{"gene":"PF3D7_1022400","run_date":"2026-09-08T12:51:28","timeline":{"discoveries":[{"year":2014,"finding":"PF3D7_1022400 (PfSFRS4) is phosphorylated by all four P. falciparum CLK kinases (PfCLK-1–4) on its Arginine/Serine (RS)-rich domain, as demonstrated by in vitro kinase assays using recombinantly expressed RS-domain-containing protein.","method":"In vitro kinase assay with recombinant protein; the RS-rich domain was required for phosphorylation (a peptide lacking the RS domain was not phosphorylated).","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 1 (in vitro kinase assay with domain-deletion control) / Weak — single lab, single study; functional consequence of SRSF4 phosphorylation itself not directly tested beyond substrate identification.","pmids":["25188378"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"PF3D7_1022400 (PfSFRS4) localizes predominantly to the nucleus of asexual blood stage trophozoites, as determined by cellular fractionation/imaging.","method":"Subcellular localization experiment (nuclear/cytoplasmic distribution assessed in blood stage trophozoites).","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single localization method described in abstract without functional link specific to SRSF4.","pmids":["25188378"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1022400 (SRSF4) is a nuclear SR protein in P. falciparum blood stage trophozoites whose RS-rich domain is phosphorylated in vitro by all four parasite CLK kinases (PfCLK-1–4), implicating it in CLK-dependent pre-mRNA processing; no direct functional experiments on SRSF4 itself beyond substrate identification and localization have been reported."},"narrative":{"mechanistic_narrative":"PF3D7_1022400 (SRSF4) is a serine/arginine-rich protein of Plasmodium falciparum implicated in CLK-dependent pre-mRNA processing during the asexual blood stage [PMID:25188378]. Its RS-rich domain is directly phosphorylated in vitro by all four parasite CLK kinases (PfCLK-1 through PfCLK-4), and this phosphorylation strictly requires the RS domain, since a peptide lacking it is not modified [PMID:25188378]. Consistent with a role in nuclear RNA processing, the protein localizes predominantly to the nucleus of asexual blood stage trophozoites [PMID:25188378]. Beyond identification as a CLK substrate and this nuclear localization, no direct functional experiments on SRSF4 itself have been characterized in the available corpus.","teleology":[{"year":2014,"claim":"To connect P. falciparum CLK kinases to a specific downstream substrate, it was shown that SRSF4's RS-rich domain is phosphorylated by all four PfCLKs, establishing SRSF4 as a physiological candidate effector of CLK signaling in the parasite.","evidence":"In vitro kinase assay with recombinant RS-domain-containing protein, with a domain-deletion peptide as negative control","pmids":["25188378"],"confidence":"Medium","gaps":["Functional consequence of SRSF4 phosphorylation on splicing activity not tested","Which specific residues within the RS domain are phosphorylated not mapped","Whether each PfCLK acts on SRSF4 in vivo, or with distinct specificity, not resolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"claim":"To place SRSF4 in a cellular compartment consistent with a splicing role, subcellular fractionation/imaging showed it is predominantly nuclear in blood stage trophozoites.","evidence":"Subcellular localization assay in asexual blood stage trophozoites","pmids":["25188378"],"confidence":"Low","gaps":["Single localization method reported without a functional link specific to SRSF4","Nuclear sub-compartment (e.g. speckle-like association) not defined","Whether localization changes with phosphorylation state or across stages not tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether SRSF4 directly regulates pre-mRNA splicing, its target transcripts, and its requirement for parasite viability or development remain unknown.","evidence":"No direct functional or loss-of-function experiments on SRSF4 reported in the corpus","pmids":[],"confidence":"Low","gaps":["No RNA targets or splicing activity demonstrated for SRSF4","No genetic knockout/knockdown phenotype established","No structural or interaction data beyond CLK phosphorylation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFCLK-1 (PFSRPK, KINASE ACTING ON SRSF4)","PFCLK-2","PFCLK-3","PFCLK-4"],"other_free_text":["SRSF4's RS-rich domain is the substrate module phosphorylated by all four P. falciparum CLK kinases in vitro; deletion of the RS domain abolishes phosphorylation [#0].","Nuclear localization in asexual blood stage trophozoites is the only cellular-context evidence for SRSF4 itself [#1].","No direct RNA-target, splicing-activity, or loss-of-function data for SRSF4 are present in the corpus."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"25188378","id":"PMC_25188378","title":"Inhibition of the SR protein-phosphorylating CLK kinases of Plasmodium falciparum impairs blood stage replication and malaria transmission.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25188378","citation_count":32,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3554,"output_tokens":620,"usd":0.009981,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5205,"output_tokens":1508,"usd":0.031863,"stage2_stop_reason":"end_turn"},"total_usd":0.041844,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"PF3D7_1022400 (PfSFRS4) is phosphorylated by all four P. falciparum CLK kinases (PfCLK-1–4) on its Arginine/Serine (RS)-rich domain, as demonstrated by in vitro kinase assays using recombinantly expressed RS-domain-containing protein.\",\n      \"method\": \"In vitro kinase assay with recombinant protein; the RS-rich domain was required for phosphorylation (a peptide lacking the RS domain was not phosphorylated).\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 (in vitro kinase assay with domain-deletion control) / Weak — single lab, single study; functional consequence of SRSF4 phosphorylation itself not directly tested beyond substrate identification.\",\n      \"pmids\": [\"25188378\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PF3D7_1022400 (PfSFRS4) localizes predominantly to the nucleus of asexual blood stage trophozoites, as determined by cellular fractionation/imaging.\",\n      \"method\": \"Subcellular localization experiment (nuclear/cytoplasmic distribution assessed in blood stage trophozoites).\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single localization method described in abstract without functional link specific to SRSF4.\",\n      \"pmids\": [\"25188378\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_1022400 (SRSF4) is a nuclear SR protein in P. falciparum blood stage trophozoites whose RS-rich domain is phosphorylated in vitro by all four parasite CLK kinases (PfCLK-1–4), implicating it in CLK-dependent pre-mRNA processing; no direct functional experiments on SRSF4 itself beyond substrate identification and localization have been reported.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1022400 (SRSF4) is a serine/arginine-rich protein of Plasmodium falciparum implicated in CLK-dependent pre-mRNA processing during the asexual blood stage [#0]. Its RS-rich domain is directly phosphorylated in vitro by all four parasite CLK kinases (PfCLK-1 through PfCLK-4), and this phosphorylation strictly requires the RS domain, since a peptide lacking it is not modified [#0]. Consistent with a role in nuclear RNA processing, the protein localizes predominantly to the nucleus of asexual blood stage trophozoites [#1]. Beyond identification as a CLK substrate and this nuclear localization, no direct functional experiments on SRSF4 itself have been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"To connect P. falciparum CLK kinases to a specific downstream substrate, it was shown that SRSF4's RS-rich domain is phosphorylated by all four PfCLKs, establishing SRSF4 as a physiological candidate effector of CLK signaling in the parasite.\",\n      \"evidence\": \"In vitro kinase assay with recombinant RS-domain-containing protein, with a domain-deletion peptide as negative control\",\n      \"pmids\": [\"25188378\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of SRSF4 phosphorylation on splicing activity not tested\",\n        \"Which specific residues within the RS domain are phosphorylated not mapped\",\n        \"Whether each PfCLK acts on SRSF4 in vivo, or with distinct specificity, not resolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"To place SRSF4 in a cellular compartment consistent with a splicing role, subcellular fractionation/imaging showed it is predominantly nuclear in blood stage trophozoites.\",\n      \"evidence\": \"Subcellular localization assay in asexual blood stage trophozoites\",\n      \"pmids\": [\"25188378\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single localization method reported without a functional link specific to SRSF4\",\n        \"Nuclear sub-compartment (e.g. speckle-like association) not defined\",\n        \"Whether localization changes with phosphorylation state or across stages not tested\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether SRSF4 directly regulates pre-mRNA splicing, its target transcripts, and its requirement for parasite viability or development remain unknown.\",\n      \"evidence\": \"No direct functional or loss-of-function experiments on SRSF4 reported in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No RNA targets or splicing activity demonstrated for SRSF4\",\n        \"No genetic knockout/knockdown phenotype established\",\n        \"No structural or interaction data beyond CLK phosphorylation\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006397\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PfCLK-1 (PfSRPK, kinase acting on SRSF4)\", \"PfCLK-2\", \"PfCLK-3\", \"PfCLK-4\"],\n    \"other_free_text\": [\n      \"SRSF4's RS-rich domain is the substrate module phosphorylated by all four P. falciparum CLK kinases in vitro; deletion of the RS domain abolishes phosphorylation [#0].\",\n      \"Nuclear localization in asexual blood stage trophozoites is the only cellular-context evidence for SRSF4 itself [#1].\",\n      \"No direct RNA-target, splicing-activity, or loss-of-function data for SRSF4 are present in the corpus.\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_1022400","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 1 of 1 cited papers name other catalogue genes (PF3D7_0503300, PF3D7_1321700). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1022400","name":null,"product":"serine/arginine-rich splicing factor 4","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0506600","name":null,"product":"serine/arginine-rich splicing factor 4, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0606700","name":null,"product":"serine/arginine-rich splicing factor 4, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"SRSF4","evaluation":null}