{"gene":"TG_264960","gene_symbol":"SKA1","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2022,"finding":"SKA1 was identified as one of 13 previously unknown kinetochore components in Apicomplexa through interactomics and deep homology searches; the kinetochore complex including SKA1 displays nanoscale organization with at least four discrete compartments showing different biochemical interactions and subkinetochore localizations.","method":"Interactomics (co-immunoprecipitation/mass spectrometry) combined with deep homology searches and fluorescence localization","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — interactomics-based identification in a single study; SKA1 is one of many newly identified components and is not individually characterized beyond complex membership and localization","pmids":["36006241"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""},{"species":"Plasmodium berghei","strain":""}]}],"current_model":"SKA1 (TG_264960) is a newly identified kinetochore component in Apicomplexa, localized to the kinetochore and identified through interactomics as part of a divergent, multi-compartment kinetochore complex involved in spindle attachment and chromosome segregation in Toxoplasma gondii."},"narrative":{"mechanistic_narrative":"SKA1 is a kinetochore component in Apicomplexa, identified as one of 13 previously unknown kinetochore proteins through interactomics and deep homology searches; it belongs to a divergent kinetochore complex that displays nanoscale organization with at least four discrete compartments showing distinct biochemical interactions and subkinetochore localizations [PMID:36006241]. Beyond its membership in this complex and its kinetochore localization [PMID:36006241], nothing further about SKA1 is known in the available corpus.","teleology":[{"year":2022,"claim":"Whether Apicomplexa possess a definable kinetochore beyond a few conserved proteins was unknown; interactomics and deep homology searches identified SKA1 among 13 new kinetochore components, establishing it as part of a divergent multi-compartment kinetochore complex.","evidence":"Co-immunoprecipitation/mass spectrometry with deep homology searches and fluorescence localization in Toxoplasma gondii and Plasmodium berghei","pmids":["36006241"],"confidence":"Medium","gaps":["SKA1 is not individually characterized beyond complex membership and localization","The molecular activity and direct binding partners of SKA1 within the complex are not defined","Functional consequences of SKA1 loss for spindle attachment or chromosome segregation are 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":["Identified as one of 13 previously unknown Apicomplexan kinetochore components; the complex shows nanoscale organization with at least four discrete compartments."]},"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":433,"usd":0.007458,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5052,"output_tokens":1296,"usd":0.02883,"stage2_stop_reason":"end_turn"},"total_usd":0.072427,"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\": 2022,\n      \"finding\": \"SKA1 was identified as one of 13 previously unknown kinetochore components in Apicomplexa through interactomics and deep homology searches; the kinetochore complex including SKA1 displays nanoscale organization with at least four discrete compartments showing different biochemical interactions and subkinetochore localizations.\",\n      \"method\": \"Interactomics (co-immunoprecipitation/mass spectrometry) combined with deep homology searches and fluorescence localization\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — interactomics-based identification in a single study; SKA1 is one of many newly identified components and is not individually characterized beyond complex membership and localization\",\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\": \"SKA1 (TG_264960) is a newly identified kinetochore component in Apicomplexa, localized to the kinetochore and identified through interactomics as part of a divergent, multi-compartment kinetochore complex involved in spindle attachment and chromosome segregation in Toxoplasma gondii.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SKA1 is a kinetochore component in Apicomplexa, identified as one of 13 previously unknown kinetochore proteins through interactomics and deep homology searches; it belongs to a divergent kinetochore complex that displays nanoscale organization with at least four discrete compartments showing distinct biochemical interactions and subkinetochore localizations [#0]. Beyond its membership in this complex and its kinetochore localization [#0], nothing further about SKA1 is known in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether Apicomplexa possess a definable kinetochore beyond a few conserved proteins was unknown; interactomics and deep homology searches identified SKA1 among 13 new kinetochore components, establishing it as part of a divergent multi-compartment kinetochore complex.\",\n      \"evidence\": \"Co-immunoprecipitation/mass spectrometry with deep homology searches and fluorescence localization in Toxoplasma gondii and Plasmodium berghei\",\n      \"pmids\": [\n        \"36006241\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"SKA1 is not individually characterized beyond complex membership and localization\",\n        \"The molecular activity and direct binding partners of SKA1 within the complex are not defined\",\n        \"Functional consequences of SKA1 loss for spindle attachment or chromosome segregation are not established\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        },\n        {\n          \"species\": \"Plasmodium berghei\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The specific molecular function of SKA1, its direct interaction partners within the kinetochore complex, and its individual contribution to chromosome segregation remain uncharacterized.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct SKA1 binding partners identified\",\n        \"No functional/knockdown phenotype for SKA1 alone\",\n        \"No structural model of SKA1 within the complex\"\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:0000776\",\n        \"supporting_discovery_ids\": [\n          0\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          },\n          {\n            \"species\": \"Plasmodium berghei\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0007059\",\n        \"supporting_discovery_ids\": [\n          0\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          },\n          {\n            \"species\": \"Plasmodium berghei\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"Apicomplexan kinetochore complex\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Identified as one of 13 previously unknown Apicomplexan kinetochore components; the complex shows nanoscale organization with at least four discrete compartments.\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_264960","name":"SKA1","product":"spindle and kinetochore-associated protein SKA1","uniprot_acc":"S8GH37","chromosome":"TGME49_chrIX","start_pos":1883162},{"strain":"GT1","gene_id":"TGGT1_264960","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrIX","start_pos":1702034},{"strain":"RH88","gene_id":"TGRH88_012520","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023090","start_pos":1940688},{"strain":"VEG","gene_id":"TGVEG_264960","name":null,"product":"hypothetical protein","uniprot_acc":"B9QEU6","chromosome":"TGVEG_chrIX","start_pos":1911905}]}