{"id":"4417a344-e7c7-54d8-8cc4-f610b5baae0b","stable_key":"research:secis-variable","predicate":"modulates","statement":"Human SECIS elements show widely differing reporter recoding activities, precluding a universal endogenous 5–10 percent efficiency inference.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"literature_reviewed:supported_interpretation","direction":"context_dependent","is_public":true,"mechanism_event_id":"e47b5160-1a2c-58e1-92db-a006a6f78b2b","mechanism_event_label":"Efficiency depends on the RNA and test conditions.","subject":{"id":"c08b3cec-7ec8-5899-ab6b-7cfbac057346","slug":"human-secis-elements","display_name":"Experimentally tested human SECIS elements","entity_type_key":"rna_set"},"object":{"id":"f71fba83-929f-5773-81f5-1796d8e5a369","slug":"uga-recoding","display_name":"UGA recoding","entity_type_key":"cellular_process"},"evidence_count":1,"mechanism_event":{"id":"e47b5160-1a2c-58e1-92db-a006a6f78b2b","stable_key":"research:secis-variable","event_type":"contextual_mechanism","label":"Efficiency depends on the RNA and test conditions.","description":"Human SECIS elements show widely differing reporter recoding activities, precluding a universal endogenous 5–10 percent efficiency inference.","status":"active","compartment":null,"participants":[{"entity":{"id":"c08b3cec-7ec8-5899-ab6b-7cfbac057346","slug":"human-secis-elements","display_name":"Experimentally tested human SECIS elements","entity_type_key":"rna_set"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"f71fba83-929f-5773-81f5-1796d8e5a369","slug":"uga-recoding","display_name":"UGA recoding","entity_type_key":"cellular_process"},"role":"object","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""}]},"contexts":[{"dimension":"cell_type","value_text":"HEK293 and HepG2 reporters","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"26 human SECIS reporters in HEK293/HepG2 and cell-free translation","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"Reporter activity is not a direct count of all endogenous translation outcomes.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"organism","value_text":"Homo sapiens","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"d98e1247-ba52-5d88-8214-f21e2522f085","evidence_kind":"curated_literature_summary","locator":"lines 1203-1213","start_line":1203,"end_line":1213,"excerpt":"## secis-variable\n\nEfficiency depends on the RNA and test conditions.\n\nHuman SECIS elements show widely differing reporter recoding activities, precluding a universal endogenous 5–10 percent efficiency inference.\n\nOrganism: Homo sapiens\nCell type: HEK293 and HepG2 reporters\nExperimental model: 26 human SECIS reporters in HEK293/HepG2 and cell-free translation\nLimitations: Reporter activity is not a direct count of all endogenous translation outcomes.\nPrimary reference: [Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine](https://pmc.ncbi.nlm.nih.gov/articles/PMC2761289/)","model_system":"26 human SECIS reporters in HEK293/HepG2 and cell-free translation","directness":"author_interpretation","verification_status":"secondary_verified","notes":"Curated summary; inspect the linked primary papers for original methods and results.","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"4f892f13-06ea-5199-a33c-a703f35c80ae","stable_key":"selenium-research-2026-09-17","title":"Selenium: literature corrections and mechanism additions","document_type":"curated_literature_review","citation_label":"Metabolic Ledger literature curation, 17 September 2026; primary papers linked individually","file_path":"","sha256":"0b818b10c1c7120e5caf7f4d4019d7bd025d745692e424f515d3ef903c9ab7f3","revision_id":"80984e03-5f0f-5877-8094-afef7637444e","review_status":"secondary_verified","notes":"Secondary curated summaries of primary experiments, with explicit models and limitations. Not archived primary full text."}}],"relations":[],"conflicts":[],"corrections":[{"id":"72ecddac-faf6-5af4-9cac-9ef792ff63d3","title":"UGA recoding does not have a universal 5–10 percent efficiency","kind":"qualification","status":"qualified","why":"Reporter/lysate efficiencies cannot establish premature termination for most endogenous translation; 95 percent efficiency still permits downward regulatory range.","resolution":"Retain transcript/condition-specific measurements; remove mathematical necessity and untested adaptive explanation. Later deficiency source already qualifies this.","created_at":"2026-09-17 07:19:34","record_type":"qualification","display_label":"Source qualification","record_url":"/corrections/72ecddac-faf6-5af4-9cac-9ef792ff63d3","literature_review":{"revision_id":"80984e03-5f0f-5877-8094-afef7637444e","start_line":1556,"end_line":1561,"papers":[{"paper_key":"secis-2009","title":"Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2761289/","doi":"10.1093/nar/gkp635","year":2009,"model":"26 human SECIS reporters in HEK293/HepG2 and cell-free translation","summary":"Large element-dependent differences preclude a universal endogenous efficiency inference."}]},"sides":[{"conflict_id":"72ecddac-faf6-5af4-9cac-9ef792ff63d3","ordinal":0,"label":"Original preserved statement","revision_id":"4cec6304-35d7-5560-9133-e6ea689db838","start_line":192,"end_line":192,"quote":"Baseline Sec insertion efficiency is shockingly bad — **roughly 5–10%** at a typical UGA. Most ribosomes on a selenoprotein mRNA terminate early. **This inefficiency is the feature**: it's what makes the system tunable at all. A process running at 95% efficiency has no dynamic range.","claim_id":null,"source_key":"corrections","source_title":"Selenium corrections and deep dive","claim_ids":[]},{"conflict_id":"72ecddac-faf6-5af4-9cac-9ef792ff63d3","ordinal":1,"label":"Original preserved statement","revision_id":"f8f97804-c1fb-56df-9c06-c02e36e2a5b8","start_line":45,"end_line":45,"quote":"UGA recoding is intrinsically less straightforward than ordinary amino-acid insertion and its efficiency varies substantially by transcript and cellular context. It should not be treated as a universal 5–10% process across all selenoprotein mRNAs.","claim_id":null,"source_key":"deficiency","source_title":"Selenium deficiency: a mechanism-first reference","claim_ids":[]},{"conflict_id":"72ecddac-faf6-5af4-9cac-9ef792ff63d3","ordinal":2,"label":"Literature correction and experimental limits","revision_id":"80984e03-5f0f-5877-8094-afef7637444e","start_line":1556,"end_line":1561,"quote":"## UGA recoding does not have a universal 5–10 percent efficiency\n\nReporter/lysate efficiencies cannot establish premature termination for most endogenous translation; 95 percent efficiency still permits downward regulatory range.\n\nRetain transcript/condition-specific measurements; remove mathematical necessity and untested adaptive explanation. Later deficiency source already qualifies this.\nPrimary reference: [Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine](https://pmc.ncbi.nlm.nih.gov/articles/PMC2761289/)","claim_id":null,"source_key":"selenium-research-2026-09-17","source_title":"Selenium: literature corrections and mechanism additions","claim_ids":[]}]}],"research":{"topic":"Selenium scientific audit","plain_language":"Efficiency depends on the RNA and test conditions.","evidence_scope":"supported_interpretation","papers":[{"key":"secis-2009","title":"Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2761289/","doi":"10.1093/nar/gkp635","year":2009,"model":"26 human SECIS reporters in HEK293/HepG2 and cell-free translation","summary":"Large element-dependent differences preclude a universal endogenous efficiency inference."}]}}