft model, Clk inhibitor treatment, and caspase-3/8 cleavage western blotting\",\n      \"pmids\": [\"37658940\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Specific splicing targets mediating the pro-tumorigenic phenotype not identified\",\n        \"Whether Clk inhibitors act directly on CLASRP-Clk complexes or through broader Clk effects unclear\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined the upstream transcriptional control of CLASRP, showing a LINC00482/E2F1 axis drives its expression and contributes to chemoresistance.\",\n      \"evidence\": \"Dual-luciferase reporter, ChIP, and RIP assays plus knockdown/rescue and xenograft in NSCLC cells with cisplatin sensitivity readout\",\n      \"pmids\": [\"37966662\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which CLASRP confers cisplatin resistance at the molecular level not established\",\n        \"Whether the splicing function of CLASRP underlies its drug-resistance role untested\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intrinsic biochemical activity of CLASRP — how it binds RNA, which spliceosome components it engages, and the splice events it controls genome-wide — remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genome-wide map of CLASRP-regulated splicing events\",\n        \"No reconstitution of CLASRP within a defined splicing reaction\",\n        \"Relationship between Clk binding, nuclear dot formation, and catalytic splicing outcome unresolved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CLK4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}