{"gene":"TG_290310","gene_symbol":"COG1","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"The conserved oligomeric Golgi (COG) complex, which includes COG1, was identified and characterized in T. gondii tachyzoites and shown to be essential for protein transport; the study also identified novel COG complex partners critical for protein trafficking in this parasite.","method":"Genetic characterization, identification of complex components and novel partners (functional/cell biological study in T. gondii tachyzoites)","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — complex identification and functional characterization in a single study; abstract is vague on specific methods but indicates direct experimental work on the COG complex including COG1 in T. gondii","pmids":["37966241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"The COG complex (including COG1) is essential in Toxoplasma gondii tachyzoites, where it functions in Golgi-based protein transport and glycosylation, and associates with novel parasite-specific partners that broaden the trafficking machinery to meet the specific needs of this apicomplexan parasite."},"narrative":{"mechanistic_narrative":"COG1 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, where the complex is essential for Golgi-based protein transport [PMID:37966241]. Characterization of the COG complex in this parasite also identified novel, parasite-specific partners that are critical for protein trafficking, indicating the trafficking machinery is elaborated to meet the specific needs of this apicomplexan [PMID:37966241]. Beyond this identification and functional characterization [PMID:37966241], no further mechanistic detail about COG1 has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"It was unknown whether an intact COG complex operates in Toxoplasma gondii; identifying and characterizing the complex including COG1 established that it is essential for protein transport in tachyzoites and revealed novel parasite-specific trafficking partners.","evidence":"Genetic and cell-biological characterization of COG complex components and partners in T. gondii tachyzoites","pmids":["37966241"],"confidence":"Medium","gaps":["The specific molecular function of the COG1 subunit alone, distinct from the assembled complex, is not defined","The identity and biochemical role of the novel parasite-specific partners are not detailed at the mechanistic level","No structural or interaction map placing COG1 within the complex is provided"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Conserved oligomeric Golgi (COG) complex"],"partners":[],"other_free_text":["COG1 is a subunit of the COG complex, which is essential for protein transport in T. gondii tachyzoites [#0].","Novel parasite-specific COG complex partners critical for protein trafficking were identified in T. gondii [#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":341,"usd":0.006642,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4920,"output_tokens":972,"usd":0.02445,"stage2_stop_reason":"end_turn"},"total_usd":0.06462,"stage1_batch_id":"msgbatch_015xmQKDRqnTh9anE4m7LiD6","stage2_batch_id":"msgbatch_01JLpkFTVhoQBNgqHCKFrVVU","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 COG1, was identified and characterized in T. gondii tachyzoites and shown to be essential for protein transport; the study also identified novel COG complex partners critical for protein trafficking in this parasite.\",\n      \"method\": \"Genetic characterization, identification of complex components and novel partners (functional/cell biological study in T. gondii tachyzoites)\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — complex identification and functional characterization in a single study; abstract is vague on specific methods but indicates direct experimental work on the COG complex including COG1 in T. gondii\",\n      \"pmids\": [\"37966241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"The COG complex (including COG1) is essential in Toxoplasma gondii tachyzoites, where it functions in Golgi-based protein transport and glycosylation, and associates with novel parasite-specific partners that broaden the trafficking machinery to meet the specific needs of this apicomplexan parasite.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"COG1 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, where the complex is essential for Golgi-based protein transport [#0]. Characterization of the COG complex in this parasite also identified novel, parasite-specific partners that are critical for protein trafficking, indicating the trafficking machinery is elaborated to meet the specific needs of this apicomplexan [#0]. Beyond this identification and functional characterization [#0], no further mechanistic detail about COG1 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"It was unknown whether an intact COG complex operates in Toxoplasma gondii; identifying and characterizing the complex including COG1 established that it is essential for protein transport in tachyzoites and revealed novel parasite-specific trafficking partners.\",\n      \"evidence\": \"Genetic and cell-biological characterization of COG complex components and partners in T. gondii tachyzoites\",\n      \"pmids\": [\"37966241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific molecular function of the COG1 subunit alone, distinct from the assembled complex, is not defined\",\n        \"The identity and biochemical role of the novel parasite-specific partners are not detailed at the mechanistic level\",\n        \"No structural or interaction map placing COG1 within the complex is provided\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How COG1 specifically contributes to COG complex assembly, glycosylation, and vesicle tethering in T. gondii, and which trafficking steps depend on it, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No subunit-resolved mechanistic role for COG1 established\",\n        \"No direct binding partners of COG1 characterized\",\n        \"No localization or structural data for COG1 in the corpus\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006886\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"Conserved oligomeric Golgi (COG) complex\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"COG1 is a subunit of the COG complex, which is essential for protein transport in T. gondii tachyzoites [#0].\",\n      \"Novel parasite-specific COG complex partners critical for protein trafficking were identified in T. gondii [#0].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_290310","name":"COG1","product":"conserved oligomeric Golgi complex subunit 1","uniprot_acc":"S8F057","chromosome":"TGME49_chrIX","start_pos":3694917},{"strain":"GT1","gene_id":"TGGT1_290310","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrIX","start_pos":3503340},{"strain":"RH88","gene_id":"TGRH88_014960","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023090","start_pos":3759257},{"strain":"VEG","gene_id":"TGVEG_290310","name":null,"product":"hypothetical protein","uniprot_acc":"V5BEZ4","chromosome":"TGVEG_chrIX","start_pos":3730570}]}