{"gene":"TG_212150","gene_symbol":"COG4","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"The conserved oligomeric Golgi (COG) complex, which includes COG4, was identified and characterized in T. gondii tachyzoites; the COG complex is essential for protein transport and Golgi function, and novel COG partners critical for protein transport were identified in T. gondii.","method":"Identification and functional characterization of the COG complex and its partners (likely including co-immunoprecipitation, loss-of-function, and subcellular localization assays based on the study scope described)","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab study characterizing the complex with functional readouts, but abstract does not detail specific orthogonal methods used for COG4 specifically","pmids":["37966241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"In Toxoplasma gondii tachyzoites, COG4 is a subunit of the conserved oligomeric Golgi (COG) complex, which is essential for protein transport and Golgi function, and associates with novel parasite-specific partners that accommodate the specific trafficking needs of T. gondii."},"narrative":{"mechanistic_narrative":"In Toxoplasma gondii tachyzoites, COG4 is a subunit of the conserved oligomeric Golgi (COG) complex, which is essential for protein transport and Golgi function [PMID:37966241]. The COG complex in T. gondii associates with novel parasite-specific partners critical for protein transport [PMID:37966241]. Beyond this identification and functional characterization of the COG complex, nothing further is known about COG4 in the available corpus.","teleology":[{"year":2023,"claim":"Whether T. gondii possesses a functional COG complex and what role it plays was unknown; identifying and characterizing the complex established that COG4 is a subunit of a COG complex essential for Golgi function and protein transport in the parasite.","evidence":"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites (co-immunoprecipitation, loss-of-function, and subcellular localization assays)","pmids":["37966241"],"confidence":"Medium","gaps":["The specific molecular activity of COG4 within the complex is not defined","The identity of the novel parasite-specific COG partners and how they bind COG4 is not detailed","Direct orthogonal validation of COG4's role independent of the complex is not established"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["conserved oligomeric Golgi (COG) complex"],"partners":["NOVEL T. GONDII-SPECIFIC COG COMPLEX PARTNERS"],"other_free_text":[]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"37966241","id":"PMC_37966241","title":"Essential role of the conserved oligomeric Golgi complex in Toxoplasma gondii.","date":"2023","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/37966241","citation_count":7,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2723,"output_tokens":361,"usd":0.006792,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4952,"output_tokens":1066,"usd":0.025705,"stage2_stop_reason":"end_turn"},"total_usd":0.066219,"stage1_batch_id":"msgbatch_01WokvBYTB6JLnYrpD4rXnyV","stage2_batch_id":"msgbatch_01M7hsQDvz6AqVC9DLVjQzzc","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"re-read with subject anchor"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"The conserved oligomeric Golgi (COG) complex, which includes COG4, was identified and characterized in T. gondii tachyzoites; the COG complex is essential for protein transport and Golgi function, and novel COG partners critical for protein transport were identified in T. gondii.\",\n      \"method\": \"Identification and functional characterization of the COG complex and its partners (likely including co-immunoprecipitation, loss-of-function, and subcellular localization assays based on the study scope described)\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab study characterizing the complex with functional readouts, but abstract does not detail specific orthogonal methods used for COG4 specifically\",\n      \"pmids\": [\"37966241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"In Toxoplasma gondii tachyzoites, COG4 is a subunit of the conserved oligomeric Golgi (COG) complex, which is essential for protein transport and Golgi function, and associates with novel parasite-specific partners that accommodate the specific trafficking needs of T. gondii.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"In Toxoplasma gondii tachyzoites, COG4 is a subunit of the conserved oligomeric Golgi (COG) complex, which is essential for protein transport and Golgi function [#0]. The COG complex in T. gondii associates with novel parasite-specific partners critical for protein transport [#0]. Beyond this identification and functional characterization of the COG complex, nothing further is known about COG4 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether T. gondii possesses a functional COG complex and what role it plays was unknown; identifying and characterizing the complex established that COG4 is a subunit of a COG complex essential for Golgi function and protein transport in the parasite.\",\n      \"evidence\": \"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites (co-immunoprecipitation, loss-of-function, and subcellular localization assays)\",\n      \"pmids\": [\n        \"37966241\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific molecular activity of COG4 within the complex is not defined\",\n        \"The identity of the novel parasite-specific COG partners and how they bind COG4 is not detailed\",\n        \"Direct orthogonal validation of COG4's role independent of the complex is not established\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular function of COG4, its binding interface with novel T. gondii-specific partners, and its individual contribution to protein transport remain uncharacterized.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of COG4 or its complex integration\",\n        \"No defined trafficking cargo dependent specifically on COG4\",\n        \"No strain-comparative analysis of COG4 function\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0005794\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0015031\",\n        \"supporting_discovery_ids\": [0],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"conserved oligomeric Golgi (COG) complex\"\n    ],\n    \"partners\": [\n      \"novel T. gondii-specific COG complex partners\"\n    ],\n    \"other_free_text\": []\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_212150","name":"COG4","product":"conserved oligomeric Golgi complex subunit 4","uniprot_acc":"S8G5D3","chromosome":"TGME49_chrX","start_pos":4006986},{"strain":"GT1","gene_id":"TGGT1_212150","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrX","start_pos":3912877},{"strain":"RH88","gene_id":"TGRH88_042900","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023091","start_pos":3530971},{"strain":"VEG","gene_id":"TGVEG_212150","name":null,"product":"COG4 transport protein","uniprot_acc":"V4YVZ3","chromosome":"TGVEG_chrX","start_pos":3917975}]}