{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.cx3cl1","code":"thing-q14907780","url":"https://ver.cy/models/thing/q14907780/","name":"CX3CL1","alternateNames":[],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.OBJ"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"CX3CL1 is a human protein-coding gene that encodes fractalkine, a chemokine whose membrane-bound and soluble forms act through CX3CR1 to regulate leukocyte adhesion and migration.","purpose":"Enable an agent to identify the human CX3CL1 gene, assess evidence about its variants and expression, and distinguish gene and transcript observations from measurements of its protein product.","scope":{"in":["Human CX3CL1 gene identity and reference genomic sequence are included.","Genomic coordinates qualified by reference assembly are included.","Gene variants and their evidence-supported annotations are included.","Transcript models, transcriptional regulation and RNA expression are included.","Relationships between the gene, its transcripts and its encoded chemokine are included."],"out":["The CX3CL1 protein's membrane-associated, soluble and engineered forms as independent molecular entities are excluded.","The CX3CR1 gene and receptor as independent entities are excluded.","Complete models of CX3CL1-producing or responding cell types are excluded.","Disease mechanisms, diagnostic criteria and treatment recommendations are excluded.","Antibodies, inhibitors and assay platforms as independent entities are excluded."],"boundaries":[]},"distinguishingFeatures":["Identity requires a human gene reference record or genomic sequence evidence specific to CX3CL1.","CX3CL1 encodes a ligand and is distinct from CX3CR1, which encodes its receptor.","Genomic coordinates and variants require an explicit reference assembly or sequence accession.","RNA expression measurements describe transcriptional output rather than directly establishing protein abundance or activity.","Membrane-bound and soluble fractalkine are protein forms rather than separate gene identities."],"structure":{"bundles":[{"id":"cx3cl1-identity","name":"CX3CL1 identity and registry boundary","description":"Resolve what the CX3CL1 label denotes before attaching molecular or functional observations.","layers":[{"id":"protein-versus-gene","name":"Protein versus gene","description":"Separate the modelled protein from the genetic entity that encodes it.","findings":[{"id":"fractalkine-reference","name":"Fractalkine reference identity","description":"Human CX3CL1 encodes fractalkine; the registry's intended molecular level needs confirmation. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)","questions":[{"text":"Does the originating registry record identify CX3CL1 protein, the encoding gene or an unresolved combination?","id":"fractalkine-reference-q01","kind":"boundary"},{"text":"Which protein accession and sequence substantiate the identity of the material being modelled?","id":"fractalkine-reference-q02","kind":"provenance"}]}]},{"id":"orthologue-and-construct","name":"Orthologue and construct","description":"Track species and engineered sequence changes within the existing registry entry.","findings":[{"id":"sequence-equivalence","name":"Sequence equivalence","description":"Make comparisons conditional on a declared species, residue interval and engineered additions.","questions":[{"text":"Which organism and reference sequence define this CX3CL1 material?","id":"sequence-equivalence-q01","kind":"definition"},{"text":"Which truncations, substitutions, tags or fusion partners distinguish it from that reference?","id":"sequence-equivalence-q02","kind":"boundary"}]}]}]},{"id":"cx3cl1-architecture","name":"CX3CL1 architecture and molecular form","description":"Describe the domains and processing state that determine how CX3CL1 is physically presented.","layers":[{"id":"domain-coverage","name":"Domain coverage","description":"Identify retained structural regions rather than relying on a product name.","findings":[{"id":"chemokine-stalk-anchor","name":"Chemokine, stalk and anchor","description":"CX3CL1 has a chemokine domain and mucin-like stalk and occurs in membrane-anchored and soluble forms. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)","questions":[{"text":"Which chemokine-domain, stalk, membrane-anchor and intracellular regions are present in this sequence?","id":"chemokine-stalk-anchor-q01","kind":"definition"},{"text":"What evidence distinguishes full-length membrane-associated material from a soluble ectodomain or isolated chemokine domain?","id":"chemokine-stalk-anchor-q02","kind":"measurement"}]}]},{"id":"cleavage-and-modification","name":"Cleavage and modification","description":"Resolve molecular heterogeneity relevant to presentation and assay interpretation.","findings":[{"id":"observed-proteoform","name":"Observed proteoform","description":"Record experimentally supported termini and modifications, separating them from predictions.","questions":[{"text":"Which cleavage termini and glycosylation features have been measured for this CX3CL1 material?","id":"observed-proteoform-q01","kind":"measurement"},{"text":"Does a mass or band-pattern difference reflect expected processing, an engineered construct or degradation?","id":"observed-proteoform-q02","kind":"boundary"}]}]}]},{"id":"cx3cl1-presentation","name":"CX3CL1 localization and release","description":"Connect the protein's measured location with its source and changes over time.","layers":[{"id":"surface-and-fluid-compartments","name":"Surface and fluid compartments","description":"Locate the measured protein within a defined biological or experimental compartment.","findings":[{"id":"compartment-specific-abundance","name":"Compartment-specific abundance","description":"Keep surface measurements, intracellular measurements and soluble concentrations distinguishable.","questions":[{"text":"Was CX3CL1 measured on a cell surface, inside cells, in tissue extract or in a specified fluid?","id":"compartment-specific-abundance-q01","kind":"measurement"},{"text":"Which cells, tissue, collection method and sampling time establish the measurement's origin?","id":"compartment-specific-abundance-q02","kind":"provenance"}]}]},{"id":"release-dynamics","name":"Release dynamics","description":"Evaluate transitions between surface-associated and soluble material.","findings":[{"id":"supported-release-mechanism","name":"Supported release mechanism","description":"Cell-surface cleavage can generate soluble CX3CL1; attribution of a particular change requires evidence from the system studied. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)","questions":[{"text":"What paired surface and soluble measurements support release rather than altered production or cell damage?","id":"supported-release-mechanism-q01","kind":"measurement"},{"text":"Which perturbation and controls would test the proposed cleavage mechanism in this system?","id":"supported-release-mechanism-q02","kind":"action"}]}]}]},{"id":"cx3cl1-receptor-function","name":"CX3CR1 interaction and functional evidence","description":"Separate ligand recognition from measured cellular outcomes.","layers":[{"id":"receptor-recognition","name":"Receptor recognition","description":"Establish the receptor and experimental basis of a CX3CL1 interaction.","findings":[{"id":"cx3cr1-binding-evidence","name":"CX3CR1 binding evidence","description":"CX3CL1 interacts with CX3CR1; a preparation's binding performance still requires assay-specific evidence. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)","questions":[{"text":"Which CX3CR1 species and expression context were used to measure binding of this CX3CL1 form?","id":"cx3cr1-binding-evidence-q01","kind":"provenance"},{"text":"What competition, receptor-negative or receptor-blocking controls establish specificity?","id":"cx3cr1-binding-evidence-q02","kind":"measurement"}]}]},{"id":"adhesion-and-migration","name":"Adhesion and migration","description":"Interpret functional outcomes against ligand presentation and responding-cell context.","findings":[{"id":"presentation-matched-function","name":"Presentation-matched function","description":"Membrane-associated CX3CL1 supports adhesion, while soluble CX3CL1 can act as a chemoattractant; test the actual form and context. [NCBI Gene](https://www.ncbi.nlm.nih.gov/gene/6376/)","questions":[{"text":"Does the assay measure adhesion, directional migration or a signaling readout, and under which dose and timing conditions?","id":"presentation-matched-function-q01","kind":"measurement"},{"text":"Which controls distinguish CX3CR1-dependent activity from nonspecific adhesion, random motility or contaminants?","id":"presentation-matched-function-q02","kind":"action"}]}]}]},{"id":"cx3cl1-assay-readiness","name":"CX3CL1 measurement and preparation readiness","description":"Determine whether detection results and prepared material support the intended experimental decision.","layers":[{"id":"detection-selectivity","name":"Detection selectivity","description":"Define which CX3CL1 forms a measurement can actually detect.","findings":[{"id":"epitope-and-calibration","name":"Epitope and calibration compatibility","description":"Assess recognition and calibration against the sample's species, sequence coverage and molecular form.","questions":[{"text":"Which CX3CL1 region does the detection reagent recognize, and is that region retained in the sample?","id":"epitope-and-calibration-q01","kind":"definition"},{"text":"Do calibration material, sample matrix and recovery checks support comparison of the reported concentrations?","id":"epitope-and-calibration-q02","kind":"measurement"}]}]},{"id":"functional-preparation-quality","name":"Functional preparation quality","description":"Assess confounders and handling effects before using CX3CL1 in cellular experiments.","findings":[{"id":"use-specific-acceptance","name":"Use-specific acceptance","description":"Base preparation acceptance on documented integrity, contamination and activity criteria for the intended assay.","questions":[{"text":"What lot-specific evidence covers CX3CL1 purity, aggregation, endotoxin and retained activity after storage?","id":"use-specific-acceptance-q01","kind":"provenance"},{"text":"Should this preparation be used, recharacterized or replaced for the proposed receptor or cellular assay?","id":"use-specific-acceptance-q02","kind":"action"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of CX3CL1 this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of CX3CL1 this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of CX3CL1 this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of CX3CL1 this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of CX3CL1 this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of CX3CL1 this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of CX3CL1 this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe the human CX3CL1 gene and the membrane-bound and soluble forms of its encoded protein, citing sources.","Report what a gene variant or RNA expression measurement shows, with method and limits."],"mustNot":["Interpret a person's CX3CL1 level as a diagnosis.","Share test or genetic results without consent.","Recommend treatments targeting it to a person.","Confuse the ligand with its receptor in reports."],"requiresHuman":["Using results in clinical decisions.","Research on patient samples without documented consent."]},"ethics":{"considerations":["Inflammation markers are often overinterpreted in commercial testing.","Lab results are private health data."],"affectedParties":["Patients","Consumers of commercial tests","Researchers"]},"owners":{"steward":"The person whose genome carries it has interests in associated samples and data; laboratories and biobanks steward the records.","roles":[],"masterSystems":["Gene and variant databases hold relevant reference records."]},"relations":[{"target":"Q20747295","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.cx3cl1","Wikidata: Q14907780 (https://www.wikidata.org/wiki/Q14907780)"]},"properties":{"applicability":"required","items":["Molecular reference: Species, protein accession with version, sequence and relationship to the encoding gene","Physical form: Membrane-associated protein; released soluble form; isolated chemokine domain; engineered fusion; unresolved","Sequence coverage: Residue interval against a named reference; length in amino acids","Processing and modification status: Observed termini, cleavage evidence, glycosylation evidence and unresolved modifications","Observed molecular mass: kDa, with analytical method and molecular form","Abundance and presentation: Soluble concentration in pg/mL or nM; calibrated surface molecules/cell; assay-relative surface signal","CX3CR1 interaction: Receptor species, binding method, measured affinity where available and specificity controls","Functional response: Assay-defined adhesion, migration or signaling response with dose, time and controls","Preparation suitability: Purity, aggregation, endotoxin result, storage history and acceptance against experiment-specific criteria"]},"recognition":{"applicability":"required","items":["The gene is identified through human genomic sequence records and reference identifiers.","Immunoassays and antibody staining detect its protein product rather than the gene.","Images of protein localization do not establish genomic variants."]},"capabilities":{"applicability":"required","items":["Resolve a CX3CL1-labelled record to a species-specific protein and molecular form.","Select detection methods that distinguish soluble CX3CL1 from surface-associated material.","Compare preparations after reconciling sequence coverage, modifications and concentration basis.","Design controlled CX3CR1 binding, adhesion or chemotaxis measurements.","Evaluate whether cleavage, degradation or sample handling explains an observed change.","Accept, qualify or reject a preparation for a stated experiment using documented criteria."]},"hazards":{"applicability":"required","items":["Overinterpretation of marker levels.","Confusion between ligand and receptor."]},"interfaces":{"applicability":"required","items":["Human gene nomenclature, HUGO Gene Nomenclature Committee (HGNC), which approves the gene symbol."]},"context":{"applicability":"required","items":["The human CX3CL1 gene is encountered in studies of immune cell recruitment, vascular inflammation and communication between cells in nervous tissue.","Its expression is studied as a contributor to production of fractalkine, while distinguishing membrane-associated and soluble protein requires additional measurements."]}},"sources":[{"title":"Wikidata item Q14907780: CX3CL1","url":"https://www.wikidata.org/wiki/Q14907780","note":"identity and sense of the item"},{"title":"Wikipedia: CX3CL1","url":"https://en.wikipedia.org/wiki/CX3CL1","note":"general description of the item"}],"openQuestions":["Does the originating registry identifier denote human CX3CL1 protein, a species-independent protein concept or the gene?","Which existing Vercy model, if any, already owns this concept and should receive the registry link?","Which native cleavage products and responsible proteases are experimentally established in each intended biological context?","How do species, glycosylation, construct boundaries and tags affect equivalence between recombinant material and endogenous CX3CL1?","Which assays and reference preparations support comparable measurements of soluble abundance, surface presentation and biological activity?"],"resources":{"spec":"/models/things/publications/thing-q14907780/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q14907780/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T08:57:10Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T12:16:28+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}