{"gene":"TG_306410","gene_symbol":"COG3","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"The conserved oligomeric Golgi (COG) complex, which includes COG3, was identified and characterized in T. gondii tachyzoites, where it plays an essential role in protein transport and Golgi function; novel partners of the COG complex critical for protein transport were also identified.","method":"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites (study implies loss-of-function and interaction experiments based on identification and characterization language)","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab characterization study with implied functional and interaction data, but abstract does not specify orthogonal methods used for COG3 specifically","pmids":["37966241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"The conserved oligomeric Golgi (COG) complex, including COG3, is essential in T. gondii tachyzoites for Golgi-mediated protein transport and glycosylation, and associates with novel parasite-specific partners that accommodate the trafficking needs of this apicomplexan parasite."},"narrative":{"mechanistic_narrative":"COG3 is a subunit of the conserved oligomeric Golgi (COG) complex, which in Toxoplasma gondii tachyzoites is essential for Golgi function and Golgi-mediated protein transport [PMID:37966241]. The COG complex in this parasite associates with novel, parasite-specific partners that are themselves critical for protein transport [PMID:37966241]. Beyond this identification and functional characterization of the COG complex, no further mechanistic detail specific to COG3 has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"Whether an intact COG complex operates in an apicomplexan parasite was unknown; identifying and characterizing the COG complex in T. gondii established that COG3 is part of a functional complex essential for Golgi-mediated protein transport.","evidence":"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites","pmids":["37966241"],"confidence":"Medium","gaps":["The specific contribution of COG3 individually, versus the complex as a whole, is not resolved","The identity of the novel COG partners and how they bind COG3 is not specified","No structural or biochemical detail of COG3 assembly into the complex is provided"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Conserved oligomeric Golgi (COG) complex"],"partners":["NOVEL PARASITE-SPECIFIC COG COMPLEX PARTNERS (IDENTITY NOT SPECIFIED) [#0]"],"other_free_text":["COG3 is essential for Golgi function and protein transport in T. gondii tachyzoites [#0]."]},"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":351,"usd":0.006717,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4938,"output_tokens":1032,"usd":0.025245,"stage2_stop_reason":"end_turn"},"total_usd":0.065544,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","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 COG3, was identified and characterized in T. gondii tachyzoites, where it plays an essential role in protein transport and Golgi function; novel partners of the COG complex critical for protein transport were also identified.\",\n      \"method\": \"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites (study implies loss-of-function and interaction experiments based on identification and characterization language)\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab characterization study with implied functional and interaction data, but abstract does not specify orthogonal methods used for COG3 specifically\",\n      \"pmids\": [\"37966241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"The conserved oligomeric Golgi (COG) complex, including COG3, is essential in T. gondii tachyzoites for Golgi-mediated protein transport and glycosylation, and associates with novel parasite-specific partners that accommodate the trafficking needs of this apicomplexan parasite.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"COG3 is a subunit of the conserved oligomeric Golgi (COG) complex, which in Toxoplasma gondii tachyzoites is essential for Golgi function and Golgi-mediated protein transport [#0]. The COG complex in this parasite associates with novel, parasite-specific partners that are themselves critical for protein transport [#0]. Beyond this identification and functional characterization of the COG complex, no further mechanistic detail specific to COG3 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether an intact COG complex operates in an apicomplexan parasite was unknown; identifying and characterizing the COG complex in T. gondii established that COG3 is part of a functional complex essential for Golgi-mediated protein transport.\",\n      \"evidence\": \"Identification and functional characterization of the COG complex and its partners in T. gondii tachyzoites\",\n      \"pmids\": [\"37966241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific contribution of COG3 individually, versus the complex as a whole, is not resolved\",\n        \"The identity of the novel COG partners and how they bind COG3 is not specified\",\n        \"No structural or biochemical detail of COG3 assembly into the complex is provided\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular activity, substrates, and direct binding interfaces of COG3 within the parasite COG complex remain undefined.\",\n      \"evidence\": \"No further discoveries in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct binding partners of COG3 specifically identified\",\n        \"No structural model of COG3 in the T. gondii COG complex\",\n        \"Glycosylation or cargo substrates dependent on COG3 not defined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006888\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"Conserved oligomeric Golgi (COG) complex\"],\n    \"partners\": [\"Novel parasite-specific COG complex partners (identity not specified) [#0]\"],\n    \"other_free_text\": [\n      \"COG3 is essential for Golgi function and protein transport in T. gondii tachyzoites [#0].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_306410","name":"COG3","product":"conserved oligomeric Golgi complex subunit 3","uniprot_acc":"A0A125YMH1","chromosome":"TGME49_chrIX","start_pos":6060077},{"strain":"GT1","gene_id":"TGGT1_306410","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrIX","start_pos":5840099},{"strain":"RH88","gene_id":"TGRH88_017870","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023090","start_pos":6183658},{"strain":"VEG","gene_id":"TGVEG_306410","name":null,"product":"Sec34-like family protein","uniprot_acc":"B6KRD0","chromosome":"TGVEG_chrIX","start_pos":6099589}]}