{"id":"abd54dcd-996a-5fb4-a763-ee15d59ff3c6","stable_key":"7de430a5-1a36-5231-b931-35cc01d8f3bf:apap-frameshift-makes-a-different-protein","predicate":"causes","statement":"The 98 base pair intron 1 of the cyclooxygenase-1 gene remains unprocessed in rat COX-1b messenger RNA, causing a frameshift mutation and a 127 amino acid open reading frame with no sequence similarity with known cyclooxygenases, and transfection of COS-7 cells produced a protein of the expected size which was also detected in rat tissues with highest expression in heart, kidney and neuronal tissue, but rat COX-1b does not have cyclooxygenase activity and does not have any effect on the inhibition of prostaglandin production by acetaminophen, leading the authors to propose the name cyclooxygenase variant protein instead.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"positive","is_public":true,"mechanism_event_id":"814e4fb9-c220-5c90-b165-2d7c0f7623b5","mechanism_event_label":"In the rat the retained intron shifts the reading frame, so what is made is a different protein altogether and not an enzyme.","subject":{"id":"0846f2e1-77d2-5173-8a11-43fc94731b53","slug":"cox1-intron-1","display_name":"Intron 1 of the cyclooxygenase-1 gene","entity_type_key":"gene"},"object":{"id":"0bd0409e-9582-5fc7-a0f7-b883eec643e2","slug":"frameshift-mutation","display_name":"A frameshift arising from retention of an unprocessed intron","entity_type_key":"cellular_process"},"evidence_count":1,"mechanism_event":{"id":"814e4fb9-c220-5c90-b165-2d7c0f7623b5","stable_key":"7de430a5-1a36-5231-b931-35cc01d8f3bf:apap-frameshift-makes-a-different-protein-event","event_type":"biochemical_relationship","label":"In the rat the retained intron shifts the reading frame, so what is made is a different protein altogether and not an enzyme.","description":"The 98 base pair intron 1 of the cyclooxygenase-1 gene remains unprocessed in rat COX-1b messenger RNA, causing a frameshift mutation and a 127 amino acid open reading frame with no sequence similarity with known cyclooxygenases, and transfection of COS-7 cells produced a protein of the expected size which was also detected in rat tissues with highest expression in heart, kidney and neuronal tissue, but rat COX-1b does not have cyclooxygenase activity and does not have any effect on the inhibition of prostaglandin production by acetaminophen, leading the authors to propose the name cyclooxygenase variant protein instead.","status":"provisional","compartment":null,"participants":[{"entity":{"id":"a4c9b287-5373-57d2-b126-f1290d79343a","slug":"cox-3","display_name":"COX-3 / COX-1b, a cyclooxygenase-1 transcript retaining intron 1","entity_type_key":"protein"},"role":"renamed_entity","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"a901be21-7915-543c-ac67-c39ef72b0d03","slug":"acetaminophen","display_name":"Paracetamol","entity_type_key":"drug"},"role":"unaffected_drug","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"6284d26c-01e2-5e12-b192-ee391dd107e2","slug":"ptgs1","display_name":"Cyclooxygenase-1 (PTGS1)","entity_type_key":"protein"},"role":"parent_gene_product","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"0846f2e1-77d2-5173-8a11-43fc94731b53","slug":"cox1-intron-1","display_name":"Intron 1 of the cyclooxygenase-1 gene","entity_type_key":"gene"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""},{"entity":{"id":"0bd0409e-9582-5fc7-a0f7-b883eec643e2","slug":"frameshift-mutation","display_name":"A frameshift arising from retention of an unprocessed intron","entity_type_key":"cellular_process"},"role":"target","stoichiometry":null,"state_label":"","sequence_order":4,"notes":""}]},"contexts":[{"dimension":"evidence_span","value_text":"{\"source_cache\": \"artifacts/paracetamol-research/15650114.abstract.txt\", \"locator\": \"Indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"1661f4d2b21244e0fc16b9a3b947cf4d09d39be35367ed263cce441f43a60563\", \"start_char\": 0, \"end_char\": 1473, \"text_sha256\": \"1661f4d2b21244e0fc16b9a3b947cf4d09d39be35367ed263cce441f43a60563\"}","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Cloning and sequencing of rat COX-1b from cerebral endothelial cells with transfection and antibody generation","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"exposure","value_text":"Rat COX-1b complementary DNA transfected into COS-7 cells, assayed for activity and for effect on acetaminophen inhibition","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"Tests the proposal in a second species by building the protein and asking whether it works. The protein is detected in rat tissue, so the finding is that it exists and is not a cyclooxygenase.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"nutrient_topic","value_text":"Paracetamol research collection; topical membership is not evidence of a direct clinical effect, and the drug is recorded separately from the metabolites NAPQI and AM404.","comparator":null,"unit":null,"notes":"","entity":{"slug":"acetaminophen","display_name":"Paracetamol","entity_type_key":"drug"}},{"dimension":"organism","value_text":"Rat","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"In the rat the retained intron shifts the reading frame, so what is made is a different protein altogether and not an enzyme.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[apap-p15650114] Cloning and characterization of cyclooxygenase-1b (putative cyclooxygenase-3) in rat. (2005). https://pubmed.ncbi.nlm.nih.gov/15650114/ DOI: 10.1124/jpet.104.079533","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Cerebral endothelial cells","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"2cb64ea2-bf5a-5f69-90c7-ced6a33385bb","evidence_kind":"source_excerpt","locator":"Lines 220-231","start_line":220,"end_line":231,"excerpt":"### apap-frameshift-makes-a-different-protein\nThe 98 base pair intron 1 of the cyclooxygenase-1 gene remains unprocessed in rat COX-1b messenger RNA, causing a frameshift mutation and a 127 amino acid open reading frame with no sequence similarity with known cyclooxygenases, and transfection of COS-7 cells produced a protein of the expected size which was also detected in rat tissues with highest expression in heart, kidney and neuronal tissue, but rat COX-1b does not have cyclooxygenase activity and does not have any effect on the inhibition of prostaglandin production by acetaminophen, leading the authors to propose the name cyclooxygenase variant protein instead.\nCondition category: normal\nnutrient_topic: Paracetamol research collection; topical membership is not evidence of a direct clinical effect, and the drug is recorded separately from the metabolites NAPQI and AM404.\nplain_language: In the rat the retained intron shifts the reading frame, so what is made is a different protein altogether and not an enzyme.\norganism: Rat\ntissue_or_cell_type: Cerebral endothelial cells\nexperimental_model: Cloning and sequencing of rat COX-1b from cerebral endothelial cells with transfection and antibody generation\nlimitations: Tests the proposal in a second species by building the protein and asking whether it works. The protein is detected in rat tissue, so the finding is that it exists and is not a cyclooxygenase.\nexposure: Rat COX-1b complementary DNA transfected into COS-7 cells, assayed for activity and for effect on acetaminophen inhibition\nevidence_span: {\"source_cache\": \"artifacts/paracetamol-research/15650114.abstract.txt\", \"locator\": \"Indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"1661f4d2b21244e0fc16b9a3b947cf4d09d39be35367ed263cce441f43a60563\", \"start_char\": 0, \"end_char\": 1473, \"text_sha256\": \"1661f4d2b21244e0fc16b9a3b947cf4d09d39be35367ed263cce441f43a60563\"}\n[apap-p15650114] Cloning and characterization of cyclooxygenase-1b (putative cyclooxygenase-3) in rat. (2005). https://pubmed.ncbi.nlm.nih.gov/15650114/ DOI: 10.1124/jpet.104.079533","model_system":"Cloning and sequencing of rat COX-1b from cerebral endothelial cells with transfection and antibody generation","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact curation-document quotation, not publisher quotation. Study references: [apap-p15650114] Cloning and characterization of cyclooxygenase-1b (putative cyclooxygenase-3) in rat. (2005). https://pubmed.ncbi.nlm.nih.gov/15650114/ DOI: 10.1124/jpet.104.079533","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"9ee11177-f860-5877-bb82-f4ee4acdc538","stable_key":"import-7de430a5-1a36-5231-b931-35cc01d8f3bf","title":"Paracetamol: the enzyme it reduces rather than blocks, the isoform that turned out not to exist, the metabolite that carries the analgesia, and the metabolite that destroys the liver (2026-09-22)","document_type":"imported_text","citation_label":"AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text.","file_path":"","sha256":"9c145887aa10fa7b85f54712e0b41fd9e04fb9544d3182793dd84414dbf8c2ae","revision_id":"c3e7827a-4f10-55e0-97b9-5782b044f7cc","review_status":"unverified_draft","notes":""}}],"relations":[],"conflicts":[{"id":"f62d9400-eaf3-577e-b4ee-47fe78629a0e","title":"Does a third cyclooxygenase explain how paracetamol works?","kind":"contradiction","status":"open","why":"A 2002 report described COX-3, a cyclooxygenase-1 transcript retaining intron 1, expressed in canine cerebral cortex and in human cerebral cortex and heart, showed the canine protein had glycosylation-dependent cyclooxygenase activity, and found it selectively inhibited by paracetamol, phenacetin, antipyrine and dipyrone, proposing this as the primary central mechanism. The proposal does not survive translation to other species. In the rat the retained 98 base pair intron causes a frameshift, giving a 127 amino acid protein with no sequence similarity to any cyclooxygenase, no cyclooxygenase activity and no effect on paracetamol inhibition of prostaglandin production. An independent survey across rat tissues found no immunoreactive protein with an anti-canine-COX-3 antibody, found no special potency of paracetamol in brain or cerebellum, and concluded that expression of an active enzyme from this transcript is apparently impossible in the rat. A review adds that even in the dog, expression level and kinetics make clinical relevance unlikely, and that in rodents and humans the encoded proteins are not cyclooxygenases. The records are recorded together because the proposal shaped a decade of writing about this drug; on the evidence here it is a species-specific curiosity rather than the mechanism.","resolution":"Unresolved; needs review.","created_at":"2026-09-22 17:05:56","record_type":"conflict","display_label":"Recorded conflict","record_url":"/conflicts/f62d9400-eaf3-577e-b4ee-47fe78629a0e","sides":[{"conflict_id":"f62d9400-eaf3-577e-b4ee-47fe78629a0e","ordinal":0,"label":"A third form of the enzyme was reported in dog brain, and it was the one this drug blocked.","revision_id":"c3e7827a-4f10-55e0-97b9-5782b044f7cc","start_line":194,"end_line":205,"quote":"### apap-cox3-proposed\nA third distinct cyclooxygenase isozyme, COX-3, made from the cyclooxygenase-1 gene but retaining intron 1 in its messenger RNA, was described as expressed in canine cerebral cortex and as an approximately 5.2 kilobase transcript most abundant in human cerebral cortex and heart, the retained intron introducing an insertion of 30 to 34 amino acids into the hydrophobic signal peptide; canine COX-3 expressed in insect cells possessed glycosylation-dependent cyclooxygenase activity and was selectively inhibited by analgesic and antipyretic drugs such as acetaminophen, phenacetin, antipyrine and dipyrone, so that inhibition of COX-3 could represent a primary central mechanism by which these drugs decrease pain and possibly fever.\nCondition category: normal\nnutrient_topic: Paracetamol research collection; topical membership is not evidence of a direct clinical effect, and the drug is recorded separately from the metabolites NAPQI and AM404.\nplain_language: A third form of the enzyme was reported in dog brain, and it was the one this drug blocked.\norganism: Dog and human\ntissue_or_cell_type: Cerebral cortex\nexperimental_model: Cloning and expression of cyclooxygenase-1-derived transcripts from canine cerebral cortex in insect cells\nlimitations: The paper that proposed the answer. Its activity data are for the canine protein expressed in insect cells; the human claim is about messenger RNA abundance, not about an active protein.\nexposure: Canine COX-3 compared with murine cyclooxygenase-1 and -2 against acetaminophen, phenacetin, antipyrine and dipyrone\nevidence_span: {\"source_cache\": \"artifacts/paracetamol-research/12242329.abstract.txt\", \"locator\": \"Indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"0c00962f9e58da9af386335ac3312d5c260d637270d80481a6f55d0ebec67a78\", \"start_char\": 0, \"end_char\": 1711, \"text_sha256\": \"0c00962f9e58da9af386335ac3312d5c260d637270d80481a6f55d0ebec67a78\"}\n[apap-p12242329] COX-3, a cyclooxygenase-1 variant inhibited by acetaminophen and other analgesic/antipyretic drugs: cloning, structure, and expression. (2002). https://pubmed.ncbi.nlm.nih.gov/12242329/ DOI: 10.1073/pnas.162468699","source_key":"import-7de430a5-1a36-5231-b931-35cc01d8f3bf","source_title":"Paracetamol: the enzyme it reduces rather than blocks, the isoform that turned out not to exist, the metabolite that carries the analgesia, and the metabolite that destroys the liver (2026-09-22)","claim_ids":["66f92b21-fb5d-5352-9c8b-ce7df9342548"]},{"conflict_id":"f62d9400-eaf3-577e-b4ee-47fe78629a0e","ordinal":1,"label":"In the rat the retained intron shifts the reading frame, so what is made is a different protein altogether and not an enzyme.","revision_id":"c3e7827a-4f10-55e0-97b9-5782b044f7cc","start_line":220,"end_line":231,"quote":"### apap-frameshift-makes-a-different-protein\nThe 98 base pair intron 1 of the cyclooxygenase-1 gene remains unprocessed in rat COX-1b messenger RNA, causing a frameshift mutation and a 127 amino acid open reading frame with no sequence similarity with known cyclooxygenases, and transfection of COS-7 cells produced a protein of the expected size which was also detected in rat tissues with highest expression in heart, kidney and neuronal tissue, but rat COX-1b does not have cyclooxygenase activity and does not have any effect on the inhibition of prostaglandin production by acetaminophen, leading the authors to propose the name cyclooxygenase variant protein instead.\nCondition category: normal\nnutrient_topic: Paracetamol research collection; topical membership is not evidence of a direct clinical effect, and the drug is recorded separately from the metabolites NAPQI and AM404.\nplain_language: In the rat the retained intron shifts the reading frame, so what is made is a different protein altogether and not an enzyme.\norganism: Rat\ntissue_or_cell_type: Cerebral endothelial cells\nexperimental_model: Cloning and sequencing of rat COX-1b from cerebral endothelial cells with transfection and antibody generation\nlimitations: Tests the proposal in a second species by building the protein and asking whether it works. The protein is detected in rat tissue, so the finding is that it exists and is not a cyclooxygenase.\nexposure: Rat COX-1b complementary DNA transfected into COS-7 cells, assayed for activity and for effect on acetaminophen inhibition\nevidence_span: {\"source_cache\": \"artifacts/paracetamol-research/15650114.abstract.txt\", \"locator\": \"Indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"1661f4d2b21244e0fc16b9a3b947cf4d09d39be35367ed263cce441f43a60563\", \"start_char\": 0, \"end_char\": 1473, \"text_sha256\": \"1661f4d2b21244e0fc16b9a3b947cf4d09d39be35367ed263cce441f43a60563\"}\n[apap-p15650114] Cloning and characterization of cyclooxygenase-1b (putative cyclooxygenase-3) in rat. (2005). https://pubmed.ncbi.nlm.nih.gov/15650114/ DOI: 10.1124/jpet.104.079533","source_key":"import-7de430a5-1a36-5231-b931-35cc01d8f3bf","source_title":"Paracetamol: the enzyme it reduces rather than blocks, the isoform that turned out not to exist, the metabolite that carries the analgesia, and the metabolite that destroys the liver (2026-09-22)","claim_ids":["abd54dcd-996a-5fb4-a763-ee15d59ff3c6"]},{"conflict_id":"f62d9400-eaf3-577e-b4ee-47fe78629a0e","ordinal":2,"label":"Nobody could find the protein, and in brain the drug showed no special selectivity at all.","revision_id":"c3e7827a-4f10-55e0-97b9-5782b044f7cc","start_line":233,"end_line":244,"quote":"### apap-no-cox3-protein-found\nProstanoid production by rat aorta, heart, lung and whole blood was inhibited by all drugs tested with the order of potency SC560 greater than naproxen greater than acetaminophen greater than or equal to rofecoxib while in brain and cerebellum no differences among drug potencies were found, Western blotting using a commercially available antibody raised against canine COX-3 failed to detect any immunoreactive proteins, and the authors conclude that cyclooxygenase-1 and -2 are the functional forms present in the rat tissues tested, that acetaminophen is not a selective inhibitor of cyclooxygenase activities in the central nervous system, and that expression of an active cyclooxygenase protein from COX-3 messenger RNA in the rat is apparently impossible.\nCondition category: normal\nnutrient_topic: Paracetamol research collection; topical membership is not evidence of a direct clinical effect, and the drug is recorded separately from the metabolites NAPQI and AM404.\nplain_language: Nobody could find the protein, and in brain the drug showed no special selectivity at all.\norganism: Rat\ntissue_or_cell_type: Multiple tissues\nexperimental_model: Comparison of acetaminophen, rofecoxib, naproxen and SC560 across rat aorta, heart, lung, brain, cerebellum and whole blood\nlimitations: Tests the proposal functionally across tissues and looks for the protein directly. A rat study, and a negative Western blot is weaker evidence than a positive one.\nexposure: Four drugs of differing isoform selectivity, with transcript and protein detection including an anti-canine-COX-3 antibody\nevidence_span: {\"source_cache\": \"artifacts/paracetamol-research/15148345.abstract.txt\", \"locator\": \"Indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"6ca43f39a9bb4cbc398f4f7f6e3401854f6c100b72fb7fdf952ee49486438d3c\", \"start_char\": 0, \"end_char\": 1940, \"text_sha256\": \"6ca43f39a9bb4cbc398f4f7f6e3401854f6c100b72fb7fdf952ee49486438d3c\"}\n[apap-p15148345] Cyclooxygenases 1, 2, and 3 and the production of prostaglandin I2: investigating the activities of acetaminophen and cyclooxygenase-2-selective inhibitors in rat tissues. (2004). https://pubmed.ncbi.nlm.nih.gov/15148345/ DOI: 10.1124/jpet.103.063875","source_key":"import-7de430a5-1a36-5231-b931-35cc01d8f3bf","source_title":"Paracetamol: the enzyme it reduces rather than blocks, the isoform that turned out not to exist, the metabolite that carries the analgesia, and the metabolite that destroys the liver (2026-09-22)","claim_ids":["f4ffe612-caf8-50f4-9dfc-9dc9d06a7fc6"]}]}],"corrections":[],"research":null}