{"gene":"PF3D7_0623100","run_date":"2026-09-08T12:51:26","timeline":{"discoveries":[{"year":2015,"finding":"PF3D7_0623100 (NAB2) was identified as a putative RNA-binding protein in P. falciparum through bioinformatic analysis of the P. falciparum genome; it was catalogued among 189 putative RBP genes belonging to recognized RBP families, suggesting a role in post-transcriptional regulation, but no direct functional characterization was performed.","method":"Bioinformatic/computational survey of the P. falciparum genome using domain-based searches and 3D modelling; no experimental validation of NAB2 specifically","journal":"BMC genomics","confidence":"Low","confidence_rationale":"Tier 4 / Weak — purely computational identification with no experimental validation of NAB2 itself","pmids":["26525978"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"PF3D7_0623100 (NAB2) was identified as an RNA-dependent protein (RDP) in P. falciparum by proteome-wide sucrose density gradient ultracentrifugation (R-DeeP) coupled with quantitative mass spectrometry, indicating that its sedimentation profile shifts in the presence versus absence of RNA. No direct functional or binding characterization of NAB2 itself was performed in this study.","method":"R-DeeP (sucrose density gradient ultracentrifugation + quantitative mass spectrometry)","journal":"Nature communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proteome-wide screen identifies NAB2 as an RDP candidate but provides no direct mechanistic follow-up for this specific protein","pmids":["38355719"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0623100 (NAB2) has been computationally predicted to be an RNA-binding protein in P. falciparum and was detected as an RNA-dependent protein in a proteome-wide screen, but no direct mechanistic characterization of its RNA-binding activity, binding partners, substrates, structure, or cellular role has been experimentally established."},"narrative":{"mechanistic_narrative":"PF3D7_0623100 (NAB2) is a putative RNA-binding protein in P. falciparum, catalogued among 189 predicted RBP genes assigned to recognized RBP families through domain-based genome analysis, implying a role in post-transcriptional regulation [PMID:26525978]. Consistent with this prediction, NAB2 was subsequently detected as an RNA-dependent protein in a proteome-wide R-DeeP screen, its sedimentation profile shifting in an RNA-dependent manner [PMID:38355719]. Beyond this computational classification and one proteome-wide RNA-dependence assignment, no direct mechanistic characterization of NAB2's RNA-binding activity, substrates, binding partners, structure, or cellular role has been established in the available corpus.","teleology":[{"year":2015,"claim":"Whether PF3D7_0623100 belongs to the RNA-binding protein repertoire of P. falciparum was unknown; a genome-wide domain survey established it as a candidate RBP, framing it as a possible post-transcriptional regulator.","evidence":"Bioinformatic/computational survey of the P. falciparum genome using domain-based searches and 3D modelling, with no experimental validation of NAB2 specifically","pmids":["26525978"],"confidence":"Low","gaps":["Purely computational assignment not experimentally validated for NAB2 itself","No RNA target or binding activity demonstrated","No cellular role or localization determined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"Whether the computationally predicted RNA association of NAB2 has any experimental support was unknown; a proteome-wide RNA-dependence screen showed its sedimentation shifts with RNA presence, providing the first experimental hint of RNA association.","evidence":"R-DeeP (sucrose density gradient ultracentrifugation coupled with quantitative mass spectrometry)","pmids":["38355719"],"confidence":"Low","gaps":["Proteome-wide screen provides no direct binding or functional follow-up for NAB2 specifically","RNA targets and whether binding is direct versus complex-mediated are unknown","No interaction partners or complex membership established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The direct RNA-binding activity, substrates, binding partners, structure, and cellular function of PF3D7_0623100 remain uncharacterized in the available corpus.","evidence":"No direct mechanistic study of NAB2 exists in the timeline","pmids":[],"confidence":"Low","gaps":["No demonstrated RNA substrate or binding specificity","No identified protein interaction partners or complex","No experimental data on localization, structure, or phenotype"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["Identified computationally as one of 189 putative RNA-binding protein genes in P. falciparum [#0].","Detected as an RNA-dependent protein by proteome-wide R-DeeP screening, indicating RNA-dependent sedimentation behavior [#1].","No direct experimental characterization of RNA targets, binding partners, structure, or cellular role of PF3D7_0623100 exists in the corpus."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"10693754","id":"PMC_10693754","title":"A simple RNA analysis method shows var and rif multigene family expression patterns in Plasmodium falciparum.","date":"2000","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/10693754","citation_count":234,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26525978","id":"PMC_26525978","title":"A bioinformatic survey of RNA-binding proteins in Plasmodium.","date":"2015","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/26525978","citation_count":62,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"4971014","id":"PMC_4971014","title":"DNA, RNA , and protein synthesis in erythrocytic forms of Plasmodium knowlesi.","date":"1968","source":"The American journal of tropical medicine and hygiene","url":"https://pubmed.ncbi.nlm.nih.gov/4971014","citation_count":56,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21935891","id":"PMC_21935891","title":"From cradle to grave: RNA biology in malaria parasites.","date":"2010","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/21935891","citation_count":25,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38355719","id":"PMC_38355719","title":"Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38355719","citation_count":12,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4651,"output_tokens":631,"usd":0.011709,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5249,"output_tokens":1405,"usd":0.030685,"stage2_stop_reason":"end_turn"},"total_usd":0.042394,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"PF3D7_0623100 (NAB2) was identified as a putative RNA-binding protein in P. falciparum through bioinformatic analysis of the P. falciparum genome; it was catalogued among 189 putative RBP genes belonging to recognized RBP families, suggesting a role in post-transcriptional regulation, but no direct functional characterization was performed.\",\n      \"method\": \"Bioinformatic/computational survey of the P. falciparum genome using domain-based searches and 3D modelling; no experimental validation of NAB2 specifically\",\n      \"journal\": \"BMC genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — purely computational identification with no experimental validation of NAB2 itself\",\n      \"pmids\": [\"26525978\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PF3D7_0623100 (NAB2) was identified as an RNA-dependent protein (RDP) in P. falciparum by proteome-wide sucrose density gradient ultracentrifugation (R-DeeP) coupled with quantitative mass spectrometry, indicating that its sedimentation profile shifts in the presence versus absence of RNA. No direct functional or binding characterization of NAB2 itself was performed in this study.\",\n      \"method\": \"R-DeeP (sucrose density gradient ultracentrifugation + quantitative mass spectrometry)\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proteome-wide screen identifies NAB2 as an RDP candidate but provides no direct mechanistic follow-up for this specific protein\",\n      \"pmids\": [\"38355719\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0623100 (NAB2) has been computationally predicted to be an RNA-binding protein in P. falciparum and was detected as an RNA-dependent protein in a proteome-wide screen, but no direct mechanistic characterization of its RNA-binding activity, binding partners, substrates, structure, or cellular role has been experimentally established.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0623100 (NAB2) is a putative RNA-binding protein in P. falciparum, catalogued among 189 predicted RBP genes assigned to recognized RBP families through domain-based genome analysis, implying a role in post-transcriptional regulation [#0]. Consistent with this prediction, NAB2 was subsequently detected as an RNA-dependent protein in a proteome-wide R-DeeP screen, its sedimentation profile shifting in an RNA-dependent manner [#1]. Beyond this computational classification and one proteome-wide RNA-dependence assignment, no direct mechanistic characterization of NAB2's RNA-binding activity, substrates, binding partners, structure, or cellular role has been established in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Whether PF3D7_0623100 belongs to the RNA-binding protein repertoire of P. falciparum was unknown; a genome-wide domain survey established it as a candidate RBP, framing it as a possible post-transcriptional regulator.\",\n      \"evidence\": \"Bioinformatic/computational survey of the P. falciparum genome using domain-based searches and 3D modelling, with no experimental validation of NAB2 specifically\",\n      \"pmids\": [\"26525978\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Purely computational assignment not experimentally validated for NAB2 itself\",\n        \"No RNA target or binding activity demonstrated\",\n        \"No cellular role or localization determined\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether the computationally predicted RNA association of NAB2 has any experimental support was unknown; a proteome-wide RNA-dependence screen showed its sedimentation shifts with RNA presence, providing the first experimental hint of RNA association.\",\n      \"evidence\": \"R-DeeP (sucrose density gradient ultracentrifugation coupled with quantitative mass spectrometry)\",\n      \"pmids\": [\"38355719\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Proteome-wide screen provides no direct binding or functional follow-up for NAB2 specifically\",\n        \"RNA targets and whether binding is direct versus complex-mediated are unknown\",\n        \"No interaction partners or complex membership established\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct RNA-binding activity, substrates, binding partners, structure, and cellular function of PF3D7_0623100 remain uncharacterized in the available corpus.\",\n      \"evidence\": \"No direct mechanistic study of NAB2 exists in the timeline\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No demonstrated RNA substrate or binding specificity\",\n        \"No identified protein interaction partners or complex\",\n        \"No experimental data on localization, structure, or phenotype\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006417\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Identified computationally as one of 189 putative RNA-binding protein genes in P. falciparum [#0].\",\n      \"Detected as an RNA-dependent protein by proteome-wide R-DeeP screening, indicating RNA-dependent sedimentation behavior [#1].\",\n      \"No direct experimental characterization of RNA targets, binding partners, structure, or cellular role of PF3D7_0623100 exists in the corpus.\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0623100","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 2 of 2 cited papers name other catalogue genes (PF3D7_0320800, PF3D7_1474900, PF3D7_0823200). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0623100","name":null,"product":"nuclear polyadenylated RNA-binding protein NAB2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1122000","name":null,"product":"nuclear polyadenylated RNA-binding protein NAB2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1127100","name":null,"product":"nuclear polyadenylated RNA-binding protein NAB2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"NAB2","evaluation":null}