{"gene":"PF3D7_API02800","run_date":"2026-09-08T15:24:04","timeline":{"discoveries":[{"year":1996,"finding":"RPS7 (PF3D7_API02800) was identified as one of 17 ribosomal protein genes encoded on the 35 kb plastid-like (apicoplast) DNA circle of P. falciparum, establishing its genomic location within the apicoplast genome and its role as a component of the apicoplast ribosomal machinery involved in gene expression within that organelle.","method":"Complete gene mapping of the 35 kb apicoplast DNA circle by sequence analysis","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — comprehensive genomic mapping with direct sequence identification, single study but systematic and definitive for genomic localization","pmids":["8757284"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"RPS7 (PF3D7_API02800) is an apicoplast-encoded ribosomal protein whose gene resides on the 35 kb circular apicoplast genome of P. falciparum and is transcribed polycistronically as part of the organelle's gene-expression machinery; beyond its membership in the apicoplast small-subunit ribosome, no further mechanistic details have been experimentally established in the available literature."},"narrative":{"mechanistic_narrative":"RPS7 (PF3D7_API02800) is a ribosomal protein gene encoded on the 35 kb plastid-like (apicoplast) DNA circle of Plasmodium falciparum, identified as one of 17 ribosomal protein genes on that genome and thereby assigned as a component of the apicoplast ribosomal machinery for organellar gene expression [PMID:8757284]. Beyond this genomic localization and inferred membership in the apicoplast ribosome, no further mechanistic detail about RPS7 has been experimentally established in the available corpus.","teleology":[{"year":1996,"claim":"Before the apicoplast genome was fully mapped, the coding content of the P. falciparum 35 kb DNA circle was unknown; sequencing it placed RPS7 among the ribosomal protein genes carried by the organelle, establishing its genomic location and implicating it in apicoplast gene expression.","evidence":"Complete gene mapping and sequence analysis of the 35 kb apicoplast DNA circle","pmids":["8757284"],"confidence":"Medium","gaps":["No direct evidence that the RPS7 protein is expressed or assembles into the apicoplast small subunit","No functional assay of RPS7 in translation or organelle biogenesis","No structural or interaction data localizing RPS7 within the ribosome"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown whether RPS7 is expressed as a functional protein, how it assembles into the apicoplast ribosome, and what role it plays in parasite viability or apicoplast function.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No protein-level detection of RPS7","No genetic knockout or knockdown phenotype","No demonstrated interaction with other ribosomal subunits or apicoplast components"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Apicoplast small ribosomal subunit"],"partners":[],"other_free_text":["Encoded on the 35 kb apicoplast DNA circle of P. falciparum as one of 17 ribosomal protein genes [#0]","No mechanistic detail beyond genomic localization and inferred ribosome membership has been established in the available corpus"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"8757284","id":"PMC_8757284","title":"Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum.","date":"1996","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8757284","citation_count":447,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19929377","id":"PMC_19929377","title":"Susceptibility of Plasmodium falciparum isolates to doxycycline is associated with pftetQ sequence polymorphisms and pftetQ and pfmdt copy numbers.","date":"2010","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/19929377","citation_count":33,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRPS7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27458998","id":"PMC_27458998","title":"Transcripts in the Plasmodium Apicoplast Undergo Cleavage at tRNAs and Editing, and Include Antisense Sequences.","date":"2016","source":"Protist","url":"https://pubmed.ncbi.nlm.nih.gov/27458998","citation_count":16,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26206143","id":"PMC_26206143","title":"Absence of correlation between ex vivo susceptibility to doxycycline and pfteQ-pfmdt gene polymorphism in French Guiana.","date":"2015","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/26206143","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRPS7"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4703,"output_tokens":381,"usd":0.009912,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4870,"output_tokens":1112,"usd":0.026075,"stage2_stop_reason":"end_turn"},"total_usd":0.035987,"stage1_batch_id":"msgbatch_01S4WrhSkksYHeZXxqf3za3o","stage2_batch_id":"msgbatch_019VBBeuW6G52X8gZfsFDfb5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"RPS7 (PF3D7_API02800) was identified as one of 17 ribosomal protein genes encoded on the 35 kb plastid-like (apicoplast) DNA circle of P. falciparum, establishing its genomic location within the apicoplast genome and its role as a component of the apicoplast ribosomal machinery involved in gene expression within that organelle.\",\n      \"method\": \"Complete gene mapping of the 35 kb apicoplast DNA circle by sequence analysis\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — comprehensive genomic mapping with direct sequence identification, single study but systematic and definitive for genomic localization\",\n      \"pmids\": [\"8757284\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"RPS7 (PF3D7_API02800) is an apicoplast-encoded ribosomal protein whose gene resides on the 35 kb circular apicoplast genome of P. falciparum and is transcribed polycistronically as part of the organelle's gene-expression machinery; beyond its membership in the apicoplast small-subunit ribosome, no further mechanistic details have been experimentally established in the available literature.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPS7 (PF3D7_API02800) is a ribosomal protein gene encoded on the 35 kb plastid-like (apicoplast) DNA circle of Plasmodium falciparum, identified as one of 17 ribosomal protein genes on that genome and thereby assigned as a component of the apicoplast ribosomal machinery for organellar gene expression [#0]. Beyond this genomic localization and inferred membership in the apicoplast ribosome, no further mechanistic detail about RPS7 has been experimentally established in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Before the apicoplast genome was fully mapped, the coding content of the P. falciparum 35 kb DNA circle was unknown; sequencing it placed RPS7 among the ribosomal protein genes carried by the organelle, establishing its genomic location and implicating it in apicoplast gene expression.\",\n      \"evidence\": \"Complete gene mapping and sequence analysis of the 35 kb apicoplast DNA circle\",\n      \"pmids\": [\n        \"8757284\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct evidence that the RPS7 protein is expressed or assembles into the apicoplast small subunit\",\n        \"No functional assay of RPS7 in translation or organelle biogenesis\",\n        \"No structural or interaction data localizing RPS7 within the ribosome\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether RPS7 is expressed as a functional protein, how it assembles into the apicoplast ribosome, and what role it plays in parasite viability or apicoplast function.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No protein-level detection of RPS7\",\n        \"No genetic knockout or knockdown phenotype\",\n        \"No demonstrated interaction with other ribosomal subunits or apicoplast components\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0003735\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0020011\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0006412\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"Apicoplast small ribosomal subunit\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Encoded on the 35 kb apicoplast DNA circle of P. falciparum as one of 17 ribosomal protein genes [#0]\",\n      \"No mechanistic detail beyond genomic localization and inferred ribosome membership has been established in the available corpus\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_API02800","name":null,"product":"apicoplast ribosomal protein S7","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPS7","evaluation":null}