{"gene":"PF3D7_1119800","run_date":"2026-09-08T12:51:28","timeline":{"discoveries":[{"year":2011,"finding":"PfASF-1 (PF3D7_1119800), the plasmodial alternative splicing factor, is phosphorylated in vitro by the cyclin-dependent kinase-like kinases PfCLK-1 (Lammer kinase homolog) and PfCLK-2, establishing these two nuclear CLKs as upstream kinases (writers) for PfASF-1.","method":"In vitro kinase assay using recombinant PfCLK-1 and PfCLK-2 with PfASF-1 as substrate","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 1 (in vitro kinase assay) / Weak — single lab, single method, no mutagenesis or site mapping of phosphorylation on PfASF-1 reported in abstract","pmids":["21312235"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1119800 (PfASF-1) is a nuclear alternative splicing factor in P. falciparum that serves as a substrate for phosphorylation by the CLK-family kinases PfCLK-1 and PfCLK-2, suggesting its activity is regulated post-translationally as part of a mRNA splicing regulatory pathway in blood-stage parasites."},"narrative":{"mechanistic_narrative":"PF3D7_1119800 (PfASF-1) is annotated as a plasmodial alternative splicing factor in Plasmodium falciparum, and the available corpus characterizes it primarily as a phosphorylation substrate within a nuclear splicing regulatory pathway [PMID:21312235]. In vitro, recombinant PfASF-1 is phosphorylated by the cyclin-dependent kinase-like kinases PfCLK-1 (a Lammer kinase homolog) and PfCLK-2, establishing these two nuclear CLKs as upstream kinases for PfASF-1 and implying that its activity is regulated post-translationally [PMID:21312235]. Beyond this kinase-substrate relationship, no direct RNA targets, splicing activity, phosphorylation sites, interaction partners, or cellular phenotypes have been characterized for PF3D7_1119800 in the available corpus.","teleology":[{"year":2011,"claim":"To determine whether the alternative splicing factor PfASF-1 is subject to post-translational control, this work asked which kinases act on it and showed that the nuclear CLK-family kinases PfCLK-1 and PfCLK-2 phosphorylate it in vitro, placing PfASF-1 downstream of CLK signaling in a putative splicing regulatory pathway.","evidence":"In vitro kinase assay with recombinant PfCLK-1 and PfCLK-2 using PfASF-1 as substrate","pmids":["21312235"],"confidence":"Medium","gaps":["Phosphorylation sites on PfASF-1 were not mapped by mutagenesis","Functional consequence of phosphorylation for splicing activity is not established","Interaction and phosphorylation shown in vitro only, not confirmed in the parasite"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown what RNA targets PfASF-1 acts on, whether it participates in a defined spliceosomal complex, and what phenotype results from disrupting it or its phosphorylation in blood-stage parasites.","evidence":"No direct experimental evidence in the available corpus","pmids":[],"confidence":"Low","gaps":["No splicing substrate or RNA target identified for PfASF-1","No stable interaction partners or complex membership established","No genetic knockout or knockdown phenotype reported"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFCLK-1 (UPSTREAM KINASE, IN VITRO) [#0]","PFCLK-2 (UPSTREAM KINASE, IN VITRO) [#0]"],"other_free_text":["PF3D7_1119800 (PfASF-1) is annotated as a plasmodial alternative splicing factor and is characterized in the available corpus only as an in vitro phosphorylation substrate of the nuclear CLK kinases PfCLK-1 and PfCLK-2 [#0].","No phosphorylation sites, RNA targets, splicing activity, or loss-of-function phenotype have been characterized for this gene in the available corpus."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"21312235","id":"PMC_21312235","title":"Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor.","date":"2011","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21312235","citation_count":38,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfASF"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3439,"output_tokens":412,"usd":0.008249,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4840,"output_tokens":1276,"usd":0.02805,"stage2_stop_reason":"end_turn"},"total_usd":0.036299,"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\": 2011,\n      \"finding\": \"PfASF-1 (PF3D7_1119800), the plasmodial alternative splicing factor, is phosphorylated in vitro by the cyclin-dependent kinase-like kinases PfCLK-1 (Lammer kinase homolog) and PfCLK-2, establishing these two nuclear CLKs as upstream kinases (writers) for PfASF-1.\",\n      \"method\": \"In vitro kinase assay using recombinant PfCLK-1 and PfCLK-2 with PfASF-1 as substrate\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 (in vitro kinase assay) / Weak — single lab, single method, no mutagenesis or site mapping of phosphorylation on PfASF-1 reported in abstract\",\n      \"pmids\": [\"21312235\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_1119800 (PfASF-1) is a nuclear alternative splicing factor in P. falciparum that serves as a substrate for phosphorylation by the CLK-family kinases PfCLK-1 and PfCLK-2, suggesting its activity is regulated post-translationally as part of a mRNA splicing regulatory pathway in blood-stage parasites.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1119800 (PfASF-1) is annotated as a plasmodial alternative splicing factor in Plasmodium falciparum, and the available corpus characterizes it primarily as a phosphorylation substrate within a nuclear splicing regulatory pathway [#0]. In vitro, recombinant PfASF-1 is phosphorylated by the cyclin-dependent kinase-like kinases PfCLK-1 (a Lammer kinase homolog) and PfCLK-2, establishing these two nuclear CLKs as upstream kinases for PfASF-1 and implying that its activity is regulated post-translationally [#0]. Beyond this kinase-substrate relationship, no direct RNA targets, splicing activity, phosphorylation sites, interaction partners, or cellular phenotypes have been characterized for PF3D7_1119800 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"To determine whether the alternative splicing factor PfASF-1 is subject to post-translational control, this work asked which kinases act on it and showed that the nuclear CLK-family kinases PfCLK-1 and PfCLK-2 phosphorylate it in vitro, placing PfASF-1 downstream of CLK signaling in a putative splicing regulatory pathway.\",\n      \"evidence\": \"In vitro kinase assay with recombinant PfCLK-1 and PfCLK-2 using PfASF-1 as substrate\",\n      \"pmids\": [\"21312235\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Phosphorylation sites on PfASF-1 were not mapped by mutagenesis\",\n        \"Functional consequence of phosphorylation for splicing activity is not established\",\n        \"Interaction and phosphorylation shown in vitro only, not confirmed in the parasite\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown what RNA targets PfASF-1 acts on, whether it participates in a defined spliceosomal complex, and what phenotype results from disrupting it or its phosphorylation in blood-stage parasites.\",\n      \"evidence\": \"No direct experimental evidence in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No splicing substrate or RNA target identified for PfASF-1\",\n        \"No stable interaction partners or complex membership established\",\n        \"No genetic knockout or knockdown phenotype reported\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008022\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008380\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PfCLK-1 (upstream kinase, in vitro) [#0]\",\n      \"PfCLK-2 (upstream kinase, in vitro) [#0]\"\n    ],\n    \"other_free_text\": [\n      \"PF3D7_1119800 (PfASF-1) is annotated as a plasmodial alternative splicing factor and is characterized in the available corpus only as an in vitro phosphorylation substrate of the nuclear CLK kinases PfCLK-1 and PfCLK-2 [#0].\",\n      \"No phosphorylation sites, RNA targets, splicing activity, or loss-of-function phenotype have been characterized for this gene in the available corpus.\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_1119800","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_1224500, PF3D7_1445400). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1119800","name":null,"product":"alternative splicing factor ASF-1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0917500","name":null,"product":"alternative splicing factor ASF-1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}