{ "model": { "rank": 11888, "code": "thing-q237218", "model_id": "vr.tr.rna-splicing", "name": "RNA splicing", "purpose": "Let an agent explain RNA splicing and its mechanisms, relay spliceosome function, alternative splicing and regulation from molecular biology references, describe disease relevance and therapies, and distinguish splicing from other RNA processing steps.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q237218/", "tier": 2, "score": 41, "payload": { "layer": "wikidata", "aliases": [ "RNA splicing, via transesterification reactions", "RNA splicing, via endonucleolytic cleavage and ligation", "snoRNA splicing", "exon skipping" ], "aliasCount": 4, "merged": 4, "knownIn": 41, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q237218", "url": "https://www.wikidata.org/wiki/Q237218", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T04:20:51Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 3, "engine": "claude" }, "metaModel": { "id": "THING-Q237218", "registryId": "vr.tr.rna-splicing", "name": "RNA splicing", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q237218/", "model": { "registry_id": "vr.tr.rna-splicing", "name": "RNA splicing", "purpose": "Let an agent explain RNA splicing and its mechanisms, relay spliceosome function, alternative splicing and regulation from molecular biology references, describe disease relevance and therapies, and distinguish splicing from other RNA processing steps.", "definition": "The process by which introns are removed from a precursor messenger RNA and exons are joined to produce mature RNA, carried out in eukaryotes mainly by the spliceosome through two transesterification reactions, and in other cases by self-splicing introns or by endonucleolytic cleavage and ligation as in tRNA splicing, with alternative splicing including exon skipping producing multiple proteins from one gene, and related processing of small nucleolar RNAs; splicing errors and mutations cause many diseases and splicing is a target of new therapies.", "what_it_is_for": "Not applicable; a molecular process.", "affordances": [ "explain mechanisms", "relay alternative splicing and regulation", "describe disease and therapy", "distinguish from other processing" ], "distinguishing_features": [ "Intron removal", "Spliceosome machinery", "Alternative splicing", "Disease relevance" ], "appearance": "Not a visible object; introns excised and exons joined.", "visual_identification": [ "Removal of introns from RNA", "Spliceosomal splicing via transesterification, self-splicing, tRNA splicing via cleavage and ligation, exon skipping, snoRNA processing", "Capping and polyadenylation are other processing steps; transcription precedes splicing" ], "physical_properties": [ { "quantity": "human genes with alternative splicing", "typical_range": "over 90", "unit": "percent", "note": "of multi-exon genes" }, { "quantity": "spliceosome components", "typical_range": "about 150", "unit": "proteins", "note": "plus five snRNAs" }, { "quantity": "splicing discovered", "typical_range": "1977", "unit": "year", "note": "Sharp and Roberts" } ], "families_and_kinds": [ "spliceosomal splicing via two transesterification reactions", "self-splicing group I and group II introns", "tRNA and archaeal splicing via endonucleolytic cleavage and ligation", "alternative splicing including exon skipping, intron retention and alternative sites", "trans-splicing", "processing of snoRNAs from introns" ], "related_models": [ { "relation": "is a kind of", "target": "RNA processing", "why": "in registry terms" }, { "relation": "is a kind of", "target": "post-transcriptional modification", "why": "in registry terms" }, { "relation": "is carried out by", "target": "spliceosome", "why": "in eukaryotes" }, { "relation": "enables", "target": "alternative splicing", "why": "and protein diversity" } ], "identifiers": [ { "scheme": "GO", "value_or_pattern": "GO:0008380", "note": "RNA splicing" }, { "scheme": "MeSH", "value_or_pattern": "D012326", "note": "RNA splicing" } ], "standards_and_regulation": [ "No regulation; standard molecular biology definitions", "Drug regulation of splicing-modulating therapies such as nusinersen and risdiplam" ], "failure_modes_and_hazards": [ "Splicing mutations causing disease", "Confusing splicing with other RNA processing", "Agents giving personal medical advice about splicing therapies" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What RNA splicing is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and mechanism.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is RNA splicing, and how does the spliceosome remove introns through two transesterification reactions?", "kind": "definition" }, { "text": "Is the question about splicing, capping, polyadenylation or transcription?", "kind": "boundary" } ] } ] }, { "id": "kinds", "name": "Kinds", "description": "Kinds.", "findings": [ { "id": "kinds-finding", "name": "Kinds", "description": "Kinds.", "questions": [ { "text": "How do spliceosomal, self-splicing and cleavage-and-ligation tRNA splicing differ, and how are snoRNAs processed?", "kind": "definition" }, { "text": "Which entry fits the specific mechanism?", "kind": "action" } ] } ] } ] }, { "id": "regulation", "name": "Regulation", "description": "Alternative splicing.", "rationale": "Science.", "layers": [ { "id": "alternative", "name": "Alternative", "description": "Alternative splicing.", "findings": [ { "id": "alternative-finding", "name": "Alternative", "description": "Alternative.", "questions": [ { "text": "How do exon skipping and other alternative splicing patterns generate protein diversity?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "control", "name": "Control", "description": "Regulation.", "findings": [ { "id": "control-finding", "name": "Control", "description": "Control.", "questions": [ { "text": "How do splicing factors, enhancers, silencers and chromatin regulate splicing?", "kind": "provenance" }, { "text": "Which entry fits splicing regulation?", "kind": "action" } ] } ] } ] }, { "id": "medicine", "name": "Medicine", "description": "Disease and therapy.", "rationale": "Clinical.", "layers": [ { "id": "disease", "name": "Disease", "description": "Splicing in disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "How do splicing mutations and dysregulation cause diseases such as spinal muscular atrophy and cancers, in general terms?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] }, { "id": "therapy", "name": "Therapy", "description": "Splicing therapies.", "findings": [ { "id": "therapy-finding", "name": "Therapy", "description": "Therapy.", "questions": [ { "text": "How do antisense oligonucleotides and small molecules modulate splicing as therapies?", "kind": "provenance" }, { "text": "Is the user asking about their own treatment, which needs their clinicians?", "kind": "boundary" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Evolution and history.", "rationale": "Context.", "layers": [ { "id": "evolution", "name": "Evolution", "description": "Evolution.", "findings": [ { "id": "evolution-finding", "name": "Evolution", "description": "Evolution.", "questions": [ { "text": "How did introns and splicing evolve, and what debates exist, with positions attributed?", "kind": "provenance" }, { "text": "Which entry fits intron evolution?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were split genes and splicing discovered by Sharp and Roberts?", "kind": "provenance" }, { "text": "Which entry fits the history of molecular biology?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should spliceosome and alternative splicing be separate primary entries?", "How should molecular biology references be linked?", "The registry entry has merged aliases naming mechanisms and processes; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "abstract concept", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a RNA splicing, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain RNA splicing and its mechanisms, relay spliceosome function, alternative splicing and regulation from molecular biology references, describe disease relevance and therapies, and distinguish splicing from other RNA processing steps.", "characteristics": { "substance": "activity", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: RNA splicing, via transesterification reactions, RNA splicing, via endonucleolytic cleavage and ligation, snoRNA splicing, exon skipping.", "4 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 41 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a RNA splicing, and on what evidence are they told apart?" ], "whatItIsMadeOf": "something that happens over time", "physicalCharacter": [ "Does nothing on its own; everything it does, something else did to it.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Nothing to see. What is recognised is an instance of it, and which instances count is exactly what is argued about." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "RNA splicing, via transesterification reactions", "RNA splicing, via endonucleolytic cleavage and ligation", "snoRNA splicing", "exon skipping" ] } ], "standing": "Described in 41 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 4 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one RNA splicing from another, and a RNA splicing from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a RNA splicing sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a RNA splicing from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a RNA splicing passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a RNA splicing between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a RNA splicing, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a RNA splicing is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "process-and-outcome", "name": "Process, inputs and outcome", "description": "How a RNA splicing proceeds, what it needs and what it leaves behind.", "rationale": "An activity is known by its steps and its results, and both have to be recordable while it is still running.", "layers": [ { "id": "steps-and-sequence", "name": "Steps and sequence", "description": "The steps of a RNA splicing, their order and what may run in parallel.", "findings": [ { "id": "steps-and-preconditions", "name": "Steps, preconditions and completion", "description": "What has to be true before each step of a RNA splicing and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "steps-and-preconditions-q02", "text": "Who or what asserted this about a step of a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "steps-and-preconditions-q03", "text": "What may an agent decide or do once a step of a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "inputs-and-results", "name": "Inputs, resources and results", "description": "What a RNA splicing consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a RNA splicing takes and the results it leaves, wanted or not.", "questions": [ { "id": "inputs-and-outputs-q01", "text": "What identifies and describes the inputs and results of a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "inputs-and-outputs-q02", "text": "Who or what asserted this about the inputs and results of a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "inputs-and-outputs-q03", "text": "What may an agent decide or do once the inputs and results of a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definitions-in-contest", "name": "Definitions and who holds them", "description": "What RNA splicing is taken to mean, and by whom.", "rationale": "When a field disagrees about a concept, the disagreement is the content. A model that picks one definition silently destroys the information.", "layers": [ { "id": "competing-definitions", "name": "Competing definitions", "description": "The main readings and the traditions behind them.", "findings": [ { "id": "definition-map", "name": "Definitions and their holders", "description": "Each definition with the school or body that holds it.", "questions": [ { "id": "definition-map-q01", "text": "Which definitions of RNA splicing are in use, and which tradition or body holds each?", "kind": "definition" }, { "id": "definition-map-q02", "text": "What turns on the difference between them in practice?", "kind": "boundary" } ] } ] }, { "id": "operationalisation", "name": "Operationalisation", "description": "How it is measured or applied when it has to be.", "findings": [ { "id": "operational-record", "name": "Measures and proxies", "description": "Instruments and indicators used to stand in for it.", "questions": [ { "id": "operational-record-q01", "text": "How is RNA splicing operationalised or measured in practice, and by what instrument?", "kind": "measurement" }, { "id": "operational-record-q02", "text": "What does that operationalisation leave out, and when does that matter?", "kind": "boundary" } ] } ] } ] }, { "id": "instances-and-use", "name": "Instances, use and consequence", "description": "What counts as an instance of RNA splicing and what follows from calling something that.", "rationale": "Applying a concept is an act with consequences, so a model must say what the label licenses and what it does not.", "layers": [ { "id": "instances", "name": "What counts as an instance", "description": "Clear cases, borderline cases and non-cases.", "findings": [ { "id": "instance-tests", "name": "Tests for an instance", "description": "What would settle whether something falls under it.", "questions": [ { "id": "instance-tests-q01", "text": "What would settle whether something is an instance of RNA splicing?", "kind": "boundary" }, { "id": "instance-tests-q02", "text": "Which borderline cases are argued about, and on what grounds?", "kind": "definition" } ] } ] }, { "id": "consequence", "name": "Consequence of application", "description": "Rights, duties or decisions that follow from the label.", "findings": [ { "id": "consequence-record", "name": "What the label licenses", "description": "What an agent may do once something is classified this way.", "questions": [ { "id": "consequence-record-q01", "text": "What follows practically once something is treated as RNA splicing?", "kind": "action" }, { "id": "consequence-record-q02", "text": "What must an agent not infer from the label alone?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a RNA splicing came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a RNA splicing and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a RNA splicing is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a RNA splicing, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a RNA splicing, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a RNA splicing is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }