{"gene":"PF3D7_0627700","run_date":"2026-09-08T12:51:26","timeline":{"discoveries":[{"year":2002,"finding":"P. falciparum transportin (PF3D7_0627700) was cloned and found to encode a 1,136 amino acid protein with conserved Ran-GTP and M9 nuclear localization signal binding domains, indicating it mediates nuclear import of M9-bearing cargo proteins; Southern blot showed it is a single-copy gene in the malaria genome.","method":"cDNA cloning, amino acid sequence analysis, Southern blot","journal":"Parasitology research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — sequence-based domain conservation plus Southern blot; no in vitro import assay or mutagenesis, but two orthogonal methods (sequence analysis + Southern) in a focused study on this specific gene","pmids":["12049453"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"finding":"In P. berghei, NAB2 (nuclear poly(A) binding protein 2) interacts with transportin as shown by immunoprecipitation coupled to mass spectrometry (IP-MS), placing transportin as a binding partner of NAB2 at the nuclear periphery.","method":"Immunoprecipitation coupled to mass spectrometry (IP-MS); live-cell fluorescence imaging","journal":"Frontiers in cellular and infection microbiology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS experiment, single lab, no reciprocal pulldown or functional validation of the transportin–NAB2 interaction specifically","pmids":["34604117"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"PF3D7_0627700 encodes a Plasmodium falciparum transportin that contains conserved Ran-GTP and M9-NLS binding domains consistent with a role in nuclear import of M9-bearing cargo proteins, and its P. berghei ortholog has been identified as a binding partner of the RNA-binding protein NAB2 by IP-MS, suggesting it participates in nuclear transport processes in malaria parasites."},"narrative":{"mechanistic_narrative":"PF3D7_0627700 encodes a putative Plasmodium falciparum transportin, a 1,136 amino acid protein whose sequence contains conserved Ran-GTP and M9 nuclear localization signal binding domains, consistent with a role in the nuclear import of M9-bearing cargo proteins; Southern blot established it as a single-copy gene [PMID:12049453]. Beyond this sequence-level and single-copy characterization, the direct functional biology of PF3D7_0627700 has not been characterized in the available corpus: no in vitro import assay, mutagenesis, or cargo identification has been reported for the P. falciparum protein. In the related parasite P. berghei, a transportin was identified as a binding partner of the nuclear poly(A) binding protein NAB2 at the nuclear periphery by IP-MS, placing a transportin within nuclear transport processes in malaria parasites [PMID:34604117].","teleology":[{"year":2002,"claim":"Establishing whether malaria parasites encode a dedicated nuclear import receptor addressed how M9-bearing cargo might reach the parasite nucleus; cloning revealed a single-copy gene with the diagnostic Ran-GTP and M9-NLS binding domains.","evidence":"cDNA cloning, amino acid sequence/domain analysis, and Southern blot in P. falciparum","pmids":["12049453"],"confidence":"Medium","gaps":["No in vitro import assay demonstrating M9-cargo binding or Ran-GTP-dependent release","No mutagenesis confirming domain function","No cargo protein identified for the P. falciparum transportin"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"To identify physiological partners of a malaria transportin, IP-MS in P. berghei placed a transportin in association with the RNA-binding protein NAB2 at the nuclear periphery, linking transportin to nuclear transport/RNA-associated processes.","evidence":"Immunoprecipitation coupled to mass spectrometry with live-cell fluorescence imaging in P. berghei","pmids":["34604117"],"confidence":"Low","gaps":["Single Co-IP/MS without reciprocal pulldown or functional validation of the transportin–NAB2 interaction","Shown in P. berghei, not directly in P. falciparum PF3D7_0627700","Functional consequence of the interaction (cargo import, RNA handling) not established"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"Whether PF3D7_0627700 functions as a bona fide nuclear import receptor in P. falciparum, what cargo it transports, and whether the NAB2 interaction seen in P. berghei applies to the P. falciparum protein remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No direct import or Ran-GTP release assay for PF3D7_0627700","No cargo repertoire defined","No genetic knockout/knockdown phenotype reported for this gene"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["NAB2 (NUCLEAR POLY(A) BINDING PROTEIN 2, P. BERGHEI ORTHOLOG INTERACTION)"],"other_free_text":["1,136 amino acid protein with conserved Ran-GTP and M9-NLS binding domains; single-copy gene by Southern blot (P. falciparum) [#0]","NAB2 interaction demonstrated for the P. berghei transportin, not directly for P. falciparum PF3D7_0627700 [#1]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"34604117","id":"PMC_34604117","title":"Roles and Cellular Localization of GBP2 and NAB2 During the Blood Stage of Malaria Parasites.","date":"2021","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/34604117","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["transportin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"12049453","id":"PMC_12049453","title":"Molecular cloning and characterization of Plasmodium falciparum transportin.","date":"2002","source":"Parasitology research","url":"https://pubmed.ncbi.nlm.nih.gov/12049453","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["transportin"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3720,"output_tokens":626,"usd":0.010275,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5194,"output_tokens":1597,"usd":0.032947,"stage2_stop_reason":"end_turn"},"total_usd":0.043222,"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\": 2002,\n      \"finding\": \"P. falciparum transportin (PF3D7_0627700) was cloned and found to encode a 1,136 amino acid protein with conserved Ran-GTP and M9 nuclear localization signal binding domains, indicating it mediates nuclear import of M9-bearing cargo proteins; Southern blot showed it is a single-copy gene in the malaria genome.\",\n      \"method\": \"cDNA cloning, amino acid sequence analysis, Southern blot\",\n      \"journal\": \"Parasitology research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — sequence-based domain conservation plus Southern blot; no in vitro import assay or mutagenesis, but two orthogonal methods (sequence analysis + Southern) in a focused study on this specific gene\",\n      \"pmids\": [\"12049453\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In P. berghei, NAB2 (nuclear poly(A) binding protein 2) interacts with transportin as shown by immunoprecipitation coupled to mass spectrometry (IP-MS), placing transportin as a binding partner of NAB2 at the nuclear periphery.\",\n      \"method\": \"Immunoprecipitation coupled to mass spectrometry (IP-MS); live-cell fluorescence imaging\",\n      \"journal\": \"Frontiers in cellular and infection microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS experiment, single lab, no reciprocal pulldown or functional validation of the transportin–NAB2 interaction specifically\",\n      \"pmids\": [\"34604117\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0627700 encodes a Plasmodium falciparum transportin that contains conserved Ran-GTP and M9-NLS binding domains consistent with a role in nuclear import of M9-bearing cargo proteins, and its P. berghei ortholog has been identified as a binding partner of the RNA-binding protein NAB2 by IP-MS, suggesting it participates in nuclear transport processes in malaria parasites.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PF3D7_0627700 encodes a putative Plasmodium falciparum transportin, a 1,136 amino acid protein whose sequence contains conserved Ran-GTP and M9 nuclear localization signal binding domains, consistent with a role in the nuclear import of M9-bearing cargo proteins; Southern blot established it as a single-copy gene [#0]. Beyond this sequence-level and single-copy characterization, the direct functional biology of PF3D7_0627700 has not been characterized in the available corpus: no in vitro import assay, mutagenesis, or cargo identification has been reported for the P. falciparum protein. In the related parasite P. berghei, a transportin was identified as a binding partner of the nuclear poly(A) binding protein NAB2 at the nuclear periphery by IP-MS, placing a transportin within nuclear transport processes in malaria parasites [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Establishing whether malaria parasites encode a dedicated nuclear import receptor addressed how M9-bearing cargo might reach the parasite nucleus; cloning revealed a single-copy gene with the diagnostic Ran-GTP and M9-NLS binding domains.\",\n      \"evidence\": \"cDNA cloning, amino acid sequence/domain analysis, and Southern blot in P. falciparum\",\n      \"pmids\": [\"12049453\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No in vitro import assay demonstrating M9-cargo binding or Ran-GTP-dependent release\",\n        \"No mutagenesis confirming domain function\",\n        \"No cargo protein identified for the P. falciparum transportin\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"To identify physiological partners of a malaria transportin, IP-MS in P. berghei placed a transportin in association with the RNA-binding protein NAB2 at the nuclear periphery, linking transportin to nuclear transport/RNA-associated processes.\",\n      \"evidence\": \"Immunoprecipitation coupled to mass spectrometry with live-cell fluorescence imaging in P. berghei\",\n      \"pmids\": [\"34604117\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single Co-IP/MS without reciprocal pulldown or functional validation of the transportin\\u2013NAB2 interaction\",\n        \"Shown in P. berghei, not directly in P. falciparum PF3D7_0627700\",\n        \"Functional consequence of the interaction (cargo import, RNA handling) not established\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PF3D7_0627700 functions as a bona fide nuclear import receptor in P. falciparum, what cargo it transports, and whether the NAB2 interaction seen in P. berghei applies to the P. falciparum protein remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct import or Ran-GTP release assay for PF3D7_0627700\",\n        \"No cargo repertoire defined\",\n        \"No genetic knockout/knockdown phenotype reported for this gene\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008536\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0008139\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0031267\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0034399\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006606\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NAB2 (nuclear poly(A) binding protein 2, P. berghei ortholog interaction)\"],\n    \"other_free_text\": [\n      \"1,136 amino acid protein with conserved Ran-GTP and M9-NLS binding domains; single-copy gene by Southern blot (P. falciparum) [#0]\",\n      \"NAB2 interaction demonstrated for the P. berghei transportin, not directly for P. falciparum PF3D7_0627700 [#1]\"\n    ]\n  }\n}\n```","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0627700","name":null,"product":"transportin","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1126400","name":null,"product":"transportin, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1122100","name":null,"product":"transportin, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}