FLC is an Arabidopsis MADS-box DNA-binding transcription factor that delays flowering by regulating genes in leaves and the shoot meristem. It binds regulatory DNA at floral integrators, including a CArG-containing region in the first intron of FT and the SOC1 promoter, and represses their expression. FLC acts in multimeric protein complexes, including complexes with other MADS proteins such as SVP. Although best characterized as a floral repressor, FLC also promotes expression of a subset of bound target genes; its transcriptional effect depends on the target and context. Prolonged cold and autonomous-pathway regulators reduce FLC expression, relieving its inhibition of floral transition. The chromatin silencing of the FLC locus is regulation of FLC expression, distinct from the DNA-binding activity of the FLC protein. Additional documented roles include juvenile-to-adult phase progression and temperature-dependent modulation of circadian period.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: FLC directly regulates RNA polymerase II target genes through sequence-specific chromatin binding. Reason: Native-target ChIP and expression experiments establish FLC occupancy at SOC1 promoter and FT intron regulatory DNA and regulation of their transcription (PMID:16623882; PMID:16600915). This supports the inherited or domain-based activity without assigning every MADS-family member the same targets or regulatory sign. Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0009910 negative regulation of flower development | IBA GO_REF:0000033 | ACCEPT | Summary: FLC represses the floral transition. Reason: Leaf and meristem expression experiments show that FLC suppresses systemic floral signaling and meristem competence. The PAINT assertion agrees with target-specific flowering repression, not merely with broad MADS-box family membership. Supporting Evidence: PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: FLC directly regulates RNA polymerase II target genes through sequence-specific chromatin binding. Reason: Native-target ChIP and expression experiments establish FLC occupancy at SOC1 promoter and FT intron regulatory DNA and regulation of their transcription (PMID:16623882; PMID:16600915). This supports the inherited or domain-based activity without assigning every MADS-family member the same targets or regulatory sign. Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: FLC directly regulates RNA polymerase II target genes through sequence-specific chromatin binding. Reason: Native-target ChIP and expression experiments establish FLC occupancy at SOC1 promoter and FT intron regulatory DNA and regulation of their transcription (PMID:16623882; PMID:16600915). This supports the inherited or domain-based activity without assigning every MADS-family member the same targets or regulatory sign. Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: FLC directly regulates RNA polymerase II target genes through sequence-specific chromatin binding. Reason: Native-target ChIP and expression experiments establish FLC occupancy at SOC1 promoter and FT intron regulatory DNA and regulation of their transcription (PMID:16623882; PMID:16600915). This supports the inherited or domain-based activity without assigning every MADS-family member the same targets or regulatory sign. Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MODIFY | Summary: Refine general DNA binding to the established cis-regulatory sequence-specific activity. Reason: FLC occupies CArG-containing cis-regulatory DNA at the FT first intron and SOC1 promoter in target-specific ChIP experiments (PMID:16623882). This localizes the otherwise general DNA-binding claim to sequence-specific regulatory-region binding at RNA polymerase II-transcribed genes, already represented by GO:0000978. The evidence identifies a transcriptional DNA-recognition role rather than nonspecific DNA association. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | MODIFY | Summary: Refine transcription factor activity to regulation of RNA polymerase II targets. Reason: The InterPro-derived DNA-binding transcription-factor claim agrees with FLC occupancy of FT/SOC1 regulatory regions and altered expression of these protein-coding targets (PMID:16623882; PMID:16600915). Specifying RNA polymerase II in GO:0000981 captures the demonstrated transcription system. This activity term does not require an exclusively repressive sign at every FLC target. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: FLC acts on nuclear chromatin. Reason: In vivo chromatin occupancy at FT and SOC1 and the curated nuclear localization support the nuclear site of FLC transcription factor activity. Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. file:ARATH/FLC/FLC-uniprot.txt SUBCELLULAR LOCATION: Nucleus |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: Refine transcription regulation to RNA polymerase II transcription. Reason: FLC regulates transcription of the RNA polymerase II targets FT and SOC1 through their regulatory chromatin, supported by target occupancy and expression experiments (PMID:16623882; PMID:16600915). GO:0006357 adds the warranted polymerase specificity to the broad transcription-regulation process. Keeping the replacement unsigned preserves the separately supported target-dependent positive as well as negative effects. Proposed replacements: regulation of transcription by RNA polymerase II Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0009908 flower development | IEA GO_REF:0000043 | MODIFY | Summary: FLC negatively regulates floral development. Reason: FLC represses floral integrator expression and limits the meristem response to the FT signal (PMID:16600915), establishing a negative regulatory role in floral development. Replace the keyword-derived process membership with the already-supported GO:0009910 regulatory role. This is a lateral process-to-regulation correction, not an is_a/part_of descendant refinement of flower development; it does not imply that FLC itself constructs floral tissues. Proposed replacements: negative regulation of flower development Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0009909 regulation of flower development | IEA GO_REF:0000117 | MODIFY | Summary: Refine unsigned flower regulation to the supported negative effect. Reason: The original assertion already places FLC in regulation of flower development but leaves the direction unspecified. Repression of SOC1 and impairment of the meristem response to FT (PMID:16600915) support the negative sign represented by GO:0009910, also present in an experimental row. This specifies the direction of floral regulation, without claiming that every transcriptional target of FLC is repressed. Proposed replacements: negative regulation of flower development Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0030154 cell differentiation | IEA GO_REF:0000043 | MODIFY | Summary: Replace the generic differentiation mapping with FLC's demonstrated inhibition of floral development. Reason: The keyword-derived developmental claim should be expressed as negative regulation of flower development, already present experimentally, rather than as an unspecified cell-differentiation program. FLC controls floral integrator transcription and meristem competence. This is a correction of developmental role/scope, not a claim that developmental regulation is false merely because it is broad. Proposed replacements: negative regulation of flower development Supporting Evidence: PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IEA GO_REF:0000002 | ACCEPT | Summary: FLC can positively regulate a subset of its direct transcriptional targets. Reason: The prior sign reversal wrongly treated a flowering repressor as an obligate transcriptional repressor. PMID:21464308 combines FLC chromatin binding with target expression in flc mutants: five tested bound genes decreased in the mutant, supporting positive as well as negative transcriptional regulation. The full primary study identifies SMZ and TOE3 among positively regulated targets. This does not reverse FLC repression of FT/SOC1 or make FLC a universal activator. Supporting Evidence: PMID:21464308 Five genes showed decreased expression in the mutant, indicating that FLC binding can result in either transcriptional repression or activation. |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | ACCEPT | Summary: FLC forms multimeric MADS-protein assemblies. Reason: The in vivo complex can contain multiple FLC polypeptides, and a specific FLC-SVP interaction is independently supported. The general dimerization activity accommodates these self/partner assembly modes without claiming a single obligatory stoichiometry. Supporting Evidence: PMID:16623882 We have shown that FLC is a component of a multimeric protein complex in vivo and that more than one FLC polypeptides can be present in the complex. PMID:19011118 Yeast two-hybrid analysis demonstrated an interaction between SVP and FLOWERING LOCUS C |
| GO:0005515 protein binding | IPI PMID:19011118 Circadian clock proteins LHY and CCA1 regulate SVP protein a... | MODIFY | Summary: FLC forms a functional MADS-protein association with SVP. Reason: The primary study directly assays the FLC-SVP pair by yeast two-hybrid and places both proteins in flowering repression. Refine uninformative protein binding to heterodimerization in this MADS-partner context; this does not assert an isolated native two-subunit stoichiometry for every FLC complex. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:19011118 Yeast two-hybrid analysis demonstrated an interaction between SVP and FLOWERING LOCUS C |
| GO:0005515 protein binding | IPI PMID:28650476 CrY2H-seq: a massively multiplexed assay for deep-coverage i... | REMOVE | Summary: Remove uninformative bare binding while preserving the interaction-screen evidence. Reason: PMID:28650476 is a multiplexed binary-interaction screen of Arabidopsis transcription factors. The measured association is not denied, but a generic binding row does not identify a distinct FLC-enabled activity. The screen alone does not make every detected partner a native obligate heterodimer; characterized FLC MADS assembly is represented separately. Supporting Evidence: PMID:28650476 uncovering a network of 8,577 interactions among 1,453 transcription factors |
| GO:0005515 protein binding | IPI PMID:38053494 FLZ13 interacts with FLC and ABI5 to negatively regulate flo... | REMOVE | Summary: FLZ13 association is real but bare protein binding is uninformative. Reason: The primary study identifies direct FLZ13-FLC association and FLC-dependent repression of FT/SOC1. Preserve that regulatory interaction in the biological account; remove only the uninformative binding claim under policy, without assigning the regulator's activity to FLC. Supporting Evidence: PMID:38053494 Biochemical analysis showed that FLZ13 directly interacts with FLOWERING LOCUS C (FLC) |
| GO:0009266 response to temperature stimulus | IDA PMID:25267112 Jumonji demethylases moderate precocious flowering at elevat... | KEEP AS NON CORE | Summary: FLC participates in the flowering response to elevated temperature. Reason: PMID:25267112 shows that JMJ30/JMJ32 maintain FLC expression at warm temperatures and that the flc mutant has precocious flowering. FLC is a regulated output of this response, not itself a demonstrated temperature sensor or histone demethylase. Retain this precise environmental context outside the central DNA-binding activity. Supporting Evidence: PMID:25267112 At elevated temperatures, the JMJ30 RNA and protein are stabilized, and FLC expression is maintained at high levels to prevent extreme precocious flowering. |
| GO:2000028 regulation of photoperiodism, flowering | IMP PMID:25267112 Jumonji demethylases moderate precocious flowering at elevat... | ACCEPT | Summary: FLC controls competence for photoperiodic floral induction. Reason: The warm-temperature genetics of PMID:25267112 concern FLC-mediated flowering repression. Independent leaf/meristem experiments in PMID:16600915 establish that FLC blocks the response to photoperiodic FT signaling. Retain regulation of photoperiodic flowering without claiming FLC perceives day length. Supporting Evidence: PMID:16600915 Vernalization, the response to winter temperatures, overcomes a block on photoperiodic floral induction. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0000976 transcription cis-regulatory region binding | IPI PMID:30356219 Transcriptional regulation of nitrogen-associated metabolism... | MODIFY | Summary: Refine regulatory-region binding to the established sequence-specific cis-regulatory DNA-binding activity. Reason: The nitrogen-network paper is cached as an abstract that does not resolve the individual FLC target pair; it is not rejected for failing to name FLC there. Independent target-specific ChIP establishes the same general molecular claim with greater specificity at FT/SOC1 CArG-containing regions. No uninspected nitrogen-metabolism target is asserted. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. |
| GO:0032991 protein-containing complex | IDA PMID:16623882 The Arabidopsis FLC protein interacts directly in vivo with ... | ACCEPT | Summary: FLC is a component of an experimentally detected protein complex. Reason: PMID:16623882 reports an in vivo multimeric FLC-containing complex, including more than one FLC polypeptide. Retain the experimentally warranted complex membership without inventing its complete composition or asserting that all complexes are chromatin-silencing machinery. Supporting Evidence: PMID:16623882 We have shown that FLC is a component of a multimeric protein complex in vivo and that more than one FLC polypeptides can be present in the complex. |
| GO:0005515 protein binding | IPI PMID:30946745 Floral regulators FLC and SOC1 directly regulate expression ... | REMOVE | Summary: Retain the FLC/SVP chromatin-regulatory mechanism, but remove bare protein binding. Reason: PMID:30946745 establishes FLC/SVP-dependent repression and chromatin changes at TFS1. Generic protein binding adds no defined FLC-enabled molecular activity beyond its separately supported transcription-factor and MADS-association functions. Removal is the bare-binding policy exception, not a rejection of the reported interactions. Supporting Evidence: PMID:30946745 FLC and SVP repress TFS1 transcription leading to deposition of trimethylation of Iysine 27 of histone 3 (H3K27me3) by the Polycomb Repressive Complex 2 at the TFS1 locus. |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:16600915 The transcription factor FLC confers a flowering response to... | MODIFY | Summary: Specify FLC's RNA polymerase II DNA-binding transcription factor activity. Reason: The original experimental, comparative or literature assertion agrees with direct FLC target occupancy and transcriptional effects. Refine to the RNA polymerase II-specific activity already present; no inference that an abstract-only family paper omitted or misidentified FLC is made. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:12837945 Molecular and phylogenetic analyses of the complete MADS-box... | MODIFY | Summary: Specify FLC's RNA polymerase II DNA-binding transcription factor activity. Reason: The original experimental, comparative or literature assertion agrees with direct FLC target occupancy and transcriptional effects. Refine to the RNA polymerase II-specific activity already present; no inference that an abstract-only family paper omitted or misidentified FLC is made. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0009266 response to temperature stimulus | IMP PMID:16473970 FLOWERING LOCUS C mediates natural variation in the high-tem... | KEEP AS NON CORE | Summary: FLC contributes to temperature-dependent clock behavior. Reason: Near-isogenic lines and induced alleles establish an FLC-dependent increase in circadian period at 27 degrees C. This is a supported temperature-response role distinct from claiming direct temperature sensing or making circadian control its principal function. Supporting Evidence: PMID:16473970 FLC lengthened the circadian period specifically at 27 degrees C, contributing to temperature compensation of the circadian clock. |
| GO:0009910 negative regulation of flower development | IMP PMID:12114624 Multiple roles of Arabidopsis VRN1 in vernalization and flow... | ACCEPT | Summary: FLC is a genetically established floral repressor. Reason: The VRN1 study places FLC as the major repressed floral inhibitor; independent FLC tissue-expression and target-binding studies directly establish the inhibitory function. Its experimental assertion is not rejected because the original abstract emphasizes the upstream regulator. Supporting Evidence: PMID:12114624 the major target of the vernalization pathway, the floral repressor FLC. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0010048 vernalization response | IEP PMID:15734903 Differential regulation of FLOWERING LOCUS C expression by v... | ACCEPT | Summary: Downregulation of FLC links prolonged cold to competence to flower. Reason: The comparative study distinguishes cabbage and Arabidopsis vernalization responses rather than implying identical timing across species. Native Arabidopsis FLC transcript and protein decline with cold, quantitatively relating FLC levels to flowering response (PMID:10716723). Retain the response claim without assigning FLC the catalytic machinery that silences its own locus. Supporting Evidence: PMID:10716723 The level of FLC determines the extent of the vernalization response in the promotion of flowering |
| GO:0042752 regulation of circadian rhythm | IMP PMID:16473970 FLOWERING LOCUS C mediates natural variation in the high-tem... | KEEP AS NON CORE | Summary: FLC modulates circadian period in a temperature-dependent context. Reason: The primary allele and mutant experiments support a genuine clock phenotype. This is a secondary regulatory role, not evidence that FLC is an obligatory central oscillator component or directly modifies clock proteins. Supporting Evidence: PMID:16473970 FLC lengthened the circadian period specifically at 27 degrees C, contributing to temperature compensation of the circadian clock. |
| GO:0003700 DNA-binding transcription factor activity | TAS PMID:10716723 The molecular basis of vernalization: the central role of FL... | MODIFY | Summary: Specify FLC's RNA polymerase II DNA-binding transcription factor activity. Reason: The original experimental, comparative or literature assertion agrees with direct FLC target occupancy and transcriptional effects. Refine to the RNA polymerase II-specific activity already present; no inference that an abstract-only family paper omitted or misidentified FLC is made. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | MODIFY | Summary: Specify FLC's RNA polymerase II DNA-binding transcription factor activity. Reason: The original experimental, comparative or literature assertion agrees with direct FLC target occupancy and transcriptional effects. Refine to the RNA polymerase II-specific activity already present; no inference that an abstract-only family paper omitted or misidentified FLC is made. Proposed replacements: DNA-binding transcription factor activity, RNA polymerase II-specific Supporting Evidence: PMID:16623882 Using chromatin immunoprecipitation, we have shown that FLC binds to a region of the first intron of FT that contains a putative CArG box, and have confirmed that FLC binds to a CArG box in the promoter of the SOC1 gene. PMID:16600915 FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. |
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Download this section (compressed HTML)Q: Which native FLC partner combinations determine whether a bound target is activated or repressed in each tissue?
Q: How do the composition and stoichiometry of native FLC complexes change during floral transition and temperature responses?
Experiment: Combine native-tag FLC complex purification, partner perturbation, chromatin occupancy and nascent transcription in matched leaf and meristem samples before and after floral induction.
Hypothesis: FLC partner composition determines target-specific transcriptional sign.
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