{"gene":"PF3D7_0606500","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2023,"finding":"PTB (PF3D7_0606500) was identified as a component of the PfPRMT5-associated protein complex in P. falciparum, co-purifying in immunoprecipitation experiments as a regulator of alternative splicing associated with the RNA splicing machinery.","method":"Co-immunoprecipitation / interactome mass spectrometry (cytosolic and nuclear IPs of PfPRMT5)","journal":"Communications biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS experiment identifying PTB as one of many co-purifying proteins; no functional follow-up on PTB itself","pmids":["37349497"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"finding":"PF3D7_0606500 is annotated as the single PTB orthologue in P. falciparum (with TGME49_090660 as its T. gondii counterpart), identified by phylogenetic/bioinformatic analysis; no functional studies on the Plasmodium PTB orthologue had been published as of this review.","method":"Phylogenetic analysis and bioinformatic annotation","journal":"mBio","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational/phylogenetic identification only, no experimental functional characterization of the Plasmodium protein","pmids":["30782661"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0606500 (PTB) is bioinformatically identified as the sole polypyrimidine tract-binding protein orthologue in P. falciparum and has been detected as a component of the PfPRMT5-associated RNA splicing machinery by co-immunoprecipitation, but no direct functional or mechanistic characterization of this protein itself has been reported."},"narrative":{"mechanistic_narrative":"PF3D7_0606500 (PTB) is annotated by phylogenetic and bioinformatic analysis as the single polypyrimidine tract-binding protein orthologue in Plasmodium falciparum [PMID:30782661]. The only experimental evidence linking it to a cellular process is its co-purification with the PfPRMT5-associated protein complex, placing it within the RNA splicing machinery implicated in alternative splicing regulation [PMID:37349497]. Beyond this complex membership, no direct functional or mechanistic characterization of PF3D7_0606500 itself — its RNA targets, splicing activity, localization, or phenotype — has been reported in the available corpus.","teleology":[{"year":2019,"claim":"Establishing whether P. falciparum encodes a PTB orthologue was the first step toward asking whether polypyrimidine-tract-based splicing regulation operates in the parasite; bioinformatics identified PF3D7_0606500 as the sole such orthologue.","evidence":"Phylogenetic analysis and bioinformatic annotation, with TGME49_090660 identified as the T. gondii counterpart","pmids":["30782661"],"confidence":"Low","gaps":["Computational identification only; no experimental confirmation of PTB activity in Plasmodium","No RNA-binding or splicing function demonstrated for the parasite protein","No expression, localization, or essentiality data"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"The question of whether PF3D7_0606500 physically associates with splicing machinery was addressed by finding it among proteins co-purifying with PfPRMT5, placing it in a complex regulating alternative splicing.","evidence":"Co-immunoprecipitation / interactome mass spectrometry of cytosolic and nuclear PfPRMT5 pulldowns","pmids":["37349497"],"confidence":"Low","gaps":["Single Co-IP/MS experiment identifying PTB as one of many co-purifying proteins, with no reciprocal validation or functional follow-up on PTB itself","Direct RNA targets and splicing role of PF3D7_0606500 not defined","Whether the association is direct or bridged by other complex members is unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The intrinsic molecular function of PF3D7_0606500 — its RNA-binding specificity, splicing substrates, subcellular localization, and requirement for parasite viability — remains uncharacterized.","evidence":"No direct functional study of the protein exists in the corpus","pmids":[],"confidence":"Low","gaps":["No demonstrated polypyrimidine-tract or RNA binding by the Plasmodium protein","No identified splicing targets or regulatory outcomes","No knockout, knockdown, or phenotypic data"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PfPRMT5-associated protein complex / RNA splicing machinery [#0]"],"partners":["PFPRMT5 (CO-PURIFYING COMPLEX, NOT SHOWN TO BE A DIRECT INTERACTION) [#0]"],"other_free_text":["Annotated as the single PTB (polypyrimidine tract-binding protein) orthologue in P. falciparum by phylogenetic analysis [#1].","No direct functional or mechanistic characterization of PF3D7_0606500 itself has been reported; its role is defined only by membership in the PfPRMT5-associated complex."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"26525978","id":"PMC_26525978","title":"A bioinformatic survey of RNA-binding proteins in Plasmodium.","date":"2015","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/26525978","citation_count":62,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"37349497","id":"","title":"A type II protein arginine methyltransferase regulates merozoite invasion in Plasmodium falciparum.","date":"2023","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/37349497","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PTB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"30782661","id":"","title":"Alternative Splicing in Apicomplexan Parasites.","date":"2019","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/30782661","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PTB"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5978,"output_tokens":588,"usd":0.013377,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5152,"output_tokens":1446,"usd":0.030955,"stage2_stop_reason":"end_turn"},"total_usd":0.044332,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"PTB (PF3D7_0606500) was identified as a component of the PfPRMT5-associated protein complex in P. falciparum, co-purifying in immunoprecipitation experiments as a regulator of alternative splicing associated with the RNA splicing machinery.\",\n      \"method\": \"Co-immunoprecipitation / interactome mass spectrometry (cytosolic and nuclear IPs of PfPRMT5)\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS experiment identifying PTB as one of many co-purifying proteins; no functional follow-up on PTB itself\",\n      \"pmids\": [\"37349497\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PF3D7_0606500 is annotated as the single PTB orthologue in P. falciparum (with TGME49_090660 as its T. gondii counterpart), identified by phylogenetic/bioinformatic analysis; no functional studies on the Plasmodium PTB orthologue had been published as of this review.\",\n      \"method\": \"Phylogenetic analysis and bioinformatic annotation\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational/phylogenetic identification only, no experimental functional characterization of the Plasmodium protein\",\n      \"pmids\": [\"30782661\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0606500 (PTB) is bioinformatically identified as the sole polypyrimidine tract-binding protein orthologue in P. falciparum and has been detected as a component of the PfPRMT5-associated RNA splicing machinery by co-immunoprecipitation, but no direct functional or mechanistic characterization of this protein itself has been reported.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0606500 (PTB) is annotated by phylogenetic and bioinformatic analysis as the single polypyrimidine tract-binding protein orthologue in Plasmodium falciparum [#1]. The only experimental evidence linking it to a cellular process is its co-purification with the PfPRMT5-associated protein complex, placing it within the RNA splicing machinery implicated in alternative splicing regulation [#0]. Beyond this complex membership, no direct functional or mechanistic characterization of PF3D7_0606500 itself — its RNA targets, splicing activity, localization, or phenotype — has been reported in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Establishing whether P. falciparum encodes a PTB orthologue was the first step toward asking whether polypyrimidine-tract-based splicing regulation operates in the parasite; bioinformatics identified PF3D7_0606500 as the sole such orthologue.\",\n      \"evidence\": \"Phylogenetic analysis and bioinformatic annotation, with TGME49_090660 identified as the T. gondii counterpart\",\n      \"pmids\": [\"30782661\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Computational identification only; no experimental confirmation of PTB activity in Plasmodium\",\n        \"No RNA-binding or splicing function demonstrated for the parasite protein\",\n        \"No expression, localization, or essentiality data\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The question of whether PF3D7_0606500 physically associates with splicing machinery was addressed by finding it among proteins co-purifying with PfPRMT5, placing it in a complex regulating alternative splicing.\",\n      \"evidence\": \"Co-immunoprecipitation / interactome mass spectrometry of cytosolic and nuclear PfPRMT5 pulldowns\",\n      \"pmids\": [\"37349497\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single Co-IP/MS experiment identifying PTB as one of many co-purifying proteins, with no reciprocal validation or functional follow-up on PTB itself\",\n        \"Direct RNA targets and splicing role of PF3D7_0606500 not defined\",\n        \"Whether the association is direct or bridged by other complex members is unknown\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intrinsic molecular function of PF3D7_0606500 — its RNA-binding specificity, splicing substrates, subcellular localization, and requirement for parasite viability — remains uncharacterized.\",\n      \"evidence\": \"No direct functional study of the protein exists in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No demonstrated polypyrimidine-tract or RNA binding by the Plasmodium protein\",\n        \"No identified splicing targets or regulatory outcomes\",\n        \"No knockout, knockdown, or phenotypic data\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0000398\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"PfPRMT5-associated protein complex / RNA splicing machinery [#0]\"],\n    \"partners\": [\"PfPRMT5 (co-purifying complex, not shown to be a direct interaction) [#0]\"],\n    \"other_free_text\": [\n      \"Annotated as the single PTB (polypyrimidine tract-binding protein) orthologue in P. falciparum by phylogenetic analysis [#1].\",\n      \"No direct functional or mechanistic characterization of PF3D7_0606500 itself has been reported; its role is defined only by membership in the PfPRMT5-associated complex.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0606500","name":null,"product":"polypyrimidine tract-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0105200","name":null,"product":"polypyrimidine tract-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1143700","name":null,"product":"polypyrimidine tract-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"PTB","evaluation":null}