{"gene":"TG_242030","gene_symbol":"COG7","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2023,"finding":"The conserved oligomeric Golgi (COG) complex, which includes COG7, was identified and characterized in T. gondii tachyzoites and shown to be essential for protein transport; the study also identified novel COG partners critical for trafficking in this parasite.","method":"Genetic characterization and functional studies in T. gondii tachyzoites (loss-of-function with phenotypic readout in protein transport)","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, single study with functional characterization of the COG complex including COG7, but abstract does not detail orthogonal methods specific to COG7 alone","pmids":["37966241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"COG7 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, where the complex plays an essential role in Golgi-mediated protein transport and glycosylation, with T. gondii appearing to have broadened the roles of conserved COG elements and evolved novel interacting partners to meet parasite-specific trafficking needs."},"narrative":{"mechanistic_narrative":"COG7 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, where the complex is essential for Golgi-mediated protein transport [PMID:37966241]. Characterization of the COG complex in this parasite, which includes COG7, additionally identified novel COG-interacting partners critical for trafficking, indicating that T. gondii has broadened the roles of conserved COG elements to meet parasite-specific trafficking needs [PMID:37966241]. Beyond this identification and functional requirement in protein transport, no further mechanistic detail specific to COG7 has been characterized in the available corpus.","teleology":[{"year":2023,"claim":"Whether a conserved oligomeric Golgi complex exists and functions in an apicomplexan parasite was unresolved; identifying COG7 as part of an essential COG complex established that Golgi-mediated protein transport in T. gondii depends on this machinery and involves parasite-specific partners.","evidence":"Genetic characterization and loss-of-function functional studies with protein-transport phenotypic readouts in T. gondii tachyzoites","pmids":["37966241"],"confidence":"Medium","gaps":["No orthogonal method specific to COG7 alone (e.g. its individual contribution versus the intact complex) is reported","The identity and molecular action of the novel COG partners are not detailed at the level of COG7","No structural, biochemical, or subcellular localization data for COG7 are provided"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["conserved oligomeric Golgi (COG) complex"],"partners":[],"other_free_text":["COG7 is essential for protein transport in T. gondii tachyzoites [#0]","The COG complex in T. gondii associates with novel parasite-specific interacting partners critical for trafficking [#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":348,"usd":0.006694,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4924,"output_tokens":1037,"usd":0.025272,"stage2_stop_reason":"end_turn"},"total_usd":0.0664,"stage1_batch_id":"msgbatch_01TEPNZ4MCzJ7xtsNwosiDRk","stage2_batch_id":"msgbatch_01FQShM7n1sfCr4pWTDShmki","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 COG7, was identified and characterized in T. gondii tachyzoites and shown to be essential for protein transport; the study also identified novel COG partners critical for trafficking in this parasite.\",\n      \"method\": \"Genetic characterization and functional studies in T. gondii tachyzoites (loss-of-function with phenotypic readout in protein transport)\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, single study with functional characterization of the COG complex including COG7, but abstract does not detail orthogonal methods specific to COG7 alone\",\n      \"pmids\": [\"37966241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"COG7 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, where the complex plays an essential role in Golgi-mediated protein transport and glycosylation, with T. gondii appearing to have broadened the roles of conserved COG elements and evolved novel interacting partners to meet parasite-specific trafficking needs.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"COG7 is a subunit of the conserved oligomeric Golgi (COG) complex in Toxoplasma gondii tachyzoites, where the complex is essential for Golgi-mediated protein transport [#0]. Characterization of the COG complex in this parasite, which includes COG7, additionally identified novel COG-interacting partners critical for trafficking, indicating that T. gondii has broadened the roles of conserved COG elements to meet parasite-specific trafficking needs [#0]. Beyond this identification and functional requirement in protein transport, no further mechanistic detail specific to COG7 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether a conserved oligomeric Golgi complex exists and functions in an apicomplexan parasite was unresolved; identifying COG7 as part of an essential COG complex established that Golgi-mediated protein transport in T. gondii depends on this machinery and involves parasite-specific partners.\",\n      \"evidence\": \"Genetic characterization and loss-of-function functional studies with protein-transport phenotypic readouts in T. gondii tachyzoites\",\n      \"pmids\": [\n        \"37966241\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No orthogonal method specific to COG7 alone (e.g. its individual contribution versus the intact complex) is reported\",\n        \"The identity and molecular action of the novel COG partners are not detailed at the level of COG7\",\n        \"No structural, biochemical, or subcellular localization data for COG7 are provided\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How COG7 individually contributes to COG complex assembly, its direct binding partners, and its role in specific glycosylation or trafficking steps remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct interaction map for COG7 established\",\n        \"No substrate or cargo specificity assigned to COG7\",\n        \"No structural model or subcellular localization determined for COG7\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0006886\",\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    \"other_free_text\": [\n      \"COG7 is essential for protein transport in T. gondii tachyzoites [#0]\",\n      \"The COG complex in T. gondii associates with novel parasite-specific interacting partners critical for trafficking [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_242030","name":"COG7","product":"conserved oligomeric Golgi complex subunit 7","uniprot_acc":"S8FAE0","chromosome":"TGME49_chrVI","start_pos":1836899},{"strain":"GT1","gene_id":"TGGT1_242030","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrVI","start_pos":1774596},{"strain":"RH88","gene_id":"TGRH88_029880","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023087","start_pos":1865414},{"strain":"VEG","gene_id":"TGVEG_242030","name":null,"product":"hypothetical protein","uniprot_acc":"A0A125YRU6","chromosome":"TGVEG_chrVI","start_pos":1850903}]}