{"gene":"TRAPPC2B","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2000,"finding":"SEDL (TRAPPC2) protein, when tagged and transiently transfected into Cos-7 cells, localizes to perinuclear structures that partly overlap with the intermediate ER-Golgi compartment (ERGIC/VTC), indicating a role in ER-to-Golgi transport. SEDLP1 (TRAPPC2B) is identified as a transcribed retropseudogene on chromosome 19q13.4 with potential to encode a protein identical to SEDL.","method":"Transient transfection of FLAG- and GFP-tagged constructs in Cos-7 cells; subcellular localization by immunofluorescence; mutant constructs with disease-causing mutations (157-158delAT and C271T(STOP)) showing mislocalization to nucleus/cytoplasm, suggesting COOH-terminus mediates proper targeting","journal":"Genomics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single-method localization study; findings are about SEDL (TRAPPC2) and only incidentally identify SEDLP1/TRAPPC2B as a transcribed pseudogene; no direct functional experiment performed on TRAPPC2B protein itself","pmids":["11031107"],"is_preprint":false}],"current_model":"TRAPPC2B (SEDLP1) is identified as a transcribed retropseudogene of TRAPPC2 (SEDL) on chromosome 19q13.4 with potential to encode a protein identical to SEDL, which localizes to ER-Golgi intermediate compartments via its C-terminus, but no direct mechanistic experiments have been performed specifically on the TRAPPC2B protein itself."},"narrative":{"mechanistic_narrative":"TRAPPC2B (SEDLP1) is a transcribed retropseudogene located on chromosome 19q13.4 with the potential to encode a protein identical to SEDL/TRAPPC2 [PMID:11031107]. In the available corpus, no direct mechanistic experiment has been performed on the TRAPPC2B protein itself; the only functional data concern its parent gene SEDL/TRAPPC2, whose tagged product localizes to perinuclear structures overlapping the ER-Golgi intermediate compartment and depends on its C-terminus for proper targeting [PMID:11031107]. Beyond this incidental identification of TRAPPC2B as a transcribed pseudogene [PMID:11031107], no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2000,"claim":"Establishing whether the SEDL locus has paralogous copies, this work identified TRAPPC2B/SEDLP1 as a transcribed retropseudogene on chromosome 19q13.4 capable of encoding a protein identical to SEDL, while characterizing the parent SEDL protein's localization to the ER-Golgi intermediate compartment.","evidence":"Transient transfection of FLAG- and GFP-tagged SEDL constructs in Cos-7 cells with immunofluorescence localization; disease-mutation constructs implicating the C-terminus in targeting; genomic identification of the SEDLP1 pseudogene","pmids":["11031107"],"confidence":"Low","gaps":["No direct functional or localization experiment was performed on the TRAPPC2B protein itself","Whether the TRAPPC2B transcript is translated into a functional protein in vivo is unaddressed","All mechanistic claims (ERGIC localization, C-terminal targeting) pertain to the parent SEDL/TRAPPC2, not TRAPPC2B"]},{"year":null,"claim":"Whether TRAPPC2B encodes a functional protein and contributes to ER-to-Golgi transport independently of its parent gene remains unknown.","evidence":"","pmids":[],"confidence":"Low","gaps":["No TRAPPC2B-specific protein expression, localization, or interaction data exist in the corpus","No evidence on tissue-specific transcription or biological role of the pseudogene transcript"]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P0DI82","full_name":"Trafficking protein particle complex subunit 2B","aliases":["MBP-1-interacting protein 2A","MIP-2A"],"length_aa":140,"mass_kda":16.4,"function":"Prevents transcriptional repression and induction of cell death by ENO1. May play a role in vesicular transport from endoplasmic reticulum to Golgi","subcellular_location":"Nucleus; Cytoplasm, perinuclear region; Endoplasmic reticulum-Golgi intermediate compartment; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P0DI82/entry"},"depmap":{"release":"DepMap","has_data":false,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRAPPC2B"},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TRAPPC2B","total_profiled":1310},"omim":[{"mim_id":"620472","title":"TRAFFICKING PROTEIN PARTICLE COMPLEX, SUBUNIT 2B; TRAPPC2B","url":"https://www.omim.org/entry/620472"},{"mim_id":"172430","title":"ENOLASE 1; ENO1","url":"https://www.omim.org/entry/172430"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Endoplasmic reticulum","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TRAPPC2B"},"hgnc":{"alias_symbol":["SEDLP1","MIP-2A"],"prev_symbol":["SEDLP","TRAPPC2P1"]},"alphafold":{"accession":"P0DI82","domains":[{"cath_id":"3.30.450.70","chopping":"4-137","consensus_level":"high","plddt":93.0203,"start":4,"end":137}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P0DI82","model_url":"https://alphafold.ebi.ac.uk/files/AF-P0DI82-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P0DI82-F1-predicted_aligned_error_v6.png","plddt_mean":92.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRAPPC2B","jax_strain_url":"https://www.jax.org/strain/search?query=TRAPPC2B"},"sequence":{"accession":"P0DI82","fasta_url":"https://rest.uniprot.org/uniprotkb/P0DI82.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P0DI82/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P0DI82"}},"corpus_meta":[{"pmid":"11031107","id":"PMC_11031107","title":"Gene structure and expression study of the SEDL gene for spondyloepiphyseal dysplasia tarda.","date":"2000","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/11031107","citation_count":41,"is_preprint":false},{"pmid":"22446932","id":"PMC_22446932","title":"A genome-wide RNAi screen identifies novel targets of neratinib resistance leading to identification of potential drug resistant genetic markers.","date":"2012","source":"Molecular bioSystems","url":"https://pubmed.ncbi.nlm.nih.gov/22446932","citation_count":28,"is_preprint":false},{"pmid":"23115970","id":"PMC_23115970","title":"[Cell surface display of Thermomyces lanuginosus lipase in Pichia pastoris and its characterization].","date":"2012","source":"Wei sheng wu xue bao = Acta microbiologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/23115970","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3988,"output_tokens":467,"usd":0.009484,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6743,"output_tokens":931,"usd":0.028495,"stage2_stop_reason":"end_turn"},"total_usd":0.037979,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"SEDL (TRAPPC2) protein, when tagged and transiently transfected into Cos-7 cells, localizes to perinuclear structures that partly overlap with the intermediate ER-Golgi compartment (ERGIC/VTC), indicating a role in ER-to-Golgi transport. SEDLP1 (TRAPPC2B) is identified as a transcribed retropseudogene on chromosome 19q13.4 with potential to encode a protein identical to SEDL.\",\n      \"method\": \"Transient transfection of FLAG- and GFP-tagged constructs in Cos-7 cells; subcellular localization by immunofluorescence; mutant constructs with disease-causing mutations (157-158delAT and C271T(STOP)) showing mislocalization to nucleus/cytoplasm, suggesting COOH-terminus mediates proper targeting\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single-method localization study; findings are about SEDL (TRAPPC2) and only incidentally identify SEDLP1/TRAPPC2B as a transcribed pseudogene; no direct functional experiment performed on TRAPPC2B protein itself\",\n      \"pmids\": [\"11031107\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRAPPC2B (SEDLP1) is identified as a transcribed retropseudogene of TRAPPC2 (SEDL) on chromosome 19q13.4 with potential to encode a protein identical to SEDL, which localizes to ER-Golgi intermediate compartments via its C-terminus, but no direct mechanistic experiments have been performed specifically on the TRAPPC2B protein itself.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TRAPPC2B (SEDLP1) is a transcribed retropseudogene located on chromosome 19q13.4 with the potential to encode a protein identical to SEDL/TRAPPC2 [#0]. In the available corpus, no direct mechanistic experiment has been performed on the TRAPPC2B protein itself; the only functional data concern its parent gene SEDL/TRAPPC2, whose tagged product localizes to perinuclear structures overlapping the ER-Golgi intermediate compartment and depends on its C-terminus for proper targeting [#0]. Beyond this incidental identification of TRAPPC2B as a transcribed pseudogene [#0], no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Establishing whether the SEDL locus has paralogous copies, this work identified TRAPPC2B/SEDLP1 as a transcribed retropseudogene on chromosome 19q13.4 capable of encoding a protein identical to SEDL, while characterizing the parent SEDL protein's localization to the ER-Golgi intermediate compartment.\",\n      \"evidence\": \"Transient transfection of FLAG- and GFP-tagged SEDL constructs in Cos-7 cells with immunofluorescence localization; disease-mutation constructs implicating the C-terminus in targeting; genomic identification of the SEDLP1 pseudogene\",\n      \"pmids\": [\"11031107\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct functional or localization experiment was performed on the TRAPPC2B protein itself\",\n        \"Whether the TRAPPC2B transcript is translated into a functional protein in vivo is unaddressed\",\n        \"All mechanistic claims (ERGIC localization, C-terminal targeting) pertain to the parent SEDL/TRAPPC2, not TRAPPC2B\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether TRAPPC2B encodes a functional protein and contributes to ER-to-Golgi transport independently of its parent gene remains unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No TRAPPC2B-specific protein expression, localization, or interaction data exist in the corpus\",\n        \"No evidence on tissue-specific transcription or biological role of the pseudogene transcript\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":2,"faith_total":2,"faith_pct":100.0}}