{"gene":"TG_259520","gene_symbol":"SKA2","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2022,"finding":"SKA2 was identified as one of 13 previously unknown kinetochore components in Apicomplexa through interactomics and deep homology searches; the apicomplexan kinetochore complex containing SKA2 is organised into at least four discrete compartments with different biochemical interactions and subkinetochore localizations, and kinetochores align at the metaphase plate in both Plasmodium berghei and Toxoplasma gondii, suggestive of a conserved hold signal preventing premature anaphase entry.","method":"Interactomics (co-immunoprecipitation/proximity labelling) combined with deep homology searches and fluorescence microscopy for subkinetochore localization","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — interactomics plus localization in two apicomplexan species, single study, multiple orthogonal methods","pmids":["36006241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""},{"species":"Plasmodium berghei","strain":""}]}],"current_model":"SKA2 is a kinetochore-associated protein in apicomplexan parasites, identified as part of a divergent multiprotein kinetochore complex organised into discrete subkinetochore compartments, where it participates in chromosome segregation control including metaphase plate alignment and prevention of premature anaphase entry."},"narrative":{"mechanistic_narrative":"SKA2 is a kinetochore-associated protein of apicomplexan parasites, identified through interactomics and deep homology searches as one of 13 previously unknown components of a divergent multiprotein kinetochore complex [PMID:36006241]. This complex is organised into at least four discrete subkinetochore compartments with distinct biochemical interactions and localizations, within which SKA2 participates in chromosome segregation control; kinetochores align at the metaphase plate in both Plasmodium berghei and Toxoplasma gondii, consistent with a conserved hold signal that prevents premature anaphase entry [PMID:36006241]. Beyond this single identification and localization study, no further mechanistic detail about SKA2 has been characterized in the available corpus.","teleology":[{"year":2022,"claim":"Whether the apicomplexan kinetochore contains uncharacterized components was unknown; identifying SKA2 as part of a divergent multiprotein kinetochore complex established its role in chromosome segregation control in these parasites.","evidence":"Interactomics (co-IP/proximity labelling) plus deep homology searches and fluorescence microscopy for subkinetochore localization in Toxoplasma gondii and Plasmodium berghei","pmids":["36006241"],"confidence":"Medium","gaps":["The specific molecular activity of SKA2 within the complex is not defined","The direct binding partners and which of the four compartments SKA2 occupies are not resolved","The molecular basis of the proposed hold signal preventing premature anaphase is not established"],"attribution":[{"species":"Toxoplasma gondii","strain":""},{"species":"Plasmodium berghei","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Apicomplexan kinetochore complex"],"partners":[],"other_free_text":["SKA2 localizes to discrete subkinetochore compartments; kinetochores align at the metaphase plate in P. berghei and T. gondii, consistent with a conserved hold signal preventing premature anaphase entry [#0]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"36006241","id":"PMC_36006241","title":"Composition and organization of kinetochores show plasticity in apicomplexan chromosome segregation.","date":"2022","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/36006241","citation_count":30,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2807,"output_tokens":416,"usd":0.007331,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5015,"output_tokens":1237,"usd":0.028,"stage2_stop_reason":"end_turn"},"total_usd":0.072231,"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\": 2022,\n      \"finding\": \"SKA2 was identified as one of 13 previously unknown kinetochore components in Apicomplexa through interactomics and deep homology searches; the apicomplexan kinetochore complex containing SKA2 is organised into at least four discrete compartments with different biochemical interactions and subkinetochore localizations, and kinetochores align at the metaphase plate in both Plasmodium berghei and Toxoplasma gondii, suggestive of a conserved hold signal preventing premature anaphase entry.\",\n      \"method\": \"Interactomics (co-immunoprecipitation/proximity labelling) combined with deep homology searches and fluorescence microscopy for subkinetochore localization\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — interactomics plus localization in two apicomplexan species, single study, multiple orthogonal methods\",\n      \"pmids\": [\"36006241\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"SKA2 is a kinetochore-associated protein in apicomplexan parasites, identified as part of a divergent multiprotein kinetochore complex organised into discrete subkinetochore compartments, where it participates in chromosome segregation control including metaphase plate alignment and prevention of premature anaphase entry.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SKA2 is a kinetochore-associated protein of apicomplexan parasites, identified through interactomics and deep homology searches as one of 13 previously unknown components of a divergent multiprotein kinetochore complex [#0]. This complex is organised into at least four discrete subkinetochore compartments with distinct biochemical interactions and localizations, within which SKA2 participates in chromosome segregation control; kinetochores align at the metaphase plate in both Plasmodium berghei and Toxoplasma gondii, consistent with a conserved hold signal that prevents premature anaphase entry [#0]. Beyond this single identification and localization study, no further mechanistic detail about SKA2 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether the apicomplexan kinetochore contains uncharacterized components was unknown; identifying SKA2 as part of a divergent multiprotein kinetochore complex established its role in chromosome segregation control in these parasites.\",\n      \"evidence\": \"Interactomics (co-IP/proximity labelling) plus deep homology searches and fluorescence microscopy for subkinetochore localization in Toxoplasma gondii and Plasmodium berghei\",\n      \"pmids\": [\"36006241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific molecular activity of SKA2 within the complex is not defined\",\n        \"The direct binding partners and which of the four compartments SKA2 occupies are not resolved\",\n        \"The molecular basis of the proposed hold signal preventing premature anaphase is not established\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular function of SKA2, its direct interactions, and how it contributes to the metaphase hold signal remain to be determined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional or loss-of-function characterization of SKA2 in the corpus\",\n        \"No structural model or defined enzymatic/binding activity\",\n        \"Mechanism of recruitment to the kinetochore unknown\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"},\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0000776\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}, {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0007059\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}, {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"Apicomplexan kinetochore complex\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"SKA2 localizes to discrete subkinetochore compartments; kinetochores align at the metaphase plate in P. berghei and T. gondii, consistent with a conserved hold signal preventing premature anaphase entry [#0]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_259520","name":"SKA2","product":"spindle and kinetochore-associated protein SKA2","uniprot_acc":"A0A125YMB5","chromosome":"TGME49_chrVIIb","start_pos":2793136},{"strain":"GT1","gene_id":"TGGT1_259520","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrVIIb","start_pos":2767419},{"strain":"RH88","gene_id":"TGRH88_070620","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023089","start_pos":2813135},{"strain":"VEG","gene_id":"TGVEG_259520","name":null,"product":"hypothetical protein","uniprot_acc":"B6KBG2","chromosome":"TGVEG_chrVIIb","start_pos":2810626}]}