CRY1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0009414 response to water deprivation	IGI PMID:16093319 From The Cover: A role for Arabidopsis cryptochromes and COP...	MARK AS OVER ANNOTATED	Summary: Water-deprivation response reflects altered stomatal aperture and water loss rather than a primary CRY1 function. Reason: The direct evidence is that CRY1/CRY2 regulate blue-light stomatal opening and water loss. Calling CRY1 a water-deprivation response gene overstates an indirect physiological consequence. Supporting Evidence: PMID:16093319 CRY functions additively with PHOT in mediating blue light-induced stomatal opening.
GO:0009416 response to light stimulus	IMP PMID:36508461 A role for brassinosteroid signalling in decision-making pro...	MODIFY	Summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A photoreception. Reason: The original cached abstract does not verify a CRY1-specific light-response claim, and the term is too broad in any case. The supported CRY1 biology should be represented by blue-light response/signaling terms. Proposed replacements: response to blue light blue light signaling pathway Supporting Evidence: PMID:36508461 The accessible abstract describes a BIN2 light/water screen, but does not mention CRY1.
GO:0009583 detection of light stimulus	IMP PMID:20668058 Cryptochrome as a sensor of the blue/green ratio of natural ...	ACCEPT	Summary: detection of light stimulus matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:20668058 Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis.
GO:0009637 response to blue light	IMP PMID:12324610 Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition ...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:12324610 Hypocotyl elongation is not inhibited in the mutant seedlings by continuous blue light.
GO:0009638 phototropism	IMP PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochro...	KEEP AS NON CORE	Summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated Inhibition of PIF4 Expression.
GO:0009640 photomorphogenesis	IMP PMID:12324610 Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition ...	ACCEPT	Summary: photomorphogenesis matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:12324610 Hypocotyl elongation is not inhibited in the mutant seedlings by continuous blue light.
GO:0009785 blue light signaling pathway	TAS PMID:10364413 Arabidopsis contains at least four independent blue-light-ac...	ACCEPT	Summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:10364413 These photoreceptors appear to activate separate signal transduction pathways.
GO:0010075 regulation of meristem growth	IGI PMID:18424613 Distinct light-initiated gene expression and cell cycle prog...	KEEP AS NON CORE	Summary: regulation of meristem growth is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:18424613 phytochromes and cryptochromes play largely redundant roles
GO:0010118 stomatal movement	IGI PMID:16093319 From The Cover: A role for Arabidopsis cryptochromes and COP...	KEEP AS NON CORE	Summary: Stomatal movement is a supported non-core output of CRY1 blue-light signaling. Reason: CRY1/CRY2 influence blue-light stomatal opening, but this physiological output is downstream of the core photoreceptor/signaling role. Supporting Evidence: PMID:16093319 CRY functions additively with PHOT in mediating blue light-induced stomatal opening.
GO:0010343 singlet oxygen-mediated programmed cell death	IMP PMID:17075038 Cryptochrome-1-dependent execution of programmed cell death ...	KEEP AS NON CORE	Summary: singlet oxygen-mediated programmed cell death is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:17075038 Cryptochrome-1-dependent execution of programmed cell death induced by singlet oxygen.
GO:0010468 regulation of gene expression	IMP PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochro...	MODIFY	Summary: Regulation of gene expression is too broad for the CRY1/PIF4 phototropism evidence. Reason: The cited work supports CRY1 control of PIF4 expression in low-blue-light phototropism, so response to blue light and phototropism capture the evidence more specifically than general gene-expression regulation. Proposed replacements: response to blue light phototropism Supporting Evidence: PMID:32554507 Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated Inhibition of PIF4 Expression.
GO:0010617 circadian regulation of calcium ion oscillation	IMP PMID:17982000 Distinct light and clock modulation of cytosolic free Ca2+ o...	KEEP AS NON CORE	Summary: circadian regulation of calcium ion oscillation is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:17982000 Plants have circadian oscillations in the concentration of cytosolic free calcium.
GO:0046283 anthocyanin-containing compound metabolic process	IMP PMID:17217468 HY5 is a point of convergence between cryptochrome and cytok...	KEEP AS NON CORE	Summary: anthocyanin-containing compound metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:17217468 downstream of cryptochrome 1 (CRY1) at the level of transcript accumulation
GO:0046777 protein autophosphorylation	IDA PMID:12846824 Novel ATP-binding and autophosphorylation activity associate...	KEEP AS NON CORE	Summary: protein autophosphorylation is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: CRY1 autophosphorylation is experimentally supported, but its in vivo regulatory significance and light dependence are less central than CRY1 photoreceptor activity. Supporting Evidence: PMID:12846824 autophosphorylation activity associated with Arabidopsis cry1 protein
GO:0051510 regulation of unidimensional cell growth	IMP PMID:12324610 Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition ...	ACCEPT	Summary: regulation of unidimensional cell growth matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:12324610 Hypocotyl elongation is not inhibited in the mutant seedlings by continuous blue light.
GO:2000652 regulation of secondary cell wall biogenesis	IDA PMID:30242037 Blue Light Regulates Secondary Cell Wall Thickening via MYC2...	KEEP AS NON CORE	Summary: regulation of secondary cell wall biogenesis is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:30242037 CRY1 overexpression led to enhanced SCW formation.
GO:0003904 deoxyribodipyrimidine photo-lyase activity	IBA GO_REF:0000033	REMOVE	Summary: Photolyase activity is not supported for Arabidopsis CRY1. Reason: CRY1 is in the cryptochrome/photolyase superfamily, but Arabidopsis CRY1 is a cryptochrome photoreceptor and published summaries state that cryptochromes lack photolyase DNA repair activity. The PANTHER family includes true photolyases, making this IBA transfer over-propagated. Supporting Evidence: PMID:11752373 lack photolyase activity file:interpro/panther/PTHR11455/PTHR11455-notes.md The family contains both cryptochromes and photolyases; subfamilies separate circadian cryptochromes from repair enzymes. file:interpro/panther/PTHR11455/PTHR11455-entries.csv Q43125,Cryptochrome-1,protein,3702,Arabidopsis thaliana,...,PTHR11455:SF50,CRYPTOCHROME-1
GO:0004672 protein kinase activity	IDA PMID:12846824 Novel ATP-binding and autophosphorylation activity associate...	KEEP AS NON CORE	Summary: protein kinase activity is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: AtCRY1 autokinase activity is experimentally supported in vitro, but the primary evolved molecular function is blue-light photoreceptor signaling. Supporting Evidence: PMID:12846824 autophosphorylation activity associated with Arabidopsis cry1 protein
GO:0005515 protein binding	IPI PMID:11509693 Direct interaction of Arabidopsis cryptochromes with COP1 in...	REMOVE	Summary: Generic protein binding from PMID:11509693 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:11509693 photoactivated cryptochromes repress COP1 activity through a direct
GO:0005515 protein binding	IPI PMID:11752373 The signaling mechanism of Arabidopsis CRY1 involves direct ...	REMOVE	Summary: Generic protein binding from PMID:11752373 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:11752373 The signaling mechanism of Arabidopsis CRY is mediated through CCT.
GO:0005515 protein binding	IPI PMID:21511871 Arabidopsis cryptochrome 1 interacts with SPA1 to suppress C...	REMOVE	Summary: Generic protein binding from PMID:21511871 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:21511871 CRY1-SPA1 interaction suppresses the SPA1-COP1 interaction
GO:0005515 protein binding	IPI PMID:21511872 Blue-light-dependent interaction of cryptochrome 1 with SPA1...	REMOVE	Summary: Generic protein binding from PMID:21511872 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:21511872 CRY1 interacts physically with SPA1 in a blue-light-dependent manner.
GO:0005515 protein binding	IPI PMID:22577138 Light-dependent, dark-promoted interaction between Arabidops...	REMOVE	Summary: Generic protein binding from PMID:22577138 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:22577138 CRY1), a UV-A/blue photoreceptor.
GO:0005515 protein binding	IPI PMID:26596765 TCP2 positively regulates HY5/HYH and photomorphogenesis in ...	REMOVE	Summary: Generic protein binding from PMID:26596765 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:26596765 TCP2 physically interacts with CRY1
GO:0005515 protein binding	IPI PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G...	REMOVE	Summary: Generic protein binding from PMID:26724867 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:26724867 CRY1 and CRY2 perceive
GO:0005515 protein binding	IPI PMID:32661061 Photoexcited Cryptochrome2 Interacts Directly with TOE1 and ...	REMOVE	Summary: Generic protein binding from PMID:32661061 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:32661061 CRY1 and CRY2 physically interact with TOE1 and TOE2 in a BL-dependent manner.
GO:0005515 protein binding	IPI PMID:9651577 The CRY1 blue light photoreceptor of Arabidopsis interacts w...	REMOVE	Summary: Generic protein binding from PMID:9651577 records a real CRY1 interaction but is not informative as a GO molecular function. Reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition, PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein binding. Supporting Evidence: PMID:9651577 The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in vitro.
GO:0005524 ATP binding	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: ATP binding is a supported biochemical property that affects CRY1 conformation and flavin photochemistry, but it is accessory to photoreceptor signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Binding to ATP mediates conformational changes which facilitate flavin binding.
GO:0005524 ATP binding	IDA PMID:12846824 Novel ATP-binding and autophosphorylation activity associate...	KEEP AS NON CORE	Summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: ATP binding is a supported biochemical property that affects CRY1 conformation and flavin photochemistry, but it is accessory to photoreceptor signaling. Supporting Evidence: PMID:12846824 autophosphorylation activity associated with Arabidopsis cry1 protein
GO:0005524 ATP binding	IDA PMID:17073458 Analysis of autophosphorylating kinase activities of Arabido...	KEEP AS NON CORE	Summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: ATP binding is a supported biochemical property that affects CRY1 conformation and flavin photochemistry, but it is accessory to photoreceptor signaling. Supporting Evidence: PMID:17073458 AtCry1, which contains near stoichiometric
GO:0005524 ATP binding	IDA PMID:19327354 Conformational change induced by ATP binding correlates with...	KEEP AS NON CORE	Summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: ATP binding is a supported biochemical property that affects CRY1 conformation and flavin photochemistry, but it is accessory to photoreceptor signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Binding to ATP mediates conformational changes which facilitate flavin binding.
GO:0009882 blue light photoreceptor activity	IEA GO_REF:0000002	ACCEPT	Summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Photoreceptor that mediates primarily blue light inhibition of hypocotyl elongation. file:ARATH/CRY1/CRY1-deep-research-falcon.md nucleo-cytoplasmic blue/UV-A photoreceptor
GO:0009882 blue light photoreceptor activity	IDA PMID:30242037 Blue Light Regulates Secondary Cell Wall Thickening via MYC2...	ACCEPT	Summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:8953250 CRY1 is a flavin-type blue type receptor of Arabidopsis PMID:30242037 CRY1 overexpression led to enhanced SCW formation.
GO:0009882 blue light photoreceptor activity	IMP PMID:8953250 Arabidopsis cryptochrome 1 is a soluble protein mediating bl...	ACCEPT	Summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:8953250 CRY1 is a flavin-type blue type receptor of Arabidopsis
GO:0016301 kinase activity	IDA PMID:17073458 Analysis of autophosphorylating kinase activities of Arabido...	MODIFY	Summary: Kinase activity is supported only as CRY1 autokinase activity and should be stated more specifically. Reason: The biochemical evidence is for protein autophosphorylation/autokinase activity of AtCRY1. Protein kinase activity is the more specific molecular-function term than generic kinase activity. Proposed replacements: protein kinase activity Supporting Evidence: PMID:17073458 AtCry1, which contains near stoichiometric
GO:0042802 identical protein binding	IPI PMID:15805487 N-terminal domain-mediated homodimerization is required for ...	MODIFY	Summary: Identical protein binding captures CRY1 self-association but the specific homodimerization term is better. Reason: The evidence concerns CRY1 homodimerization, and GO:0042803 directly states this activity whereas identical protein binding is less precise. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:15805487 N-terminal domain-mediated homodimerization is required for photoreceptor activity of Arabidopsis CRYPTOCHROME 1.
GO:0042803 protein homodimerization activity	IEA GO_REF:0000117	ACCEPT	Summary: protein homodimerization activity matches the core CRY1 photoreceptor/signaling role. Reason: CRY1 homodimerization/oligomerization is an activation mechanism required for photoreceptor signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subunit: Homodimer.
GO:0042803 protein homodimerization activity	IPI PMID:15805487 N-terminal domain-mediated homodimerization is required for ...	ACCEPT	Summary: protein homodimerization activity matches the core CRY1 photoreceptor/signaling role. Reason: CRY1 homodimerization/oligomerization is an activation mechanism required for photoreceptor signaling. Supporting Evidence: PMID:15805487 N-terminal domain-mediated homodimerization is required for photoreceptor activity of Arabidopsis CRYPTOCHROME 1.
GO:0071949 FAD binding	IEA GO_REF:0000117	ACCEPT	Summary: FAD binding matches the core CRY1 photoreceptor/signaling role. Reason: FAD binding is central to CRY1 blue-light absorption and flavin photoredox signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Name=FAD; Binds 1 FAD per subunit.
GO:0071949 FAD binding	IDA PMID:17073458 Analysis of autophosphorylating kinase activities of Arabido...	ACCEPT	Summary: FAD binding matches the core CRY1 photoreceptor/signaling role. Reason: FAD binding is central to CRY1 blue-light absorption and flavin photoredox signaling. Supporting Evidence: PMID:17073458 AtCry1, which contains near stoichiometric
GO:0140517 protein-RNA adaptor activity	IPI PMID:36305219 The blue light receptor CRY1 interacts with FIP37 to promote...	KEEP AS NON CORE	Summary: protein-RNA adaptor activity is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The CRY1-FIP37 interaction supports a specific adaptor role in blue-light m6A regulation, but this appears to be a specialized signaling branch rather than the primary CRY1 molecular function. Supporting Evidence: PMID:36305219 CRY1 physically interacted with FIP37
GO:0007623 circadian rhythm	IEP PMID:11743105 Circadian clock-regulated expression of phytochrome and cryp...	KEEP AS NON CORE	Summary: circadian rhythm is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:11743105 display circadian oscillations under constant conditions
GO:0009266 response to temperature stimulus	IMP PMID:30635559 Daytime temperature is sensed by phytochrome B in Arabidopsi...	KEEP AS NON CORE	Summary: response to temperature stimulus is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:30635559 the PHYB-dependent hypocotyl thermoresponse is masked by CRY1
GO:0009414 response to water deprivation	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: Water-deprivation response reflects altered stomatal aperture and water loss rather than a primary CRY1 function. Reason: The direct evidence is that CRY1/CRY2 regulate blue-light stomatal opening and water loss. Calling CRY1 a water-deprivation response gene overstates an indirect physiological consequence. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0009416 response to light stimulus	IEP PMID:11743105 Circadian clock-regulated expression of phytochrome and cryp...	MODIFY	Summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A photoreception. Reason: This IEP row reflects light/circadian regulation of CRY1 expression, while the gene-product function is better captured by direct blue-light response and blue-light signaling terms. Proposed replacements: response to blue light blue light signaling pathway Supporting Evidence: PMID:11743105 display circadian oscillations under constant conditions
GO:0009416 response to light stimulus	IMP PMID:15751956 Role of structural plasticity in signal transduction by the ...	MODIFY	Summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A photoreception. Reason: CRY1 is a blue/UV-A photoreceptor. The broad parent term loses the relevant spectral and signaling specificity. Proposed replacements: response to blue light blue light signaling pathway Supporting Evidence: PMID:15751956 light-dependent conformational change in the C-terminal domain of Arabidopsis
GO:0009416 response to light stimulus	IDA PMID:21467031 Light-activated cryptochrome reacts with molecular oxygen to...	MODIFY	Summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A photoreception. Reason: CRY1 is a blue/UV-A photoreceptor. The broad parent term loses the relevant spectral and signaling specificity. Proposed replacements: response to blue light blue light signaling pathway Supporting Evidence: PMID:21467031 Light-activated cryptochrome reacts with molecular oxygen to form a flavin-superoxide radical pair.
GO:0009637 response to blue light	IMP PMID:12857830 Second positive phototropism results from coordinated co-act...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:12857830 phototropins and cryptochromes function
GO:0009637 response to blue light	IMP PMID:21511871 Arabidopsis cryptochrome 1 interacts with SPA1 to suppress C...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:21511871 CRY1-SPA1 interaction suppresses the SPA1-COP1 interaction
GO:0009637 response to blue light	IDA PMID:21511872 Blue-light-dependent interaction of cryptochrome 1 with SPA1...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:21511872 CRY1 interacts physically with SPA1 in a blue-light-dependent manner.
GO:0009637 response to blue light	IMP PMID:22147516 Phototropins but not cryptochromes mediate the blue light-sp...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:22147516 effects of cry on stomatal conductance are largely indirect
GO:0009637 response to blue light	IMP PMID:23511208 Network balance via CRY signalling controls the Arabidopsis ...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:23511208 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures.
GO:0009637 response to blue light	IMP PMID:25721730 The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to M...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:25721730 The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to Mediate Blue Light Inhibition of Hypocotyl Elongation.
GO:0009637 response to blue light	IDA PMID:25728686 Blue-light dependent reactive oxygen species formation by Ar...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:25728686 Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome.
GO:0009637 response to blue light	IMP PMID:26313597 Cellular metabolites modulate in vivo signaling of Arabidops...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:26313597 These pathways are potentiated by metabolites in the intracellular
GO:0009637 response to blue light	IMP PMID:8528277 Mutations throughout an Arabidopsis blue-light photoreceptor...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:8528277 CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated inhibition
GO:0009637 response to blue light	IMP PMID:9733523 Genetic interactions between phytochrome A, phytochrome B, a...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:9733523 cry1 activity in a phyAphyB mutant
GO:0009637 response to blue light	IMP PMID:9765547 Two genetically separable phases of growth inhibition induce...	ACCEPT	Summary: response to blue light matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: PMID:9765547 High fluence-rate blue light (BL) rapidly inhibits hypocotyl growth
GO:0009638 phototropism	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0009638 phototropism	IMP PMID:12857830 Second positive phototropism results from coordinated co-act...	KEEP AS NON CORE	Summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:12857830 phototropins and cryptochromes function
GO:0009638 phototropism	IMP PMID:8528277 Mutations throughout an Arabidopsis blue-light photoreceptor...	KEEP AS NON CORE	Summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:8528277 CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated inhibition
GO:0009644 response to high light intensity	IMP PMID:22786870 The CRYPTOCHROME1-dependent response to excess light is medi...	KEEP AS NON CORE	Summary: response to high light intensity is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:22786870 components of the cry1-mediated photoprotective response
GO:0009646 response to absence of light	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: response to absence of light is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0009646 response to absence of light	IMP PMID:22855128 cry1 and GPA1 signaling genetically interact in hook opening...	KEEP AS NON CORE	Summary: response to absence of light is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:22855128 cry1 and GPA1 signaling genetically interact in hook opening and anthocyanin synthesis.
GO:0009785 blue light signaling pathway	IEA GO_REF:0000002	ACCEPT	Summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0009785 blue light signaling pathway	IEA GO_REF:0000117	ACCEPT	Summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role. Reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light signaling and photomorphogenesis. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0009791 post-embryonic development	IEA GO_REF:0000117	MODIFY	Summary: post-embryonic development is a broad developmental consequence of CRY1 light signaling. Reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent growth, not a generic role in overall development. Proposed replacements: photomorphogenesis response to blue light Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0010075 regulation of meristem growth	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: regulation of meristem growth is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0010114 response to red light	IMP PMID:9733523 Genetic interactions between phytochrome A, phytochrome B, a...	KEEP AS NON CORE	Summary: response to red light is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:9733523 cry1 activity in a phyAphyB mutant
GO:0010117 photoprotection	IMP PMID:22786870 The CRYPTOCHROME1-dependent response to excess light is medi...	KEEP AS NON CORE	Summary: photoprotection is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:22786870 components of the cry1-mediated photoprotective response
GO:0010118 stomatal movement	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: Stomatal movement is a supported non-core output of CRY1 blue-light signaling. Reason: CRY1/CRY2 influence blue-light stomatal opening, but this physiological output is downstream of the core photoreceptor/signaling role. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0010118 stomatal movement	IMP PMID:22147516 Phototropins but not cryptochromes mediate the blue light-sp...	KEEP AS NON CORE	Summary: Stomatal movement is retained as a non-core CRY1 output, with this study supporting an indirect ABA-linked effect on conductance. Reason: The paper argues cry effects on stomatal conductance are largely indirect rather than direct blue-light stomatal photoreception, so the term should not be treated as core CRY1 function. Supporting Evidence: PMID:22147516 effects of cry on stomatal conductance are largely indirect
GO:0010218 response to far red light	IMP PMID:9733523 Genetic interactions between phytochrome A, phytochrome B, a...	KEEP AS NON CORE	Summary: response to far red light is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:9733523 cry1 activity in a phyAphyB mutant
GO:0010244 response to low fluence blue light stimulus by blue low-fluence system	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: response to low fluence blue light stimulus by blue low-fluence system is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0010244 response to low fluence blue light stimulus by blue low-fluence system	IMP PMID:19558423 Differential petiole growth in Arabidopsis thaliana: photoco...	KEEP AS NON CORE	Summary: response to low fluence blue light stimulus by blue low-fluence system is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Reduced hyponastic growth (differential growth-driven upward leaf movement) in low blue light fluence.
GO:0010244 response to low fluence blue light stimulus by blue low-fluence system	IEP PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G...	KEEP AS NON CORE	Summary: response to low fluence blue light stimulus by blue low-fluence system is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:26724867 CRY1 and CRY2 perceive
GO:0010310 regulation of hydrogen peroxide metabolic process	IDA PMID:25728686 Blue-light dependent reactive oxygen species formation by Ar...	KEEP AS NON CORE	Summary: regulation of hydrogen peroxide metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:25728686 Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome.
GO:0010617 circadian regulation of calcium ion oscillation	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: circadian regulation of calcium ion oscillation is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0032922 circadian regulation of gene expression	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: circadian regulation of gene expression is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0042752 regulation of circadian rhythm	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: regulation of circadian rhythm is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0042752 regulation of circadian rhythm	IMP PMID:23511208 Network balance via CRY signalling controls the Arabidopsis ...	KEEP AS NON CORE	Summary: regulation of circadian rhythm is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:23511208 Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures.
GO:0043153 entrainment of circadian clock by photoperiod	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: entrainment of circadian clock by photoperiod is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0046283 anthocyanin-containing compound metabolic process	IMP PMID:8528277 Mutations throughout an Arabidopsis blue-light photoreceptor...	KEEP AS NON CORE	Summary: anthocyanin-containing compound metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:8528277 CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated inhibition
GO:0046777 protein autophosphorylation	IDA PMID:17073458 Analysis of autophosphorylating kinase activities of Arabido...	KEEP AS NON CORE	Summary: protein autophosphorylation is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: CRY1 autophosphorylation is experimentally supported, but its in vivo regulatory significance and light dependence are less central than CRY1 photoreceptor activity. Supporting Evidence: PMID:17073458 AtCry1, which contains near stoichiometric
GO:0048580 regulation of post-embryonic development	IEA GO_REF:0000117	MODIFY	Summary: regulation of post-embryonic development is a broad developmental consequence of CRY1 light signaling. Reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent growth, not a generic role in overall development. Proposed replacements: photomorphogenesis response to blue light Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0048731 system development	IEA GO_REF:0000117	MODIFY	Summary: system development is a broad developmental consequence of CRY1 light signaling. Reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent growth, not a generic role in overall development. Proposed replacements: photomorphogenesis response to blue light Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:0060918 auxin transport	IMP PMID:20133010 Arabidopsis cryptochrome-1 restrains lateral roots growth by...	KEEP AS NON CORE	Summary: auxin transport is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:20133010 Arabidopsis CRY1 restrains lateral roots growth by inhibiting auxin transport.
GO:0071000 response to magnetism	IDA PMID:22421133 Magnetically sensitive light-induced reactions in cryptochro...	KEEP AS NON CORE	Summary: response to magnetism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:22421133 Magnetically sensitive light-induced reactions in cryptochrome are consistent with its proposed role as a magnetoreceptor.
GO:0071000 response to magnetism	IMP PMID:26095447 Suppression of Arabidopsis flowering by near-null magnetic f...	KEEP AS NON CORE	Summary: response to magnetism is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:26095447 The effect of near-null magnetic field on Arabidopsis flowering is associated with CRY.
GO:0072387 flavin adenine dinucleotide metabolic process	ISS GO_REF:0000024	MODIFY	Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Blue-light absorbing flavoprotein that activates reversible flavin photoreduction.
GO:0072387 flavin adenine dinucleotide metabolic process	IEA GO_REF:0000117	MODIFY	Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Blue-light absorbing flavoprotein that activates reversible flavin photoreduction.
GO:0072387 flavin adenine dinucleotide metabolic process	IDA PMID:21467031 Light-activated cryptochrome reacts with molecular oxygen to...	MODIFY	Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: PMID:21467031 Light-activated cryptochrome reacts with molecular oxygen to form a flavin-superoxide radical pair.
GO:0072387 flavin adenine dinucleotide metabolic process	IDA PMID:25157750 ATP binding and aspartate protonation enhance photoinduced e...	MODIFY	Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: PMID:25157750 ATP binding and aspartate protonation enhance photoinduced electron transfer in plant cryptochrome.
GO:0072387 flavin adenine dinucleotide metabolic process	IMP PMID:26313597 Cellular metabolites modulate in vivo signaling of Arabidops...	MODIFY	Summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function, not FAD metabolic process. Reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling, but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor metabolism as a biological process. Proposed replacements: FAD binding blue light photoreceptor activity Supporting Evidence: PMID:26313597 These pathways are potentiated by metabolites in the intracellular
GO:0099402 plant organ development	IMP PMID:25721730 The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to M...	MODIFY	Summary: plant organ development is a broad developmental consequence of CRY1 light signaling. Reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent growth, not a generic role in overall development. Proposed replacements: photomorphogenesis response to blue light Supporting Evidence: PMID:25721730 The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to Mediate Blue Light Inhibition of Hypocotyl Elongation.
GO:1900426 positive regulation of defense response to bacterium	IMP PMID:20053798 CRYPTOCHROME 1 is implicated in promoting R protein-mediated...	KEEP AS NON CORE	Summary: positive regulation of defense response to bacterium is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Promotes systemic acquired resistance (SAR) and PR gene expression triggered by P.syringae.
GO:1901332 negative regulation of lateral root development	IMP PMID:20133010 Arabidopsis cryptochrome-1 restrains lateral roots growth by...	KEEP AS NON CORE	Summary: negative regulation of lateral root development is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:20133010 Arabidopsis CRY1 restrains lateral roots growth by inhibiting auxin transport.
GO:1901371 regulation of leaf morphogenesis	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: regulation of leaf morphogenesis is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:1901371 regulation of leaf morphogenesis	IMP PMID:19558423 Differential petiole growth in Arabidopsis thaliana: photoco...	KEEP AS NON CORE	Summary: regulation of leaf morphogenesis is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Reduced hyponastic growth (differential growth-driven upward leaf movement) in low blue light fluence.
GO:1901529 positive regulation of anion channel activity	IMP PMID:9765547 Two genetically separable phases of growth inhibition induce...	KEEP AS NON CORE	Summary: positive regulation of anion channel activity is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:9765547 High fluence-rate blue light (BL) rapidly inhibits hypocotyl growth
GO:1901672 positive regulation of systemic acquired resistance	IMP PMID:20053798 CRYPTOCHROME 1 is implicated in promoting R protein-mediated...	KEEP AS NON CORE	Summary: positive regulation of systemic acquired resistance is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Promotes systemic acquired resistance (SAR) and PR gene expression triggered by P.syringae.
GO:1902347 response to strigolactone	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: response to strigolactone is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:1902347 response to strigolactone	IMP PMID:24126495 Strigolactone-regulated hypocotyl elongation is dependent on...	KEEP AS NON CORE	Summary: response to strigolactone is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:24126495 Strigolactone-regulated hypocotyl elongation is dependent on cryptochrome and phytochrome signaling pathways.
GO:1902448 positive regulation of shade avoidance	IMP PMID:21457375 Cryptochrome 1 and phytochrome B control shade-avoidance res...	KEEP AS NON CORE	Summary: positive regulation of shade avoidance is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:21457375 Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis.
GO:2000377 regulation of reactive oxygen species metabolic process	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: regulation of reactive oxygen species metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
GO:2000377 regulation of reactive oxygen species metabolic process	IDA PMID:25728686 Blue-light dependent reactive oxygen species formation by Ar...	KEEP AS NON CORE	Summary: regulation of reactive oxygen species metabolic process is supported for CRY1 but is a non-core output or accessory biochemical property. Reason: The annotation is supported as a downstream or context-specific output of CRY1 blue-light signaling, but it should not be treated as the core molecular role of CRY1. Supporting Evidence: PMID:25728686 Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome.
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005634 nucleus	IDA PMID:10221900 Cryptochromes: blue light receptors for plants and animals.	ACCEPT	Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005634 nucleus	HDA PMID:15610358 High-throughput protein localization in Arabidopsis using Ag...	ACCEPT	Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005634 nucleus	EXP PMID:18003924 Separate functions for nuclear and cytoplasmic cryptochrome ...	ACCEPT	Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005634 nucleus	IDA PMID:26724867 Cryptochromes Interact Directly with PIFs to Control Plant G...	ACCEPT	Summary: nucleus matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: cytoplasm matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005737 cytoplasm	IEA GO_REF:0000117	ACCEPT	Summary: cytoplasm matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005737 cytoplasm	IDA PMID:18003924 Separate functions for nuclear and cytoplasmic cryptochrome ...	ACCEPT	Summary: cytoplasm matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0005829 cytosol	HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati...	UNDECIDED	Summary: Cytosol localization is plausible for CRY1 but the high-throughput dataset support is not accessible in the cached text. Reason: CRY1 has independent cytoplasm evidence, but this specific HDA cytosol assertion cannot be checked from the accessible publication text. Supporting Evidence: PMID:28887381 The accessible cache describes a global protein-correlation profiling dataset, but not the CRY1 cytosol call.
GO:0016604 nuclear body	IEA GO_REF:0000117	ACCEPT	Summary: nuclear body matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0016604 nuclear body	IDA PMID:21511872 Blue-light-dependent interaction of cryptochrome 1 with SPA1...	ACCEPT	Summary: nuclear body matches the core CRY1 photoreceptor/signaling role. Reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body accumulation during photomorphogenic signaling. Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.
GO:0016605 PML body	IEA GO_REF:0000044	MODIFY	Summary: PML body is an animal-centric mapping; the plant evidence supports CRY1 nuclear bodies. Reason: Arabidopsis CRY1 is reported in nuclear bodies. PML body is too specific for plant CRY1 and should be replaced by nuclear body. Proposed replacements: nuclear body Supporting Evidence: file:ARATH/CRY1/CRY1-uniprot.txt Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies.

Core Functions

CRY1 is a FAD-dependent blue/UV-A photoreceptor whose light-driven flavin photoredox, conformational change, and oligomerization initiate blue-light signaling outputs including photomorphogenesis, hypocotyl growth inhibition, circadian modulation, and regulation of transcription-factor stability or activity.

Molecular Function:

blue light photoreceptor activity

Directly Involved In:

blue light signaling pathway photomorphogenesis regulation of unidimensional cell growth

Cellular Locations:

nucleus cytoplasm nuclear body

Supporting Evidence:

PMID:8953250
CRY1 is a flavin-type blue type receptor of Arabidopsis
PMID:15805487
N-terminal domain-mediated homodimerization is required for photoreceptor activity of Arabidopsis CRYPTOCHROME 1.
PMID:21511872
CRY1 interacts physically with SPA1 in a blue-light-dependent manner.
PMID:26724867
CRY1 and CRY2 perceive
file:ARATH/CRY1/CRY1-uniprot.txt
Blue-light absorbing flavoprotein that activates reversible flavin photoreduction.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000024

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000122

AtSubP analysis

PMID:10221900

Cryptochromes: blue light receptors for plants and animals.

PMID:10364413

Arabidopsis contains at least four independent blue-light-activated signal transduction pathways.

PMID:11509693

Direct interaction of Arabidopsis cryptochromes with COP1 in light control development.

PMID:11743105

Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis.

PMID:11752373

The signaling mechanism of Arabidopsis CRY1 involves direct interaction with COP1.

Arabidopsis CRY1 and CRY2 are cryptochrome photoreceptors rather than DNA repair photolyases.

"lack photolyase activity"

PMID:12324610

Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition of Hypocotyl Elongation.

PMID:12846824

Novel ATP-binding and autophosphorylation activity associated with Arabidopsis and human cryptochrome-1.

CRY1 has ATP-binding/autophosphorylation activity.

"autophosphorylation activity associated with Arabidopsis cry1 protein"

PMID:12857830

Second positive phototropism results from coordinated co-action of the phototropins and cryptochromes.

PMID:15610358

High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions.

PMID:15751956

Role of structural plasticity in signal transduction by the cryptochrome blue-light photoreceptor.

PMID:15805487

N-terminal domain-mediated homodimerization is required for photoreceptor activity of Arabidopsis CRYPTOCHROME 1.

PMID:16093319

From The Cover: A role for Arabidopsis cryptochromes and COP1 in the regulation of stomatal opening.

CRY1/CRY2 contribute to blue-light-induced stomatal opening through COP1-related signaling.

"CRY functions additively with PHOT in mediating blue light-induced stomatal opening."

PMID:17073458

Analysis of autophosphorylating kinase activities of Arabidopsis and human cryptochromes.

AtCRY1 contains FAD and has autokinase activity in vitro.

"AtCry1, which contains near stoichiometric"

PMID:17075038

Cryptochrome-1-dependent execution of programmed cell death induced by singlet oxygen in Arabidopsis thaliana.

PMID:17217468

HY5 is a point of convergence between cryptochrome and cytokinin signalling pathways in Arabidopsis thaliana.

PMID:17982000

Distinct light and clock modulation of cytosolic free Ca2+ oscillations and rhythmic CHLOROPHYLL A/B BINDING PROTEIN2 promoter activity in Arabidopsis.

PMID:18003924

Separate functions for nuclear and cytoplasmic cryptochrome 1 during photomorphogenesis of Arabidopsis seedlings.

PMID:18424613

Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis.

PMID:19327354

Conformational change induced by ATP binding correlates with enhanced biological function of Arabidopsis cryptochrome.

PMID:19558423

Differential petiole growth in Arabidopsis thaliana: photocontrol and hormonal regulation.

PMID:20053798

CRYPTOCHROME 1 is implicated in promoting R protein-mediated plant resistance to Pseudomonas syringae in Arabidopsis.

PMID:20133010

Arabidopsis cryptochrome-1 restrains lateral roots growth by inhibiting auxin transport.

PMID:20668058

Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis.

CRY1 contributes to detection of blue/green light ratio.

"Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis."

PMID:21457375

Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis via partially independent hormonal cascades.

PMID:21467031

Light-activated cryptochrome reacts with molecular oxygen to form a flavin-superoxide radical pair consistent with magnetoreception.

PMID:21511871

Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response to blue light.

PMID:21511872

Blue-light-dependent interaction of cryptochrome 1 with SPA1 defines a dynamic signaling mechanism.

CRY1 interacts with SPA1 in a blue-light-dependent signaling mechanism.

"CRY1 interacts physically with SPA1 in a blue-light-dependent manner."

PMID:22147516

Phototropins but not cryptochromes mediate the blue light-specific promotion of stomatal conductance, while both enhance photosynthesis and transpiration under full sunlight.

CRY effects on stomatal conductance can be indirect and ABA-linked.

"effects of cry on stomatal conductance are largely indirect"

PMID:22421133

Magnetically sensitive light-induced reactions in cryptochrome are consistent with its proposed role as a magnetoreceptor.

PMID:22577138

Light-dependent, dark-promoted interaction between Arabidopsis cryptochrome 1 and phytochrome B proteins.

PMID:22786870

The CRYPTOCHROME1-dependent response to excess light is mediated through the transcriptional activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis.

PMID:22855128

cry1 and GPA1 signaling genetically interact in hook opening and anthocyanin synthesis in Arabidopsis.

PMID:23511208

Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures.

PMID:24126495

Strigolactone-regulated hypocotyl elongation is dependent on cryptochrome and phytochrome signaling pathways in Arabidopsis.

PMID:25157750

ATP binding and aspartate protonation enhance photoinduced electron transfer in plant cryptochrome.

PMID:25721730

The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to Mediate Blue Light Inhibition of Hypocotyl Elongation.

PMID:25728686

Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome may define a novel evolutionarily conserved signaling mechanism.

Photoactivated Arabidopsis cryptochrome can promote ROS formation.

"Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome."

PMID:26095447

Suppression of Arabidopsis flowering by near-null magnetic field is affected by light.

PMID:26313597

Cellular metabolites modulate in vivo signaling of Arabidopsis cryptochrome-1.

PMID:26596765

TCP2 positively regulates HY5/HYH and photomorphogenesis in Arabidopsis.

PMID:26724867

Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light.

CRY1/CRY2 directly contact PIF4 and PIF5 under limiting blue light.

"CRY1 and CRY2 perceive"

PMID:28887381

Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling.

PMID:30242037

Blue Light Regulates Secondary Cell Wall Thickening via MYC2/MYC4 Activation of the NST1-Directed Transcriptional Network in Arabidopsis.

CRY1 links blue light to secondary cell wall thickening through MYC2/MYC4/NST1.

"CRY1 overexpression led to enhanced SCW formation."

PMID:30635559

Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional activator HEMERA.

PMID:32554507

Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated Inhibition of PIF4 Expression.

CRY1 modulates low-blue-light phototropism through PIF4 expression.

"Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated Inhibition of PIF4 Expression."

PMID:32661061

Photoexcited Cryptochrome2 Interacts Directly with TOE1 and TOE2 in Flowering Regulation.

PMID:36305219

The blue light receptor CRY1 interacts with FIP37 to promote N(6) -methyladenosine RNA modification and photomorphogenesis in Arabidopsis.

CRY1 interacts with FIP37 to promote blue-light m6A RNA modification.

"CRY1 physically interacted with FIP37"

PMID:36508461

A role for brassinosteroid signalling in decision-making processes in the Arabidopsis seedling.

PMID:8528277

Mutations throughout an Arabidopsis blue-light photoreceptor impair blue-light-responsive anthocyanin accumulation and inhibition of hypocotyl elongation.

CRY1 mutations impair blue-light hypocotyl inhibition and anthocyanin accumulation.

"CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated inhibition"

PMID:8953250

Arabidopsis cryptochrome 1 is a soluble protein mediating blue light-dependent regulation of plant growth and development.

CRY1 is a blue-light photoreceptor controlling growth and gene expression.

"CRY1 is a flavin-type blue type receptor of Arabidopsis"

PMID:9651577

The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in vitro.

PMID:9733523

Genetic interactions between phytochrome A, phytochrome B, and cryptochrome 1 during Arabidopsis development.

PMID:9765547

Two genetically separable phases of growth inhibition induced by blue light in Arabidopsis seedlings.

file:ARATH/CRY1/CRY1-uniprot.txt

UniProtKB record for Arabidopsis thaliana CRY1 (Q43125)

UniProt summarizes CRY1 as a blue-light absorbing flavoprotein with nucleo-cytoplasmic signaling roles.

"Blue-light absorbing flavoprotein that activates reversible flavin photoreduction."
UniProt records CRY1 in cytoplasm, nucleus, and nuclear bodies.

"Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present in nuclear bodies."

file:ARATH/CRY1/CRY1-deep-research-falcon.md

Falcon deep-research report for Arabidopsis CRY1

The deep-research synthesis supports CRY1 as a FAD-dependent photoreceptor signaling switch.

"CRY1 binds FAD in its PHR domain and undergoes light-driven flavin redox cycling and conformational change."

file:interpro/panther/PTHR11455/PTHR11455-notes.md

PANTHER PTHR11455 cryptochrome family notes

PANTHER context warns that the family mixes cryptochromes and photolyases.

"The family contains both cryptochromes and photolyases; subfamilies separate circadian cryptochromes from repair enzymes."

file:interpro/panther/PTHR11455/PTHR11455-entries.csv

PANTHER PTHR11455 reviewed entry table

The cached PANTHER entry table places Q43125 in a CRYPTOCHROME-1 subfamily.

"Q43125,Cryptochrome-1,protein,3702,Arabidopsis thaliana,...,PTHR11455:SF50,CRYPTOCHROME-1"

Suggested Experiments

Experiment: Complement cry1 mutants with native-promoter CRY1 phosphorylation-site and kinase-impaired variants, then assay hypocotyl inhibition, SPA/COP1 association, HY5 stability, and FAD photoreduction kinetics under matched blue-light fluence.

Hypothesis: CRY1 autophosphorylation is required for a subset of photomorphogenic outputs but not for initial FAD photoreduction.

Type: native-promoter rescue with phosphosite mutagenesis

Experiment: Express CRY1 specifically in guard cells versus mesophyll/epidermal tissues in a cry1 cry2 background and measure stomatal aperture, ABA abundance, transpiration, and photosynthesis after acute and acclimated blue-light treatments.

Hypothesis: CRY1 regulation of stomatal conductance is partly indirect through ABA and long-term acclimation rather than direct blue-light guard-cell photoreception.

Type: cell-type-specific complementation and physiology

Experiment: Combine CRY1-FIP37 interaction-defective CRY1 alleles with m6A profiling and RNA decay measurements under blue light to separate FIP37-dependent RNA regulation from COP1/SPA-dependent proteostasis outputs.

Hypothesis: The CRY1-FIP37 branch controls a defined subset of m6A-modified PIF and photomorphogenesis transcripts.

Type: interaction-mutant m6A profiling

Deep Research

Falcon

(CRY1-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 21 citations 2026-05-05T03:58:49.944036

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Comprehensive Research Report: Arabidopsis thaliana CRY1 (UniProt Q43125; HY4/BLU1)

Executive summary

Arabidopsis thaliana cryptochrome-1 (CRY1) is a flavin-dependent blue/UV-A light photoreceptor in the DNA photolyase class-1 superfamily. Current evidence supports a functional model in which light-driven FAD photoredox chemistry triggers conformational change and oligomerization, enabling CRY1 to regulate gene expression largely by antagonizing the COP1/SPA E3 ubiquitin ligase and stabilizing downstream transcriptional regulators such as HY5. In addition to this canonical proteasome-linked pathway, recent work shows CRY1 can also regulate HY5 via selective autophagy, through blue-light-dependent interaction with ATG8. (fraikin2023molecularbasesof pages 4-5, volna2024bridgingthegap pages 5-6, jiang2025photoexcitedcry1physically pages 1-1)

1) Key concepts and definitions (current understanding)

1.1 Target identity verification and disambiguation

The target in this report is Arabidopsis thaliana CRY1 corresponding to UniProt accession Q43125 (historical aliases HY4/BLU1), a plant cryptochrome photoreceptor. The reviewed literature describing plant CRY1 matches the UniProt-provided identity as a cryptochrome with a photolyase-like core and plant-specific signaling extension, rather than animal CRY1 circadian repressors or other taxon-specific “CRY1” genes. (fraikin2023molecularbasesof pages 1-2, deoliveira2025astructuraldecryption pages 1-2)

1.2 Domain architecture and what it implies for function

Plant cryptochromes are described as modular proteins consisting of:
- an N-terminal photolyase-homologous region (PHR) (reported ~500 aa) that binds FAD and provides conformationally responsive interaction surfaces, and
- a C-terminal cryptochrome C-terminal extension (CCE) (reported ~180 aa in CRY1) that is absent from DNA photolyases and contributes to signaling outputs, including interactions with the COP1/SPA complex. (fraikin2023molecularbasesof pages 1-2, deoliveira2025astructuraldecryption pages 1-2, volna2024bridgingthegap pages 5-6)

These features support functional annotation of CRY1 as a signal-transducing photoreceptor (not an enzyme catalyzing a metabolic conversion), whose primary biochemical activity is light-triggered redox/conformational switching of a flavoprotein scaffold to regulate protein–protein interaction networks. (fraikin2023molecularbasesof pages 4-5, deoliveira2025astructuraldecryption pages 4-5)

1.3 Photochemistry terminology and redox states

A central concept for CRY1 functional annotation is that the cofactor FAD can exist in multiple redox states with distinct absorption spectra, and these redox transitions are tied to signaling competence. Plant cryptochromes are described as populating oxidized FAD, the anionic semiquinone FAD•−, the neutral radical FADH•, and the fully reduced FADH− state. Absorbance properties reported include:
- oxidized FAD peak near ~450 nm,
- all redox forms peaking in UVA 360–370 nm,
- FAD•− peaks near ~410 and ~470 nm, and
- FADH• absorbance shifted into ~500–650 nm (treated as a signaling-competent form). (fraikin2023molecularbasesof pages 1-2, fraikin2023molecularbasesof pages 4-5)

2) Recent developments and latest research (prioritizing 2023–2024)

2.1 2023: Mechanistic consolidation of plant CRY photochemistry and coupling to signaling

A 2023 mechanistic review synthesizes how blue-light absorption by FAD in CRY1 can drive photoreduction through a conserved Trp-triad electron-transfer chain, producing FAD•− and then (after protonation) FADH•. It further connects these photochemical steps to PHR–CCE disengagement, increased disorder in a portion of the CCE, and oligomerization, which together enable binding to signaling partners and downstream regulators. (fraikin2023molecularbasesof pages 4-5)

2.2 2024: Structural framework for cryptochrome signaling specificity

A 2024 structural review provides an updated framework emphasizing that cryptochrome outputs arise from a conserved PHR fold (Rossmann-like α/β plus α-helical domains) that binds FAD (in a characteristic U-shaped conformation), plus variable C-terminal regions (“CTT/CCE”) that tune partner recognition and signaling specificity. The review also highlights that signaling can be coupled to changes in homo/hetero-oligomerization and/or post-translational modifications, framing how plant CRY1 can convert photochemistry into changes in protein–protein interaction networks. (deoliveira2025astructuraldecryption pages 1-2, deoliveira2025astructuraldecryption pages 4-5)

2.3 2024: Translational framing—light control of metabolism and stress-protective compounds

A 2024 review linking photoperception to transcriptional control of phenolic compound pathways explicitly positions plant photoreceptors (including cryptochromes) as actionable levers for manipulating gene expression programs relevant to UV screening and antioxidative metabolism, with stated relevance to horticulture and indoor cultivation as implementation contexts. (volna2024bridgingthegap pages 2-5, volna2024bridgingthegap pages 6-8)

3) Molecular function and pathways (functional annotation focus)

3.1 Primary molecular function: light-sensing flavoprotein switch

CRY1 is best annotated as a blue/UV-A photoreceptor whose functional core is a FAD-binding PHR domain that undergoes light-dependent redox chemistry and downstream conformational switching. Blue-light absorption by oxidized FAD leads to electron transfer via the Trp triad with reported ultrafast time constants (0.4 ps and 31 ps). The resulting semiquinone can be protonated within microseconds to FADH•; the FADH• lifetime is reported to extend to milliseconds in vitro and minutes in vivo, consistent with a state capable of sustained signaling. Green light is described as able to antagonize blue-light signaling by further photoreducing FADH• to FADH−. (fraikin2023molecularbasesof pages 4-5)

3.2 Canonical signaling axis: CRY1 → COP1/SPA → HY5 (proteasome-linked)

A commonly used mechanistic model in recent reviews describes: light-triggered CRY activation and dimerization/oligomerization, followed by phosphorylation and interaction with the COP1/SPA ubiquitin ligase complex. The CCE is specifically described as required for COP1/SPA interaction (and absent in CRY3), supporting a CRY1-specific signaling role for the C-terminal region. (volna2024bridgingthegap pages 5-6, volna2024complexroleof pages 4-7)

Primary evidence (outside the 2023–2024 window but highly relevant mechanistically) reiterates that CRY signaling suppresses COP1–SPA-mediated 26S proteasome degradation of HY5, enabling HY5 accumulation and photomorphogenic transcriptional programs. (jiang2025photoexcitedcry1physically pages 1-1)

3.3 Additional signaling branch: CRY1 → ATG8 → HY5 (selective autophagy)

A major recent mechanistic advance is the discovery of a CRY1 link to the autophagy system: photoexcited CRY1 physically interacts with ATG8 in a blue-light-dependent manner and thereby inhibits ATG8–HY5 association, reducing HY5 trafficking to autophagosomes and suppressing vacuolar degradation of HY5. Genetic analysis places ATG8 and core autophagy factors ATG5/ATG7 downstream of CRY1 and upstream of HY5. This establishes that CRY1 can regulate HY5 through both proteasomal and autophagic degradation routes. (jiang2025photoexcitedcry1physically pages 1-1, jiang2025photoexcitedcry1physically pages 2-2)

A notable quantitative/structural detail from this work is the identification of multiple putative ATG8-interacting motifs (AIMs) in CRY1, including an AIM1 motif at AA111–114 (YDPL); mutation of AIM1 is reported to weaken CRY1’s ability to inhibit ATG8–HY5 interaction and to compromise complementation of cry1 hypocotyl phenotypes, supporting functional importance of this interface. (jiang2025photoexcitedcry1physically pages 2-2, jiang2025photoexcitedcry1physically pages 13-14)

3.4 Negative regulators and network architecture

Recent reviews highlight the BIC1/BIC2 proteins as negative regulators that repress CRY activation by inhibiting the monomer-to-dimer transition/photooligomerization. This provides a mechanistic “brake” that can be used to interpret variability in blue-light response amplitude. (volna2024bridgingthegap pages 5-6, volna2024complexroleof pages 4-7)

4) Subcellular localization and site of action

4.1 Nucleo-cytoplasmic distribution

CRY1 is described as nucleo-cytoplasmic, functioning in both nucleus and cytoplasm, consistent with a protein that can both influence nuclear transcriptional programs (via COP1/SPA/HY5) and participate in broader cytoplasmic signaling and trafficking processes. (fraikin2023molecularbasesof pages 1-2, kong2025complexsignalingnetworks pages 2-4)

4.2 Localization dynamics linked to autophagy regulation

In the CRY1–ATG8 mechanism, CRY1 activity is linked to nuclear–cytoplasmic trafficking control: under blue light, CRY1 interaction with ATG8 is described to prevent ATG8–HY5 binding and to inhibit ATG8 nuclear export, thereby reducing ATG8/HY5 co-localization on autophagosomes and limiting HY5 vacuolar degradation. (jiang2025photoexcitedcry1physically pages 19-19, jiang2025photoexcitedcry1physically pages 1-1)

5) Current applications and real-world implementations

5.1 Controlled-environment agriculture (CEA) and indoor cultivation

Recent review-level synthesis explicitly positions light signaling (including cryptochrome pathways) as a route to manipulate transcriptional regulators controlling phenolic compound biosynthesis. These pathways contribute to UV screening and antioxidative capacity, motivating “real-world” implementations in horticulture and indoor cultivation, where spectral composition, intensity, and timing of light can be precisely controlled to steer protective metabolite profiles. (volna2024bridgingthegap pages 2-5, volna2024bridgingthegap pages 6-8)

5.2 Crop and trait engineering relevance (mechanistic rationale)

While the retrieved 2023–2024 sources in this run did not provide a CRY1-specific engineering case study with quantitative yield outcomes, the mechanistic evidence supports clear translational strategies: manipulating CRY1 activation state (or its negative regulators BIC1/BIC2) and downstream degradation pathways (COP1/SPA proteasome axis; ATG8-mediated autophagy axis) provides defined intervention points for tuning photomorphogenesis-associated traits and metabolite programs. (volna2024bridgingthegap pages 5-6, jiang2025photoexcitedcry1physically pages 1-1, jiang2025photoexcitedcry1physically pages 2-2)

6) Expert opinions and authoritative synthesis

Authoritative reviews converge on several interpretive points:
- Cryptochrome signaling is fundamentally structure-enabled: a conserved FAD-binding PHR provides photochemistry and responsive surfaces, while the variable C-terminal region tunes partner interactions and output specificity. (deoliveira2025astructuraldecryption pages 1-2)
- Photochemistry and signaling are coupled through redox-state transitions, conformational rearrangements, and oligomerization, rather than through classical enzymatic catalysis. (fraikin2023molecularbasesof pages 4-5, deoliveira2025astructuraldecryption pages 4-5)
- The COP1/SPA interaction paradigm remains central for understanding how photoreceptors reshape proteostasis of transcription factors, and recent work expands this framework by adding autophagy as a second regulated proteolytic route for a key output factor (HY5). (jiang2025photoexcitedcry1physically pages 1-1, jiang2025photoexcitedcry1physically pages 2-2)

7) Relevant statistics and data points (from recent literature)

Key quantitative values reported in the cited sources include:
- Domain sizes: PHR ~500 aa; CRY1 CCE ~180 aa. (fraikin2023molecularbasesof pages 1-2)
- Ultrafast electron transfer during photoreduction: 0.4 ps and 31 ps steps; subsequent protonation within microseconds. (fraikin2023molecularbasesof pages 4-5)
- Signaling-state lifetime: FADH• lifetime reported to extend from milliseconds (in vitro) to minutes (in vivo). (fraikin2023molecularbasesof pages 4-5)
- Spectral characteristics of FAD redox states: oxidized FAD peak ~450 nm; FAD•− peaks ~410 and ~470 nm; FADH• absorbance ~500–650 nm; UVA peaks 360–370 nm across redox states. (fraikin2023molecularbasesof pages 1-2, fraikin2023molecularbasesof pages 4-5)
- Regulatory scope statistic (review-level): cryptochrome signaling can influence expression of approximately 10–20% of Arabidopsis coding genes. (volna2024bridgingthegap pages 5-6, volna2024complexroleof pages 4-7)
- ATG8-interacting motif mapping (CRY1): AIM1 AA111–114 (YDPL) and other motifs (AA341–344; AA385–388; AA400–403) implicated in blue-light-dependent CRY1–ATG8 interaction. (jiang2025photoexcitedcry1physically pages 2-2)

8) Concise functional annotation statement (recommended)

CRY1 (At4g08920; UniProt Q43125) encodes a nucleo-cytoplasmic blue/UV-A photoreceptor of the cryptochrome/photolyase family. CRY1 binds FAD in its PHR domain and undergoes light-driven flavin redox cycling and conformational change that promote oligomerization and exposure of signaling interfaces. Activated CRY1 modulates plant transcriptional programs by engaging the COP1/SPA ubiquitin ligase axis to stabilize transcription factors such as HY5, and (as newly described) by interacting with ATG8 to inhibit selective autophagy-mediated HY5 degradation under blue light. (fraikin2023molecularbasesof pages 1-2, fraikin2023molecularbasesof pages 4-5, volna2024bridgingthegap pages 5-6, jiang2025photoexcitedcry1physically pages 1-1, jiang2025photoexcitedcry1physically pages 2-2)

Summary table

Aspect	Key points	Evidence source (author-year)	Publication date	URL
Identity/domains	• Verified target is Arabidopsis thaliana CRY1 (HY4/BLU1), a plant cryptochrome with a conserved PHR region and a CCE/C-terminal extension. • PHR is ~500 aa and binds FAD; CRY1 CCE is ~180 aa and is absent from photolyases. • Structural reviews describe the PHR as comprising α/β and α-helical domains that provide cofactor-binding and interaction surfaces. (fraikin2023molecularbasesof pages 1-2, deoliveira2025astructuraldecryption pages 1-2)	Fraikin et al. 2023; DeOliveira & Crane 2024	2023-06; 2024-08	https://doi.org/10.1134/s0006297923060056 ; https://doi.org/10.3389/fchem.2024.1436322
Cofactors/photochemistry	• FAD is the primary chromophore/cofactor in a U-shaped conformation; plant cryptochromes populate oxidized FAD, FAD•−, FADH•, and FADH− states. • Oxidized FAD absorbs at ~450 nm; all redox forms absorb in UVA 360–370 nm; FAD•− peaks near ~410 and ~470 nm; FADH• absorbs at ~500–650 nm and is treated as a signaling state. • Blue-light photoreduction proceeds through a conserved Trp triad/tetrad, followed by protonation to FADH•; green light can further reduce FADH• to inactive FADH−. (fraikin2023molecularbasesof pages 1-2, fraikin2023molecularbasesof pages 4-5, deoliveira2025astructuraldecryption pages 4-5)	Fraikin et al. 2023; DeOliveira & Crane 2024	2023-06; 2024-08	https://doi.org/10.1134/s0006297923060056 ; https://doi.org/10.3389/fchem.2024.1436322
Activation/oligomerization	• In darkness, CRYs are described as monomeric/inactive; light causes conformational change, PHR-CCE disengagement, and formation of active homooligomers/homodimers; tetramers are also discussed in reviews. • Blue-light-dependent phosphorylation accompanies activation and correlates with light intensity/duration in review-level summaries. • Photooligomerization is linked to formation of signaling complexes with downstream proteins. (fraikin2023molecularbasesof pages 4-5, kong2025complexsignalingnetworks pages 2-4, volna2024bridgingthegap pages 5-6, volna2024complexroleof pages 4-7)	Fraikin et al. 2023; Kong & Zheng 2025; Volná et al. 2024	2023-06; 2024-06; 2025-05	https://doi.org/10.1134/s0006297923060056 ; https://doi.org/10.3390/ijms25137066 ; https://doi.org/10.3390/plants14101533
Core signaling axis	• A central CRY1 pathway is blue-light activation → CRY oligomer/phosphorylation → interaction with COP1/SPA E3 ligase complex. • Review evidence states the CCE is needed for COP1/SPA interaction. • Recent primary evidence reiterates that CRY signaling inhibits COP1-SPA-dependent proteasomal degradation of HY5, thereby promoting photomorphogenesis. (volna2024bridgingthegap pages 5-6, volna2024complexroleof pages 4-7, jiang2025photoexcitedcry1physically pages 1-1)	Volná et al. 2024; Jiang et al. 2025	2024-06; 2025-08	https://doi.org/10.3390/ijms25137066 ; https://doi.org/10.1093/plcell/koaf196
Additional pathways	• A 2025 Arabidopsis study adds a second CRY1 branch: photoexcited CRY1 directly interacts with ATG8 in blue light. • This interaction inhibits ATG8-HY5 association, suppresses HY5 vacuolar/autophagic degradation, and places ATG8/ATG5/ATG7 genetically downstream of CRY1 and upstream of HY5. • Thus CRY1 can regulate HY5 through both proteasome-linked and autophagy-linked routes. (jiang2025photoexcitedcry1physically pages 1-1, jiang2025photoexcitedcry1physically pages 13-14, jiang2025photoexcitedcry1physically pages 2-2)	Jiang et al. 2025	2025-08	https://doi.org/10.1093/plcell/koaf196
Localization	• Review evidence describes CRY1 as nucleo-cytoplasmic, functioning in both nucleus and cytoplasm. • In the autophagy study, CRY1 signaling is linked to inhibition of ATG8 nuclear export, consistent with a nuclear role in protecting HY5. • Photobody/nuclear-body behavior is well established for plant cryptochromes in broader structural reviews, though the provided snippets are more explicit for CRY2 than CRY1. (fraikin2023molecularbasesof pages 1-2, kong2025complexsignalingnetworks pages 2-4, jiang2025photoexcitedcry1physically pages 19-19, deoliveira2025astructuraldecryption pages 17-18)	Fraikin et al. 2023; Kong & Zheng 2025; Jiang et al. 2025; DeOliveira & Crane 2024	2023-06; 2024-08; 2025-05; 2025-08	https://doi.org/10.1134/s0006297923060056 ; https://doi.org/10.3389/fchem.2024.1436322 ; https://doi.org/10.3390/plants14101533 ; https://doi.org/10.1093/plcell/koaf196
Negative/positive regulators	• BIC1/BIC2 are identified as negative regulators that repress CRY monomer-to-dimer transition/photooligomerization. • COP1/SPA acts as the major repressive E3 ligase complex opposed by activated CRY signaling. • HY5 is the major positive output highlighted in the snippets, stabilized by CRY-mediated inhibition of its degradation. (volna2024bridgingthegap pages 5-6, volna2024complexroleof pages 4-7, jiang2025photoexcitedcry1physically pages 1-1, volna2024bridgingthegap pages 6-8)	Volná et al. 2024; Jiang et al. 2025	2024-06; 2025-08	https://doi.org/10.3390/ijms25137066 ; https://doi.org/10.1093/plcell/koaf196
Quantitative data	• Domain sizes reported: PHR ~500 aa and CRY1 CCE ~180 aa. • Ultrafast electron-transfer steps during photoreduction were reported at 0.4 ps and 31 ps; protonation to FADH• occurs within microseconds; FADH• lifetime extends to milliseconds in vitro and minutes in vivo. • Review-level gene-regulatory scope: CRY signaling may affect ~10–20% of Arabidopsis coding genes. (fraikin2023molecularbasesof pages 1-2, fraikin2023molecularbasesof pages 4-5, volna2024bridgingthegap pages 5-6, volna2024complexroleof pages 4-7)	Fraikin et al. 2023; Volná et al. 2024	2023-06; 2024-06	https://doi.org/10.1134/s0006297923060056 ; https://doi.org/10.3390/ijms25137066
Applications/implementation	• 2024 reviews frame cryptochrome signaling as relevant to light-controlled transcriptional regulation of phenolic-compound biosynthesis and stress-protective metabolites. • They explicitly point to horticulture/indoor cultivation and manipulation of light environments as translational contexts for producing plants with adjusted protective metabolite content. • These application statements are review-level and not specific to a direct CRY1 engineering implementation in the provided snippets. (volna2024bridgingthegap pages 2-5, volna2024bridgingthegap pages 6-8)	Volná et al. 2024	2024-06	https://doi.org/10.3390/ijms25137066

Table: This table summarizes the supported functional annotation of Arabidopsis thaliana CRY1 (UniProt Q43125; HY4/BLU1), including domains, photochemistry, signaling partners, localization, regulators, quantitative findings, and translational relevance. It only uses claims supported by the provided evidence snippets and cites the corresponding context IDs.

Key sources (publication date; URL)

Fraikin G.Y., Belenikina N.S., Rubin A.B. (2023-06). Molecular Bases of Signaling Processes Regulated by Cryptochrome Sensory Photoreceptors in Plants. Biochemistry (Moscow). https://doi.org/10.1134/s0006297923060056 (fraikin2023molecularbasesof pages 1-2, fraikin2023molecularbasesof pages 4-5)
DeOliveira C.C., Crane B.R. (2024-08). A structural decryption of cryptochromes. Frontiers in Chemistry. https://doi.org/10.3389/fchem.2024.1436322 (deoliveira2025astructuraldecryption pages 1-2, deoliveira2025astructuraldecryption pages 4-5)
Volná A. et al. (2024-06). Bridging the Gap: From Photoperception to the Transcription Control of Genes Related to the Production of Phenolic Compounds. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms25137066 (volna2024bridgingthegap pages 5-6, volna2024bridgingthegap pages 2-5, volna2024bridgingthegap pages 6-8)
Jiang L. et al. (2025-08). Photoexcited CRY1 physically interacts with ATG8 to regulate selective autophagy of HY5 and photomorphogenesis in Arabidopsis. The Plant Cell. https://doi.org/10.1093/plcell/koaf196 (jiang2025photoexcitedcry1physically pages 1-1, jiang2025photoexcitedcry1physically pages 2-2)

References

(fraikin2023molecularbasesof pages 4-5): Grigori Ya. Fraikin, Natalia S. Belenikina, and Andrey B. Rubin. Molecular bases of signaling processes regulated by cryptochrome sensory photoreceptors in plants. Biochemistry (Moscow), 88:770-782, Jun 2023. URL: https://doi.org/10.1134/s0006297923060056, doi:10.1134/s0006297923060056. This article has 5 citations.
(volna2024bridgingthegap pages 5-6): Adriana Volná, Jiří Červeň, Jakub Nezval, Radomír Pech, and Vladimír Špunda. Bridging the gap: from photoperception to the transcription control of genes related to the production of phenolic compounds. International Journal of Molecular Sciences, 25:7066, Jun 2024. URL: https://doi.org/10.3390/ijms25137066, doi:10.3390/ijms25137066. This article has 6 citations.
(jiang2025photoexcitedcry1physically pages 1-1): Lu Jiang, Shilong Zhang, Yuting Niu, Guangqiong Yang, Jiachen Zhao, Huishan Liu, Minyu Xiong, Lingyi Xie, Zhilei Mao, Tongtong Guo, Hong-Quan Yang, and Wenxiu Wang. Photoexcited cry1 physically interacts with atg8 to regulate selective autophagy of hy5 and photomorphogenesis in arabidopsis. The Plant cell, Aug 2025. URL: https://doi.org/10.1093/plcell/koaf196, doi:10.1093/plcell/koaf196. This article has 7 citations.
(fraikin2023molecularbasesof pages 1-2): Grigori Ya. Fraikin, Natalia S. Belenikina, and Andrey B. Rubin. Molecular bases of signaling processes regulated by cryptochrome sensory photoreceptors in plants. Biochemistry (Moscow), 88:770-782, Jun 2023. URL: https://doi.org/10.1134/s0006297923060056, doi:10.1134/s0006297923060056. This article has 5 citations.
(deoliveira2025astructuraldecryption pages 1-2): Cristina C. DeOliveira and Brian R. Crane. A structural decryption of cryptochromes. Frontiers in Chemistry, Aug 2024. URL: https://doi.org/10.3389/fchem.2024.1436322, doi:10.3389/fchem.2024.1436322. This article has 17 citations.
(deoliveira2025astructuraldecryption pages 4-5): Cristina C. DeOliveira and Brian R. Crane. A structural decryption of cryptochromes. Frontiers in Chemistry, Aug 2024. URL: https://doi.org/10.3389/fchem.2024.1436322, doi:10.3389/fchem.2024.1436322. This article has 17 citations.
(volna2024bridgingthegap pages 2-5): Adriana Volná, Jiří Červeň, Jakub Nezval, Radomír Pech, and Vladimír Špunda. Bridging the gap: from photoperception to the transcription control of genes related to the production of phenolic compounds. International Journal of Molecular Sciences, 25:7066, Jun 2024. URL: https://doi.org/10.3390/ijms25137066, doi:10.3390/ijms25137066. This article has 6 citations.
(volna2024bridgingthegap pages 6-8): Adriana Volná, Jiří Červeň, Jakub Nezval, Radomír Pech, and Vladimír Špunda. Bridging the gap: from photoperception to the transcription control of genes related to the production of phenolic compounds. International Journal of Molecular Sciences, 25:7066, Jun 2024. URL: https://doi.org/10.3390/ijms25137066, doi:10.3390/ijms25137066. This article has 6 citations.
(volna2024complexroleof pages 4-7): Adriana Volná, Jiří Červeň, Jakub Nezval, Radomír Pech, and Vladimír Špunda. Complex role of photoreceptors in light and temperature sensing: from mechanism to the target genes regulation. a focus on the genes related to the biosynthesis of phenolic compounds. Unknown journal, Jan 2024. URL: https://doi.org/10.20944/preprints202401.2145.v1, doi:10.20944/preprints202401.2145.v1.
(jiang2025photoexcitedcry1physically pages 2-2): Lu Jiang, Shilong Zhang, Yuting Niu, Guangqiong Yang, Jiachen Zhao, Huishan Liu, Minyu Xiong, Lingyi Xie, Zhilei Mao, Tongtong Guo, Hong-Quan Yang, and Wenxiu Wang. Photoexcited cry1 physically interacts with atg8 to regulate selective autophagy of hy5 and photomorphogenesis in arabidopsis. The Plant cell, Aug 2025. URL: https://doi.org/10.1093/plcell/koaf196, doi:10.1093/plcell/koaf196. This article has 7 citations.
(jiang2025photoexcitedcry1physically pages 13-14): Lu Jiang, Shilong Zhang, Yuting Niu, Guangqiong Yang, Jiachen Zhao, Huishan Liu, Minyu Xiong, Lingyi Xie, Zhilei Mao, Tongtong Guo, Hong-Quan Yang, and Wenxiu Wang. Photoexcited cry1 physically interacts with atg8 to regulate selective autophagy of hy5 and photomorphogenesis in arabidopsis. The Plant cell, Aug 2025. URL: https://doi.org/10.1093/plcell/koaf196, doi:10.1093/plcell/koaf196. This article has 7 citations.
(kong2025complexsignalingnetworks pages 2-4): Yun Kong and Youbin Zheng. Complex signaling networks underlying blue-light-mediated floral transition in plants. Plants, 14:1533, May 2025. URL: https://doi.org/10.3390/plants14101533, doi:10.3390/plants14101533. This article has 12 citations.
(jiang2025photoexcitedcry1physically pages 19-19): Lu Jiang, Shilong Zhang, Yuting Niu, Guangqiong Yang, Jiachen Zhao, Huishan Liu, Minyu Xiong, Lingyi Xie, Zhilei Mao, Tongtong Guo, Hong-Quan Yang, and Wenxiu Wang. Photoexcited cry1 physically interacts with atg8 to regulate selective autophagy of hy5 and photomorphogenesis in arabidopsis. The Plant cell, Aug 2025. URL: https://doi.org/10.1093/plcell/koaf196, doi:10.1093/plcell/koaf196. This article has 7 citations.
(deoliveira2025astructuraldecryption pages 17-18): Cristina C. DeOliveira and Brian R. Crane. A structural decryption of cryptochromes. Frontiers in Chemistry, Aug 2024. URL: https://doi.org/10.3389/fchem.2024.1436322, doi:10.3389/fchem.2024.1436322. This article has 17 citations.

Citations

fraikin2023molecularbasesof pages 4-5
deoliveira2025astructuraldecryption pages 1-2
fraikin2023molecularbasesof pages 1-2
volna2024bridgingthegap pages 5-6
deoliveira2025astructuraldecryption pages 4-5
volna2024bridgingthegap pages 2-5
volna2024bridgingthegap pages 6-8
volna2024complexroleof pages 4-7
kong2025complexsignalingnetworks pages 2-4
deoliveira2025astructuraldecryption pages 17-18
https://doi.org/10.1134/s0006297923060056
https://doi.org/10.3389/fchem.2024.1436322
https://doi.org/10.3390/ijms25137066
https://doi.org/10.3390/plants14101533
https://doi.org/10.1093/plcell/koaf196
https://doi.org/10.1134/s0006297923060056,
https://doi.org/10.3390/ijms25137066,
https://doi.org/10.1093/plcell/koaf196,
https://doi.org/10.3389/fchem.2024.1436322,
https://doi.org/10.20944/preprints202401.2145.v1,
https://doi.org/10.3390/plants14101533,

📄 View Raw YAML

id: Q43125
gene_symbol: CRY1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:3702
  label: Arabidopsis thaliana
aliases:
- HY4
- BLU1
- OOP2
- At4g08920
description: Arabidopsis thaliana CRY1 encodes cryptochrome-1, a soluble blue/UV-A light photoreceptor
  in the cryptochrome/photolyase superfamily. CRY1 binds FAD in a photolyase-homology region
  and uses blue-light-driven flavin photoredox and conformational changes to form signaling-competent
  oligomers. Activated CRY1 acts in the nucleus and cytoplasm to regulate photomorphogenesis,
  hypocotyl and petiole growth, circadian outputs, stomatal behavior, stress responses, and
  gene expression, chiefly through partner interactions including COP1/SPA, PIF4/PIF5, HY5-linked
  pathways, and FIP37-mediated m6A regulation. Despite its photolyase-like fold, Arabidopsis
  CRY1 is not a DNA photolyase; inherited photolyase annotations should be treated as over-propagation
  from mixed cryptochrome/photolyase family context.
existing_annotations:
- term:
    id: GO:0009414
    label: response to water deprivation
  evidence_type: IGI
  original_reference_id: PMID:16093319
  review:
    summary: Water-deprivation response reflects altered stomatal aperture and water loss
      rather than a primary CRY1 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: The direct evidence is that CRY1/CRY2 regulate blue-light stomatal opening and
      water loss. Calling CRY1 a water-deprivation response gene overstates an indirect physiological
      consequence.
    supported_by:
    - reference_id: PMID:16093319
      supporting_text: CRY functions additively with PHOT in mediating blue light-induced
        stomatal opening.
      reference_section_type: ABSTRACT
- term:
    id: GO:0009416
    label: response to light stimulus
  evidence_type: IMP
  original_reference_id: PMID:36508461
  review:
    summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A
      photoreception.
    action: MODIFY
    reason: The original cached abstract does not verify a CRY1-specific light-response claim,
      and the term is too broad in any case. The supported CRY1 biology should be represented
      by blue-light response/signaling terms.
    supported_by:
    - reference_id: PMID:36508461
      supporting_text: The accessible abstract describes a BIN2 light/water screen, but does
        not mention CRY1.
      full_text_unavailable: true
      reference_section_type: ABSTRACT
    proposed_replacement_terms:
    - id: GO:0009637
      label: response to blue light
    - id: GO:0009785
      label: blue light signaling pathway
- term:
    id: GO:0009583
    label: detection of light stimulus
  evidence_type: IMP
  original_reference_id: PMID:20668058
  review:
    summary: detection of light stimulus matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:20668058
      supporting_text: Cryptochrome as a sensor of the blue/green ratio of natural radiation
        in Arabidopsis.
      reference_section_type: TITLE
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:12324610
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:12324610
      supporting_text: Hypocotyl elongation is not inhibited in the mutant seedlings by continuous
        blue light.
      reference_section_type: ABSTRACT
- term:
    id: GO:0009638
    label: phototropism
  evidence_type: IMP
  original_reference_id: PMID:32554507
  review:
    summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:32554507
      supporting_text: Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated
        Inhibition of PIF4 Expression.
      reference_section_type: TITLE
- term:
    id: GO:0009640
    label: photomorphogenesis
  evidence_type: IMP
  original_reference_id: PMID:12324610
  review:
    summary: photomorphogenesis matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:12324610
      supporting_text: Hypocotyl elongation is not inhibited in the mutant seedlings by continuous
        blue light.
      reference_section_type: ABSTRACT
- term:
    id: GO:0009785
    label: blue light signaling pathway
  evidence_type: TAS
  original_reference_id: PMID:10364413
  review:
    summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:10364413
      supporting_text: These photoreceptors appear to activate separate signal transduction
        pathways.
      reference_section_type: ABSTRACT
- term:
    id: GO:0010075
    label: regulation of meristem growth
  evidence_type: IGI
  original_reference_id: PMID:18424613
  review:
    summary: regulation of meristem growth is supported for CRY1 but is a non-core output
      or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:18424613
      supporting_text: phytochromes and cryptochromes play largely redundant roles
      reference_section_type: ABSTRACT
- term:
    id: GO:0010118
    label: stomatal movement
  evidence_type: IGI
  original_reference_id: PMID:16093319
  review:
    summary: Stomatal movement is a supported non-core output of CRY1 blue-light signaling.
    action: KEEP_AS_NON_CORE
    reason: CRY1/CRY2 influence blue-light stomatal opening, but this physiological output
      is downstream of the core photoreceptor/signaling role.
    supported_by:
    - reference_id: PMID:16093319
      supporting_text: CRY functions additively with PHOT in mediating blue light-induced
        stomatal opening.
      reference_section_type: ABSTRACT
- term:
    id: GO:0010343
    label: singlet oxygen-mediated programmed cell death
  evidence_type: IMP
  original_reference_id: PMID:17075038
  review:
    summary: singlet oxygen-mediated programmed cell death is supported for CRY1 but is a
      non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:17075038
      supporting_text: Cryptochrome-1-dependent execution of programmed cell death induced
        by singlet oxygen.
      reference_section_type: TITLE
- term:
    id: GO:0010468
    label: regulation of gene expression
  evidence_type: IMP
  original_reference_id: PMID:32554507
  review:
    summary: Regulation of gene expression is too broad for the CRY1/PIF4 phototropism evidence.
    action: MODIFY
    reason: The cited work supports CRY1 control of PIF4 expression in low-blue-light phototropism,
      so response to blue light and phototropism capture the evidence more specifically than
      general gene-expression regulation.
    proposed_replacement_terms:
    - id: GO:0009637
      label: response to blue light
    - id: GO:0009638
      label: phototropism
    supported_by:
    - reference_id: PMID:32554507
      supporting_text: Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated
        Inhibition of PIF4 Expression.
      reference_section_type: TITLE
- term:
    id: GO:0010617
    label: circadian regulation of calcium ion oscillation
  evidence_type: IMP
  original_reference_id: PMID:17982000
  review:
    summary: circadian regulation of calcium ion oscillation is supported for CRY1 but is
      a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:17982000
      supporting_text: Plants have circadian oscillations in the concentration of cytosolic
        free calcium.
      reference_section_type: ABSTRACT
- term:
    id: GO:0046283
    label: anthocyanin-containing compound metabolic process
  evidence_type: IMP
  original_reference_id: PMID:17217468
  review:
    summary: anthocyanin-containing compound metabolic process is supported for CRY1 but is
      a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:17217468
      supporting_text: downstream of cryptochrome 1 (CRY1) at the level of transcript accumulation
      reference_section_type: ABSTRACT
- term:
    id: GO:0046777
    label: protein autophosphorylation
  evidence_type: IDA
  original_reference_id: PMID:12846824
  review:
    summary: protein autophosphorylation is supported for CRY1 but is a non-core output or
      accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: CRY1 autophosphorylation is experimentally supported, but its in vivo regulatory
      significance and light dependence are less central than CRY1 photoreceptor activity.
    supported_by:
    - reference_id: PMID:12846824
      supporting_text: autophosphorylation activity associated with Arabidopsis cry1 protein
      reference_section_type: ABSTRACT
- term:
    id: GO:0051510
    label: regulation of unidimensional cell growth
  evidence_type: IMP
  original_reference_id: PMID:12324610
  review:
    summary: regulation of unidimensional cell growth matches the core CRY1 photoreceptor/signaling
      role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:12324610
      supporting_text: Hypocotyl elongation is not inhibited in the mutant seedlings by continuous
        blue light.
      reference_section_type: ABSTRACT
- term:
    id: GO:2000652
    label: regulation of secondary cell wall biogenesis
  evidence_type: IDA
  original_reference_id: PMID:30242037
  review:
    summary: regulation of secondary cell wall biogenesis is supported for CRY1 but is a non-core
      output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:30242037
      supporting_text: CRY1 overexpression led to enhanced SCW formation.
      reference_section_type: TITLE
- term:
    id: GO:0003904
    label: deoxyribodipyrimidine photo-lyase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Photolyase activity is not supported for Arabidopsis CRY1.
    action: REMOVE
    reason: CRY1 is in the cryptochrome/photolyase superfamily, but Arabidopsis CRY1 is a
      cryptochrome photoreceptor and published summaries state that cryptochromes lack photolyase
      DNA repair activity. The PANTHER family includes true photolyases, making this IBA transfer
      over-propagated.
    supported_by:
    - reference_id: PMID:11752373
      supporting_text: lack photolyase activity
      reference_section_type: INTRODUCTION
    - reference_id: file:interpro/panther/PTHR11455/PTHR11455-notes.md
      supporting_text: The family contains both cryptochromes and photolyases; subfamilies
        separate circadian cryptochromes from repair enzymes.
      reference_section_type: LITERATURE_REVIEW
    - reference_id: file:interpro/panther/PTHR11455/PTHR11455-entries.csv
      supporting_text: Q43125,Cryptochrome-1,protein,3702,Arabidopsis thaliana,...,PTHR11455:SF50,CRYPTOCHROME-1
      reference_section_type: RESULTS
- term:
    id: GO:0004672
    label: protein kinase activity
  evidence_type: IDA
  original_reference_id: PMID:12846824
  review:
    summary: protein kinase activity is supported for CRY1 but is a non-core output or accessory
      biochemical property.
    action: KEEP_AS_NON_CORE
    reason: AtCRY1 autokinase activity is experimentally supported in vitro, but the primary
      evolved molecular function is blue-light photoreceptor signaling.
    supported_by:
    - reference_id: PMID:12846824
      supporting_text: autophosphorylation activity associated with Arabidopsis cry1 protein
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11509693
  review:
    summary: Generic protein binding from PMID:11509693 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:11509693
      supporting_text: photoactivated cryptochromes repress COP1 activity through a direct
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11752373
  review:
    summary: Generic protein binding from PMID:11752373 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:11752373
      supporting_text: The signaling mechanism of Arabidopsis CRY is mediated through CCT.
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21511871
  review:
    summary: Generic protein binding from PMID:21511871 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:21511871
      supporting_text: CRY1-SPA1 interaction suppresses the SPA1-COP1 interaction
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21511872
  review:
    summary: Generic protein binding from PMID:21511872 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:21511872
      supporting_text: CRY1 interacts physically with SPA1 in a blue-light-dependent manner.
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22577138
  review:
    summary: Generic protein binding from PMID:22577138 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:22577138
      supporting_text: CRY1), a UV-A/blue photoreceptor.
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26596765
  review:
    summary: Generic protein binding from PMID:26596765 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:26596765
      supporting_text: TCP2 physically interacts with CRY1
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26724867
  review:
    summary: Generic protein binding from PMID:26724867 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:26724867
      supporting_text: CRY1 and CRY2 perceive
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32661061
  review:
    summary: Generic protein binding from PMID:32661061 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:32661061
      supporting_text: CRY1 and CRY2 physically interact with TOE1 and TOE2 in a BL-dependent
        manner.
      reference_section_type: ABSTRACT
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:9651577
  review:
    summary: Generic protein binding from PMID:9651577 records a real CRY1 interaction but
      is not informative as a GO molecular function.
    action: REMOVE
    reason: GO:0005515 does not describe the biological role of CRY1. The interaction evidence
      is better used to support CRY1 blue-light signaling mechanisms such as COP1/SPA inhibition,
      PIF regulation, or FIP37-mediated RNA modification rather than retained as generic protein
      binding.
    supported_by:
    - reference_id: PMID:9651577
      supporting_text: The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome
        A in vitro.
      reference_section_type: TITLE
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: ATP binding is a supported biochemical property that affects CRY1 conformation
      and flavin photochemistry, but it is accessory to photoreceptor signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Binding to ATP mediates conformational changes which facilitate flavin
        binding.
      reference_section_type: RESULTS
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IDA
  original_reference_id: PMID:12846824
  review:
    summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: ATP binding is a supported biochemical property that affects CRY1 conformation
      and flavin photochemistry, but it is accessory to photoreceptor signaling.
    supported_by:
    - reference_id: PMID:12846824
      supporting_text: autophosphorylation activity associated with Arabidopsis cry1 protein
      reference_section_type: ABSTRACT
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IDA
  original_reference_id: PMID:17073458
  review:
    summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: ATP binding is a supported biochemical property that affects CRY1 conformation
      and flavin photochemistry, but it is accessory to photoreceptor signaling.
    supported_by:
    - reference_id: PMID:17073458
      supporting_text: AtCry1, which contains near stoichiometric
      reference_section_type: ABSTRACT
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IDA
  original_reference_id: PMID:19327354
  review:
    summary: ATP binding is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: ATP binding is a supported biochemical property that affects CRY1 conformation
      and flavin photochemistry, but it is accessory to photoreceptor signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Binding to ATP mediates conformational changes which facilitate flavin
        binding.
      reference_section_type: RESULTS
- term:
    id: GO:0009882
    label: blue light photoreceptor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling
      role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Photoreceptor that mediates primarily blue light inhibition of hypocotyl
        elongation.
      reference_section_type: RESULTS
    - reference_id: file:ARATH/CRY1/CRY1-deep-research-falcon.md
      supporting_text: nucleo-cytoplasmic blue/UV-A photoreceptor
      reference_section_type: RESULTS
- term:
    id: GO:0009882
    label: blue light photoreceptor activity
  evidence_type: IDA
  original_reference_id: PMID:30242037
  review:
    summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling
      role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:8953250
      supporting_text: CRY1 is a flavin-type blue type receptor of Arabidopsis
      reference_section_type: ABSTRACT
    - reference_id: PMID:30242037
      supporting_text: CRY1 overexpression led to enhanced SCW formation.
      reference_section_type: TITLE
- term:
    id: GO:0009882
    label: blue light photoreceptor activity
  evidence_type: IMP
  original_reference_id: PMID:8953250
  review:
    summary: blue light photoreceptor activity matches the core CRY1 photoreceptor/signaling
      role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:8953250
      supporting_text: CRY1 is a flavin-type blue type receptor of Arabidopsis
      reference_section_type: ABSTRACT
- term:
    id: GO:0016301
    label: kinase activity
  evidence_type: IDA
  original_reference_id: PMID:17073458
  review:
    summary: Kinase activity is supported only as CRY1 autokinase activity and should be stated
      more specifically.
    action: MODIFY
    reason: The biochemical evidence is for protein autophosphorylation/autokinase activity
      of AtCRY1. Protein kinase activity is the more specific molecular-function term than
      generic kinase activity.
    proposed_replacement_terms:
    - id: GO:0004672
      label: protein kinase activity
    supported_by:
    - reference_id: PMID:17073458
      supporting_text: AtCry1, which contains near stoichiometric
      reference_section_type: ABSTRACT
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IPI
  original_reference_id: PMID:15805487
  review:
    summary: Identical protein binding captures CRY1 self-association but the specific homodimerization
      term is better.
    action: MODIFY
    reason: The evidence concerns CRY1 homodimerization, and GO:0042803 directly states this
      activity whereas identical protein binding is less precise.
    proposed_replacement_terms:
    - id: GO:0042803
      label: protein homodimerization activity
    supported_by:
    - reference_id: PMID:15805487
      supporting_text: N-terminal domain-mediated homodimerization is required for photoreceptor
        activity of Arabidopsis CRYPTOCHROME 1.
      reference_section_type: TITLE
- term:
    id: GO:0042803
    label: protein homodimerization activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: protein homodimerization activity matches the core CRY1 photoreceptor/signaling
      role.
    action: ACCEPT
    reason: CRY1 homodimerization/oligomerization is an activation mechanism required for
      photoreceptor signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subunit: Homodimer.'
      reference_section_type: RESULTS
- term:
    id: GO:0042803
    label: protein homodimerization activity
  evidence_type: IPI
  original_reference_id: PMID:15805487
  review:
    summary: protein homodimerization activity matches the core CRY1 photoreceptor/signaling
      role.
    action: ACCEPT
    reason: CRY1 homodimerization/oligomerization is an activation mechanism required for
      photoreceptor signaling.
    supported_by:
    - reference_id: PMID:15805487
      supporting_text: N-terminal domain-mediated homodimerization is required for photoreceptor
        activity of Arabidopsis CRYPTOCHROME 1.
      reference_section_type: TITLE
- term:
    id: GO:0071949
    label: FAD binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: FAD binding matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: FAD binding is central to CRY1 blue-light absorption and flavin photoredox signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Name=FAD; Binds 1 FAD per subunit.
      reference_section_type: RESULTS
- term:
    id: GO:0071949
    label: FAD binding
  evidence_type: IDA
  original_reference_id: PMID:17073458
  review:
    summary: FAD binding matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: FAD binding is central to CRY1 blue-light absorption and flavin photoredox signaling.
    supported_by:
    - reference_id: PMID:17073458
      supporting_text: AtCry1, which contains near stoichiometric
      reference_section_type: ABSTRACT
- term:
    id: GO:0140517
    label: protein-RNA adaptor activity
  evidence_type: IPI
  original_reference_id: PMID:36305219
  review:
    summary: protein-RNA adaptor activity is supported for CRY1 but is a non-core output or
      accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The CRY1-FIP37 interaction supports a specific adaptor role in blue-light m6A
      regulation, but this appears to be a specialized signaling branch rather than the primary
      CRY1 molecular function.
    supported_by:
    - reference_id: PMID:36305219
      supporting_text: CRY1 physically interacted with FIP37
      reference_section_type: ABSTRACT
- term:
    id: GO:0007623
    label: circadian rhythm
  evidence_type: IEP
  original_reference_id: PMID:11743105
  review:
    summary: circadian rhythm is supported for CRY1 but is a non-core output or accessory
      biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:11743105
      supporting_text: display circadian oscillations under constant conditions
      reference_section_type: ABSTRACT
- term:
    id: GO:0009266
    label: response to temperature stimulus
  evidence_type: IMP
  original_reference_id: PMID:30635559
  review:
    summary: response to temperature stimulus is supported for CRY1 but is a non-core output
      or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:30635559
      supporting_text: the PHYB-dependent hypocotyl thermoresponse is masked by CRY1
      reference_section_type: INTRODUCTION
- term:
    id: GO:0009414
    label: response to water deprivation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: Water-deprivation response reflects altered stomatal aperture and water loss
      rather than a primary CRY1 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: The direct evidence is that CRY1/CRY2 regulate blue-light stomatal opening and
      water loss. Calling CRY1 a water-deprivation response gene overstates an indirect physiological
      consequence.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0009416
    label: response to light stimulus
  evidence_type: IEP
  original_reference_id: PMID:11743105
  review:
    summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A
      photoreception.
    action: MODIFY
    reason: This IEP row reflects light/circadian regulation of CRY1 expression, while the
      gene-product function is better captured by direct blue-light response and blue-light
      signaling terms.
    supported_by:
    - reference_id: PMID:11743105
      supporting_text: display circadian oscillations under constant conditions
      reference_section_type: ABSTRACT
    proposed_replacement_terms:
    - id: GO:0009637
      label: response to blue light
    - id: GO:0009785
      label: blue light signaling pathway
- term:
    id: GO:0009416
    label: response to light stimulus
  evidence_type: IMP
  original_reference_id: PMID:15751956
  review:
    summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A
      photoreception.
    action: MODIFY
    reason: CRY1 is a blue/UV-A photoreceptor. The broad parent term loses the relevant spectral
      and signaling specificity.
    proposed_replacement_terms:
    - id: GO:0009637
      label: response to blue light
    - id: GO:0009785
      label: blue light signaling pathway
    supported_by:
    - reference_id: PMID:15751956
      supporting_text: light-dependent conformational change in the C-terminal domain of Arabidopsis
      reference_section_type: ABSTRACT
- term:
    id: GO:0009416
    label: response to light stimulus
  evidence_type: IDA
  original_reference_id: PMID:21467031
  review:
    summary: Response to light stimulus is too broad for CRY1, whose direct evidence is blue/UV-A
      photoreception.
    action: MODIFY
    reason: CRY1 is a blue/UV-A photoreceptor. The broad parent term loses the relevant spectral
      and signaling specificity.
    proposed_replacement_terms:
    - id: GO:0009637
      label: response to blue light
    - id: GO:0009785
      label: blue light signaling pathway
    supported_by:
    - reference_id: PMID:21467031
      supporting_text: Light-activated cryptochrome reacts with molecular oxygen to form a
        flavin-superoxide radical pair.
      reference_section_type: TITLE
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:12857830
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:12857830
      supporting_text: phototropins and cryptochromes function
      reference_section_type: ABSTRACT
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:21511871
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:21511871
      supporting_text: CRY1-SPA1 interaction suppresses the SPA1-COP1 interaction
      reference_section_type: ABSTRACT
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IDA
  original_reference_id: PMID:21511872
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:21511872
      supporting_text: CRY1 interacts physically with SPA1 in a blue-light-dependent manner.
      reference_section_type: ABSTRACT
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:22147516
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:22147516
      supporting_text: effects of cry on stomatal conductance are largely indirect
      reference_section_type: ABSTRACT
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:23511208
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:23511208
      supporting_text: Network balance via CRY signalling controls the Arabidopsis circadian
        clock over ambient temperatures.
      reference_section_type: TITLE
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:25721730
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:25721730
      supporting_text: The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to Mediate
        Blue Light Inhibition of Hypocotyl Elongation.
      reference_section_type: TITLE
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IDA
  original_reference_id: PMID:25728686
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:25728686
      supporting_text: Blue-light dependent reactive oxygen species formation by Arabidopsis
        cryptochrome.
      reference_section_type: TITLE
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:26313597
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:26313597
      supporting_text: These pathways are potentiated by metabolites in the intracellular
      reference_section_type: ABSTRACT
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:8528277
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:8528277
      supporting_text: CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated
        inhibition
      reference_section_type: ABSTRACT
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:9733523
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:9733523
      supporting_text: cry1 activity in a phyAphyB mutant
      reference_section_type: ABSTRACT
- term:
    id: GO:0009637
    label: response to blue light
  evidence_type: IMP
  original_reference_id: PMID:9765547
  review:
    summary: response to blue light matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: PMID:9765547
      supporting_text: High fluence-rate blue light (BL) rapidly inhibits hypocotyl growth
      reference_section_type: ABSTRACT
- term:
    id: GO:0009638
    label: phototropism
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0009638
    label: phototropism
  evidence_type: IMP
  original_reference_id: PMID:12857830
  review:
    summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:12857830
      supporting_text: phototropins and cryptochromes function
      reference_section_type: ABSTRACT
- term:
    id: GO:0009638
    label: phototropism
  evidence_type: IMP
  original_reference_id: PMID:8528277
  review:
    summary: phototropism is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:8528277
      supporting_text: CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated
        inhibition
      reference_section_type: ABSTRACT
- term:
    id: GO:0009644
    label: response to high light intensity
  evidence_type: IMP
  original_reference_id: PMID:22786870
  review:
    summary: response to high light intensity is supported for CRY1 but is a non-core output
      or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:22786870
      supporting_text: components of the cry1-mediated photoprotective response
      reference_section_type: TITLE
- term:
    id: GO:0009646
    label: response to absence of light
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: response to absence of light is supported for CRY1 but is a non-core output or
      accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0009646
    label: response to absence of light
  evidence_type: IMP
  original_reference_id: PMID:22855128
  review:
    summary: response to absence of light is supported for CRY1 but is a non-core output or
      accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:22855128
      supporting_text: cry1 and GPA1 signaling genetically interact in hook opening and anthocyanin
        synthesis.
      reference_section_type: TITLE
- term:
    id: GO:0009785
    label: blue light signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0009785
    label: blue light signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: blue light signaling pathway matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This captures the core CRY1 role as a blue/UV-A photoreceptor that mediates blue-light
      signaling and photomorphogenesis.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0009791
    label: post-embryonic development
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: post-embryonic development is a broad developmental consequence of CRY1 light
      signaling.
    action: MODIFY
    reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent
      growth, not a generic role in overall development.
    proposed_replacement_terms:
    - id: GO:0009640
      label: photomorphogenesis
    - id: GO:0009637
      label: response to blue light
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0010075
    label: regulation of meristem growth
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: regulation of meristem growth is supported for CRY1 but is a non-core output
      or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0010114
    label: response to red light
  evidence_type: IMP
  original_reference_id: PMID:9733523
  review:
    summary: response to red light is supported for CRY1 but is a non-core output or accessory
      biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:9733523
      supporting_text: cry1 activity in a phyAphyB mutant
      reference_section_type: ABSTRACT
- term:
    id: GO:0010117
    label: photoprotection
  evidence_type: IMP
  original_reference_id: PMID:22786870
  review:
    summary: photoprotection is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:22786870
      supporting_text: components of the cry1-mediated photoprotective response
      reference_section_type: TITLE
- term:
    id: GO:0010118
    label: stomatal movement
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: Stomatal movement is a supported non-core output of CRY1 blue-light signaling.
    action: KEEP_AS_NON_CORE
    reason: CRY1/CRY2 influence blue-light stomatal opening, but this physiological output
      is downstream of the core photoreceptor/signaling role.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0010118
    label: stomatal movement
  evidence_type: IMP
  original_reference_id: PMID:22147516
  review:
    summary: Stomatal movement is retained as a non-core CRY1 output, with this study supporting
      an indirect ABA-linked effect on conductance.
    action: KEEP_AS_NON_CORE
    reason: The paper argues cry effects on stomatal conductance are largely indirect rather
      than direct blue-light stomatal photoreception, so the term should not be treated as
      core CRY1 function.
    supported_by:
    - reference_id: PMID:22147516
      supporting_text: effects of cry on stomatal conductance are largely indirect
      reference_section_type: ABSTRACT
- term:
    id: GO:0010218
    label: response to far red light
  evidence_type: IMP
  original_reference_id: PMID:9733523
  review:
    summary: response to far red light is supported for CRY1 but is a non-core output or accessory
      biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:9733523
      supporting_text: cry1 activity in a phyAphyB mutant
      reference_section_type: ABSTRACT
- term:
    id: GO:0010244
    label: response to low fluence blue light stimulus by blue low-fluence system
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: response to low fluence blue light stimulus by blue low-fluence system is supported
      for CRY1 but is a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0010244
    label: response to low fluence blue light stimulus by blue low-fluence system
  evidence_type: IMP
  original_reference_id: PMID:19558423
  review:
    summary: response to low fluence blue light stimulus by blue low-fluence system is supported
      for CRY1 but is a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Reduced hyponastic growth (differential growth-driven upward leaf movement)
        in low blue light fluence.
      reference_section_type: RESULTS
- term:
    id: GO:0010244
    label: response to low fluence blue light stimulus by blue low-fluence system
  evidence_type: IEP
  original_reference_id: PMID:26724867
  review:
    summary: response to low fluence blue light stimulus by blue low-fluence system is supported
      for CRY1 but is a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:26724867
      supporting_text: CRY1 and CRY2 perceive
      reference_section_type: ABSTRACT
- term:
    id: GO:0010310
    label: regulation of hydrogen peroxide metabolic process
  evidence_type: IDA
  original_reference_id: PMID:25728686
  review:
    summary: regulation of hydrogen peroxide metabolic process is supported for CRY1 but is
      a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:25728686
      supporting_text: Blue-light dependent reactive oxygen species formation by Arabidopsis
        cryptochrome.
      reference_section_type: TITLE
- term:
    id: GO:0010617
    label: circadian regulation of calcium ion oscillation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: circadian regulation of calcium ion oscillation is supported for CRY1 but is
      a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0032922
    label: circadian regulation of gene expression
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: circadian regulation of gene expression is supported for CRY1 but is a non-core
      output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0042752
    label: regulation of circadian rhythm
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: regulation of circadian rhythm is supported for CRY1 but is a non-core output
      or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0042752
    label: regulation of circadian rhythm
  evidence_type: IMP
  original_reference_id: PMID:23511208
  review:
    summary: regulation of circadian rhythm is supported for CRY1 but is a non-core output
      or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:23511208
      supporting_text: Network balance via CRY signalling controls the Arabidopsis circadian
        clock over ambient temperatures.
      reference_section_type: TITLE
- term:
    id: GO:0043153
    label: entrainment of circadian clock by photoperiod
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: entrainment of circadian clock by photoperiod is supported for CRY1 but is a
      non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0046283
    label: anthocyanin-containing compound metabolic process
  evidence_type: IMP
  original_reference_id: PMID:8528277
  review:
    summary: anthocyanin-containing compound metabolic process is supported for CRY1 but is
      a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:8528277
      supporting_text: CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated
        inhibition
      reference_section_type: ABSTRACT
- term:
    id: GO:0046777
    label: protein autophosphorylation
  evidence_type: IDA
  original_reference_id: PMID:17073458
  review:
    summary: protein autophosphorylation is supported for CRY1 but is a non-core output or
      accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: CRY1 autophosphorylation is experimentally supported, but its in vivo regulatory
      significance and light dependence are less central than CRY1 photoreceptor activity.
    supported_by:
    - reference_id: PMID:17073458
      supporting_text: AtCry1, which contains near stoichiometric
      reference_section_type: ABSTRACT
- term:
    id: GO:0048580
    label: regulation of post-embryonic development
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: regulation of post-embryonic development is a broad developmental consequence
      of CRY1 light signaling.
    action: MODIFY
    reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent
      growth, not a generic role in overall development.
    proposed_replacement_terms:
    - id: GO:0009640
      label: photomorphogenesis
    - id: GO:0009637
      label: response to blue light
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0048731
    label: system development
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: system development is a broad developmental consequence of CRY1 light signaling.
    action: MODIFY
    reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent
      growth, not a generic role in overall development.
    proposed_replacement_terms:
    - id: GO:0009640
      label: photomorphogenesis
    - id: GO:0009637
      label: response to blue light
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:0060918
    label: auxin transport
  evidence_type: IMP
  original_reference_id: PMID:20133010
  review:
    summary: auxin transport is supported for CRY1 but is a non-core output or accessory biochemical
      property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:20133010
      supporting_text: Arabidopsis CRY1 restrains lateral roots growth by inhibiting auxin
        transport.
      reference_section_type: ABSTRACT
- term:
    id: GO:0071000
    label: response to magnetism
  evidence_type: IDA
  original_reference_id: PMID:22421133
  review:
    summary: response to magnetism is supported for CRY1 but is a non-core output or accessory
      biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:22421133
      supporting_text: Magnetically sensitive light-induced reactions in cryptochrome are
        consistent with its proposed role as a magnetoreceptor.
      reference_section_type: TITLE
- term:
    id: GO:0071000
    label: response to magnetism
  evidence_type: IMP
  original_reference_id: PMID:26095447
  review:
    summary: response to magnetism is supported for CRY1 but is a non-core output or accessory
      biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:26095447
      supporting_text: The effect of near-null magnetic field on Arabidopsis flowering is
        associated with CRY.
      reference_section_type: ABSTRACT
- term:
    id: GO:0072387
    label: flavin adenine dinucleotide metabolic process
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function,
      not FAD metabolic process.
    action: MODIFY
    reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling,
      but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor
      metabolism as a biological process.
    proposed_replacement_terms:
    - id: GO:0071949
      label: FAD binding
    - id: GO:0009882
      label: blue light photoreceptor activity
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Blue-light absorbing flavoprotein that activates reversible flavin
        photoreduction.
      reference_section_type: RESULTS
- term:
    id: GO:0072387
    label: flavin adenine dinucleotide metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function,
      not FAD metabolic process.
    action: MODIFY
    reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling,
      but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor
      metabolism as a biological process.
    proposed_replacement_terms:
    - id: GO:0071949
      label: FAD binding
    - id: GO:0009882
      label: blue light photoreceptor activity
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Blue-light absorbing flavoprotein that activates reversible flavin
        photoreduction.
      reference_section_type: RESULTS
- term:
    id: GO:0072387
    label: flavin adenine dinucleotide metabolic process
  evidence_type: IDA
  original_reference_id: PMID:21467031
  review:
    summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function,
      not FAD metabolic process.
    action: MODIFY
    reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling,
      but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor
      metabolism as a biological process.
    proposed_replacement_terms:
    - id: GO:0071949
      label: FAD binding
    - id: GO:0009882
      label: blue light photoreceptor activity
    supported_by:
    - reference_id: PMID:21467031
      supporting_text: Light-activated cryptochrome reacts with molecular oxygen to form a
        flavin-superoxide radical pair.
      reference_section_type: TITLE
- term:
    id: GO:0072387
    label: flavin adenine dinucleotide metabolic process
  evidence_type: IDA
  original_reference_id: PMID:25157750
  review:
    summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function,
      not FAD metabolic process.
    action: MODIFY
    reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling,
      but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor
      metabolism as a biological process.
    proposed_replacement_terms:
    - id: GO:0071949
      label: FAD binding
    - id: GO:0009882
      label: blue light photoreceptor activity
    supported_by:
    - reference_id: PMID:25157750
      supporting_text: ATP binding and aspartate protonation enhance photoinduced electron
        transfer in plant cryptochrome.
      reference_section_type: TITLE
- term:
    id: GO:0072387
    label: flavin adenine dinucleotide metabolic process
  evidence_type: IMP
  original_reference_id: PMID:26313597
  review:
    summary: FAD photochemistry in CRY1 supports cofactor binding and photoreceptor function,
      not FAD metabolic process.
    action: MODIFY
    reason: CRY1 binds FAD and undergoes flavin photoreduction during blue-light signaling,
      but there is no evidence that CRY1 is part of FAD biosynthesis, degradation, or cofactor
      metabolism as a biological process.
    proposed_replacement_terms:
    - id: GO:0071949
      label: FAD binding
    - id: GO:0009882
      label: blue light photoreceptor activity
    supported_by:
    - reference_id: PMID:26313597
      supporting_text: These pathways are potentiated by metabolites in the intracellular
      reference_section_type: ABSTRACT
- term:
    id: GO:0099402
    label: plant organ development
  evidence_type: IMP
  original_reference_id: PMID:25721730
  review:
    summary: plant organ development is a broad developmental consequence of CRY1 light signaling.
    action: MODIFY
    reason: The evidence supports CRY1 regulation of photomorphogenesis and light-dependent
      growth, not a generic role in overall development.
    proposed_replacement_terms:
    - id: GO:0009640
      label: photomorphogenesis
    - id: GO:0009637
      label: response to blue light
    supported_by:
    - reference_id: PMID:25721730
      supporting_text: The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to Mediate
        Blue Light Inhibition of Hypocotyl Elongation.
      reference_section_type: TITLE
- term:
    id: GO:1900426
    label: positive regulation of defense response to bacterium
  evidence_type: IMP
  original_reference_id: PMID:20053798
  review:
    summary: positive regulation of defense response to bacterium is supported for CRY1 but
      is a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Promotes systemic acquired resistance (SAR) and PR gene expression
        triggered by P.syringae.
      reference_section_type: RESULTS
- term:
    id: GO:1901332
    label: negative regulation of lateral root development
  evidence_type: IMP
  original_reference_id: PMID:20133010
  review:
    summary: negative regulation of lateral root development is supported for CRY1 but is
      a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:20133010
      supporting_text: Arabidopsis CRY1 restrains lateral roots growth by inhibiting auxin
        transport.
      reference_section_type: ABSTRACT
- term:
    id: GO:1901371
    label: regulation of leaf morphogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: regulation of leaf morphogenesis is supported for CRY1 but is a non-core output
      or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:1901371
    label: regulation of leaf morphogenesis
  evidence_type: IMP
  original_reference_id: PMID:19558423
  review:
    summary: regulation of leaf morphogenesis is supported for CRY1 but is a non-core output
      or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Reduced hyponastic growth (differential growth-driven upward leaf movement)
        in low blue light fluence.
      reference_section_type: RESULTS
- term:
    id: GO:1901529
    label: positive regulation of anion channel activity
  evidence_type: IMP
  original_reference_id: PMID:9765547
  review:
    summary: positive regulation of anion channel activity is supported for CRY1 but is a
      non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:9765547
      supporting_text: High fluence-rate blue light (BL) rapidly inhibits hypocotyl growth
      reference_section_type: ABSTRACT
- term:
    id: GO:1901672
    label: positive regulation of systemic acquired resistance
  evidence_type: IMP
  original_reference_id: PMID:20053798
  review:
    summary: positive regulation of systemic acquired resistance is supported for CRY1 but
      is a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: Promotes systemic acquired resistance (SAR) and PR gene expression
        triggered by P.syringae.
      reference_section_type: RESULTS
- term:
    id: GO:1902347
    label: response to strigolactone
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: response to strigolactone is supported for CRY1 but is a non-core output or accessory
      biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:1902347
    label: response to strigolactone
  evidence_type: IMP
  original_reference_id: PMID:24126495
  review:
    summary: response to strigolactone is supported for CRY1 but is a non-core output or accessory
      biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:24126495
      supporting_text: Strigolactone-regulated hypocotyl elongation is dependent on cryptochrome
        and phytochrome signaling pathways.
      reference_section_type: TITLE
- term:
    id: GO:1902448
    label: positive regulation of shade avoidance
  evidence_type: IMP
  original_reference_id: PMID:21457375
  review:
    summary: positive regulation of shade avoidance is supported for CRY1 but is a non-core
      output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:21457375
      supporting_text: Cryptochrome 1 and phytochrome B control shade-avoidance responses
        in Arabidopsis.
      reference_section_type: TITLE
- term:
    id: GO:2000377
    label: regulation of reactive oxygen species metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: regulation of reactive oxygen species metabolic process is supported for CRY1
      but is a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: CRY1 is a blue-light absorbing flavoprotein that regulates light responses.
      reference_section_type: RESULTS
- term:
    id: GO:2000377
    label: regulation of reactive oxygen species metabolic process
  evidence_type: IDA
  original_reference_id: PMID:25728686
  review:
    summary: regulation of reactive oxygen species metabolic process is supported for CRY1
      but is a non-core output or accessory biochemical property.
    action: KEEP_AS_NON_CORE
    reason: The annotation is supported as a downstream or context-specific output of CRY1
      blue-light signaling, but it should not be treated as the core molecular role of CRY1.
    supported_by:
    - reference_id: PMID:25728686
      supporting_text: Blue-light dependent reactive oxygen species formation by Arabidopsis
        cryptochrome.
      reference_section_type: TITLE
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: nucleus matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: ISM
  original_reference_id: GO_REF:0000122
  review:
    summary: nucleus matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:10221900
  review:
    summary: nucleus matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: HDA
  original_reference_id: PMID:15610358
  review:
    summary: nucleus matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: EXP
  original_reference_id: PMID:18003924
  review:
    summary: nucleus matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:26724867
  review:
    summary: nucleus matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: cytoplasm matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: cytoplasm matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:18003924
  review:
    summary: cytoplasm matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: HDA
  original_reference_id: PMID:28887381
  review:
    summary: Cytosol localization is plausible for CRY1 but the high-throughput dataset support
      is not accessible in the cached text.
    action: UNDECIDED
    reason: CRY1 has independent cytoplasm evidence, but this specific HDA cytosol assertion
      cannot be checked from the accessible publication text.
    supported_by:
    - reference_id: PMID:28887381
      supporting_text: The accessible cache describes a global protein-correlation profiling
        dataset, but not the CRY1 cytosol call.
      full_text_unavailable: true
      reference_section_type: ABSTRACT
- term:
    id: GO:0016604
    label: nuclear body
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: nuclear body matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0016604
    label: nuclear body
  evidence_type: IDA
  original_reference_id: PMID:21511872
  review:
    summary: nuclear body matches the core CRY1 photoreceptor/signaling role.
    action: ACCEPT
    reason: This localization is consistent with CRY1 nucleo-cytoplasmic signaling and nuclear-body
      accumulation during photomorphogenic signaling.
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
- term:
    id: GO:0016605
    label: PML body
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: PML body is an animal-centric mapping; the plant evidence supports CRY1 nuclear
      bodies.
    action: MODIFY
    reason: Arabidopsis CRY1 is reported in nuclear bodies. PML body is too specific for plant
      CRY1 and should be replaced by nuclear body.
    proposed_replacement_terms:
    - id: GO:0016604
      label: nuclear body
    supported_by:
    - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
      supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
        in nuclear bodies.'
      reference_section_type: RESULTS
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary
    mapping, accompanied by conservative changes to GO terms applied by UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000122
  title: AtSubP analysis
  findings: []
- id: PMID:10221900
  title: 'Cryptochromes: blue light receptors for plants and animals.'
  findings: []
- id: PMID:10364413
  title: Arabidopsis contains at least four independent blue-light-activated signal transduction
    pathways.
  findings: []
- id: PMID:11509693
  title: Direct interaction of Arabidopsis cryptochromes with COP1 in light control development.
  findings: []
- id: PMID:11743105
  title: Circadian clock-regulated expression of phytochrome and cryptochrome genes in Arabidopsis.
  findings: []
- id: PMID:11752373
  title: The signaling mechanism of Arabidopsis CRY1 involves direct interaction with COP1.
  findings:
  - statement: Arabidopsis CRY1 and CRY2 are cryptochrome photoreceptors rather than DNA repair
      photolyases.
    supporting_text: lack photolyase activity
    reference_section_type: INTRODUCTION
- id: PMID:12324610
  title: Arabidopsis Mutants Lacking Blue Light-Dependent Inhibition of Hypocotyl Elongation.
  findings: []
- id: PMID:12846824
  title: Novel ATP-binding and autophosphorylation activity associated with Arabidopsis and
    human cryptochrome-1.
  findings:
  - statement: CRY1 has ATP-binding/autophosphorylation activity.
    supporting_text: autophosphorylation activity associated with Arabidopsis cry1 protein
    reference_section_type: ABSTRACT
- id: PMID:12857830
  title: Second positive phototropism results from coordinated co-action of the phototropins
    and cryptochromes.
  findings: []
- id: PMID:15610358
  title: High-throughput protein localization in Arabidopsis using Agrobacterium-mediated
    transient expression of GFP-ORF fusions.
  findings: []
- id: PMID:15751956
  title: Role of structural plasticity in signal transduction by the cryptochrome blue-light
    photoreceptor.
  findings: []
- id: PMID:15805487
  title: N-terminal domain-mediated homodimerization is required for photoreceptor activity
    of Arabidopsis CRYPTOCHROME 1.
  findings: []
- id: PMID:16093319
  title: 'From The Cover: A role for Arabidopsis cryptochromes and COP1 in the regulation
    of stomatal opening.'
  findings:
  - statement: CRY1/CRY2 contribute to blue-light-induced stomatal opening through COP1-related
      signaling.
    supporting_text: CRY functions additively with PHOT in mediating blue light-induced stomatal
      opening.
    reference_section_type: ABSTRACT
- id: PMID:17073458
  title: Analysis of autophosphorylating kinase activities of Arabidopsis and human cryptochromes.
  findings:
  - statement: AtCRY1 contains FAD and has autokinase activity in vitro.
    supporting_text: AtCry1, which contains near stoichiometric
    reference_section_type: ABSTRACT
- id: PMID:17075038
  title: Cryptochrome-1-dependent execution of programmed cell death induced by singlet oxygen
    in Arabidopsis thaliana.
  findings: []
- id: PMID:17217468
  title: HY5 is a point of convergence between cryptochrome and cytokinin signalling pathways
    in Arabidopsis thaliana.
  findings: []
- id: PMID:17982000
  title: Distinct light and clock modulation of cytosolic free Ca2+ oscillations and rhythmic
    CHLOROPHYLL A/B BINDING PROTEIN2 promoter activity in Arabidopsis.
  findings: []
- id: PMID:18003924
  title: Separate functions for nuclear and cytoplasmic cryptochrome 1 during photomorphogenesis
    of Arabidopsis seedlings.
  findings: []
- id: PMID:18424613
  title: Distinct light-initiated gene expression and cell cycle programs in the shoot apex
    and cotyledons of Arabidopsis.
  findings: []
- id: PMID:19327354
  title: Conformational change induced by ATP binding correlates with enhanced biological
    function of Arabidopsis cryptochrome.
  findings: []
- id: PMID:19558423
  title: 'Differential petiole growth in Arabidopsis thaliana: photocontrol and hormonal regulation.'
  findings: []
- id: PMID:20053798
  title: CRYPTOCHROME 1 is implicated in promoting R protein-mediated plant resistance to
    Pseudomonas syringae in Arabidopsis.
  findings: []
- id: PMID:20133010
  title: Arabidopsis cryptochrome-1 restrains lateral roots growth by inhibiting auxin transport.
  findings: []
- id: PMID:20668058
  title: Cryptochrome as a sensor of the blue/green ratio of natural radiation in Arabidopsis.
  findings:
  - statement: CRY1 contributes to detection of blue/green light ratio.
    supporting_text: Cryptochrome as a sensor of the blue/green ratio of natural radiation
      in Arabidopsis.
    reference_section_type: ABSTRACT
- id: PMID:21457375
  title: Cryptochrome 1 and phytochrome B control shade-avoidance responses in Arabidopsis
    via partially independent hormonal cascades.
  findings: []
- id: PMID:21467031
  title: Light-activated cryptochrome reacts with molecular oxygen to form a flavin-superoxide
    radical pair consistent with magnetoreception.
  findings: []
- id: PMID:21511871
  title: Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response
    to blue light.
  findings: []
- id: PMID:21511872
  title: Blue-light-dependent interaction of cryptochrome 1 with SPA1 defines a dynamic signaling
    mechanism.
  findings:
  - statement: CRY1 interacts with SPA1 in a blue-light-dependent signaling mechanism.
    supporting_text: CRY1 interacts physically with SPA1 in a blue-light-dependent manner.
    reference_section_type: ABSTRACT
- id: PMID:22147516
  title: Phototropins but not cryptochromes mediate the blue light-specific promotion of stomatal
    conductance, while both enhance photosynthesis and transpiration under full sunlight.
  findings:
  - statement: CRY effects on stomatal conductance can be indirect and ABA-linked.
    supporting_text: effects of cry on stomatal conductance are largely indirect
    reference_section_type: ABSTRACT
- id: PMID:22421133
  title: Magnetically sensitive light-induced reactions in cryptochrome are consistent with
    its proposed role as a magnetoreceptor.
  findings: []
- id: PMID:22577138
  title: Light-dependent, dark-promoted interaction between Arabidopsis cryptochrome 1 and
    phytochrome B proteins.
  findings: []
- id: PMID:22786870
  title: The CRYPTOCHROME1-dependent response to excess light is mediated through the transcriptional
    activators ZINC FINGER PROTEIN EXPRESSED IN INFLORESCENCE MERISTEM LIKE1 and ZML2 in Arabidopsis.
  findings: []
- id: PMID:22855128
  title: cry1 and GPA1 signaling genetically interact in hook opening and anthocyanin synthesis
    in Arabidopsis.
  findings: []
- id: PMID:23511208
  title: Network balance via CRY signalling controls the Arabidopsis circadian clock over
    ambient temperatures.
  findings: []
- id: PMID:24126495
  title: Strigolactone-regulated hypocotyl elongation is dependent on cryptochrome and phytochrome
    signaling pathways in Arabidopsis.
  findings: []
- id: PMID:25157750
  title: ATP binding and aspartate protonation enhance photoinduced electron transfer in plant
    cryptochrome.
  findings: []
- id: PMID:25721730
  title: The CNT1 Domain of Arabidopsis CRY1 Alone Is Sufficient to Mediate Blue Light Inhibition
    of Hypocotyl Elongation.
  findings: []
- id: PMID:25728686
  title: Blue-light dependent reactive oxygen species formation by Arabidopsis cryptochrome
    may define a novel evolutionarily conserved signaling mechanism.
  findings:
  - statement: Photoactivated Arabidopsis cryptochrome can promote ROS formation.
    supporting_text: Blue-light dependent reactive oxygen species formation by Arabidopsis
      cryptochrome.
    reference_section_type: ABSTRACT
- id: PMID:26095447
  title: Suppression of Arabidopsis flowering by near-null magnetic field is affected by light.
  findings: []
- id: PMID:26313597
  title: Cellular metabolites modulate in vivo signaling of Arabidopsis cryptochrome-1.
  findings: []
- id: PMID:26596765
  title: TCP2 positively regulates HY5/HYH and photomorphogenesis in Arabidopsis.
  findings: []
- id: PMID:26724867
  title: Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue
    Light.
  findings:
  - statement: CRY1/CRY2 directly contact PIF4 and PIF5 under limiting blue light.
    supporting_text: CRY1 and CRY2 perceive
    reference_section_type: ABSTRACT
- id: PMID:28887381
  title: Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation
    Profiling.
  findings: []
- id: PMID:30242037
  title: Blue Light Regulates Secondary Cell Wall Thickening via MYC2/MYC4 Activation of the
    NST1-Directed Transcriptional Network in Arabidopsis.
  findings:
  - statement: CRY1 links blue light to secondary cell wall thickening through MYC2/MYC4/NST1.
    supporting_text: CRY1 overexpression led to enhanced SCW formation.
    reference_section_type: ABSTRACT
- id: PMID:30635559
  title: Daytime temperature is sensed by phytochrome B in Arabidopsis through a transcriptional
    activator HEMERA.
  findings: []
- id: PMID:32554507
  title: Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated Inhibition
    of PIF4 Expression.
  findings:
  - statement: CRY1 modulates low-blue-light phototropism through PIF4 expression.
    supporting_text: Low Blue Light Enhances Phototropism by Releasing Cryptochrome1-Mediated
      Inhibition of PIF4 Expression.
    reference_section_type: ABSTRACT
- id: PMID:32661061
  title: Photoexcited Cryptochrome2 Interacts Directly with TOE1 and TOE2 in Flowering Regulation.
  findings: []
- id: PMID:36305219
  title: The blue light receptor CRY1 interacts with FIP37 to promote N(6) -methyladenosine
    RNA modification and photomorphogenesis in Arabidopsis.
  findings:
  - statement: CRY1 interacts with FIP37 to promote blue-light m6A RNA modification.
    supporting_text: CRY1 physically interacted with FIP37
    reference_section_type: ABSTRACT
- id: PMID:36508461
  title: A role for brassinosteroid signalling in decision-making processes in the Arabidopsis
    seedling.
  findings: []
- id: PMID:8528277
  title: Mutations throughout an Arabidopsis blue-light photoreceptor impair blue-light-responsive
    anthocyanin accumulation and inhibition of hypocotyl elongation.
  findings:
  - statement: CRY1 mutations impair blue-light hypocotyl inhibition and anthocyanin accumulation.
    supporting_text: CRY1 was originally defined as the photoreceptor responsible for blue-light-mediated
      inhibition
    reference_section_type: ABSTRACT
- id: PMID:8953250
  title: Arabidopsis cryptochrome 1 is a soluble protein mediating blue light-dependent regulation
    of plant growth and development.
  findings:
  - statement: CRY1 is a blue-light photoreceptor controlling growth and gene expression.
    supporting_text: CRY1 is a flavin-type blue type receptor of Arabidopsis
    reference_section_type: ABSTRACT
- id: PMID:9651577
  title: The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in
    vitro.
  findings: []
- id: PMID:9733523
  title: Genetic interactions between phytochrome A, phytochrome B, and cryptochrome 1 during
    Arabidopsis development.
  findings: []
- id: PMID:9765547
  title: Two genetically separable phases of growth inhibition induced by blue light in Arabidopsis
    seedlings.
  findings: []
- id: file:ARATH/CRY1/CRY1-uniprot.txt
  title: UniProtKB record for Arabidopsis thaliana CRY1 (Q43125)
  findings:
  - statement: UniProt summarizes CRY1 as a blue-light absorbing flavoprotein with nucleo-cytoplasmic
      signaling roles.
    supporting_text: Blue-light absorbing flavoprotein that activates reversible flavin photoreduction.
    reference_section_type: RESULTS
  - statement: UniProt records CRY1 in cytoplasm, nucleus, and nuclear bodies.
    supporting_text: 'Subcellular location: Cytoplasm; Nucleus; Nucleus, PML body; present
      in nuclear bodies.'
    reference_section_type: RESULTS
- id: file:ARATH/CRY1/CRY1-deep-research-falcon.md
  title: Falcon deep-research report for Arabidopsis CRY1
  findings:
  - statement: The deep-research synthesis supports CRY1 as a FAD-dependent photoreceptor
      signaling switch.
    supporting_text: CRY1 binds FAD in its PHR domain and undergoes light-driven flavin redox
      cycling and conformational change.
    reference_section_type: RESULTS
- id: file:interpro/panther/PTHR11455/PTHR11455-notes.md
  title: PANTHER PTHR11455 cryptochrome family notes
  findings:
  - statement: PANTHER context warns that the family mixes cryptochromes and photolyases.
    supporting_text: The family contains both cryptochromes and photolyases; subfamilies separate
      circadian cryptochromes from repair enzymes.
    reference_section_type: RESULTS
- id: file:interpro/panther/PTHR11455/PTHR11455-entries.csv
  title: PANTHER PTHR11455 reviewed entry table
  findings:
  - statement: The cached PANTHER entry table places Q43125 in a CRYPTOCHROME-1 subfamily.
    supporting_text: Q43125,Cryptochrome-1,protein,3702,Arabidopsis thaliana,...,PTHR11455:SF50,CRYPTOCHROME-1
    reference_section_type: RESULTS
core_functions:
- description: CRY1 is a FAD-dependent blue/UV-A photoreceptor whose light-driven flavin photoredox,
    conformational change, and oligomerization initiate blue-light signaling outputs including
    photomorphogenesis, hypocotyl growth inhibition, circadian modulation, and regulation
    of transcription-factor stability or activity.
  molecular_function:
    id: GO:0009882
    label: blue light photoreceptor activity
  directly_involved_in:
  - id: GO:0009785
    label: blue light signaling pathway
  - id: GO:0009640
    label: photomorphogenesis
  - id: GO:0051510
    label: regulation of unidimensional cell growth
  locations:
  - id: GO:0005634
    label: nucleus
  - id: GO:0005737
    label: cytoplasm
  - id: GO:0016604
    label: nuclear body
  supported_by:
  - reference_id: PMID:8953250
    supporting_text: CRY1 is a flavin-type blue type receptor of Arabidopsis
    reference_section_type: ABSTRACT
  - reference_id: PMID:15805487
    supporting_text: N-terminal domain-mediated homodimerization is required for photoreceptor
      activity of Arabidopsis CRYPTOCHROME 1.
    reference_section_type: TITLE
  - reference_id: PMID:21511872
    supporting_text: CRY1 interacts physically with SPA1 in a blue-light-dependent manner.
    reference_section_type: ABSTRACT
  - reference_id: PMID:26724867
    supporting_text: CRY1 and CRY2 perceive
    reference_section_type: ABSTRACT
  - reference_id: file:ARATH/CRY1/CRY1-uniprot.txt
    supporting_text: Blue-light absorbing flavoprotein that activates reversible flavin photoreduction.
    reference_section_type: RESULTS
proposed_new_terms: []
suggested_questions:
- question: Which CRY1 phosphorylation sites or kinase-active residues are required in vivo
    for blue-light signaling, given conflicting in vitro reports on light-stimulated autokinase
    activity?
  experts:
  - Bouly JP
  - Sancar A
  - Ahmad M
- question: How much of the CRY1 stomatal and water-loss phenotype is direct guard-cell signaling
    versus indirect ABA or developmental acclimation?
  experts:
  - Mao J
  - Boccalandro HE
  - Casal JJ
- question: Should plant CRY1 nuclear bodies be represented only as nuclear bodies rather
    than PML bodies in GO-derived mappings?
  experts:
  - Lian HL
  - Yang HQ
suggested_experiments:
- hypothesis: CRY1 autophosphorylation is required for a subset of photomorphogenic outputs
    but not for initial FAD photoreduction.
  description: Complement cry1 mutants with native-promoter CRY1 phosphorylation-site and
    kinase-impaired variants, then assay hypocotyl inhibition, SPA/COP1 association, HY5 stability,
    and FAD photoreduction kinetics under matched blue-light fluence.
  experiment_type: native-promoter rescue with phosphosite mutagenesis
- hypothesis: CRY1 regulation of stomatal conductance is partly indirect through ABA and long-term
    acclimation rather than direct blue-light guard-cell photoreception.
  description: Express CRY1 specifically in guard cells versus mesophyll/epidermal tissues
    in a cry1 cry2 background and measure stomatal aperture, ABA abundance, transpiration,
    and photosynthesis after acute and acclimated blue-light treatments.
  experiment_type: cell-type-specific complementation and physiology
- hypothesis: The CRY1-FIP37 branch controls a defined subset of m6A-modified PIF and photomorphogenesis
    transcripts.
  description: Combine CRY1-FIP37 interaction-defective CRY1 alleles with m6A profiling and
    RNA decay measurements under blue light to separate FIP37-dependent RNA regulation from
    COP1/SPA-dependent proteostasis outputs.
  experiment_type: interaction-mutant m6A profiling

Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Comprehensive Research Report: Arabidopsis thaliana CRY1 (UniProt Q43125; HY4/BLU1)

Executive summary

1) Key concepts and definitions (current understanding)

1.1 Target identity verification and disambiguation

1.2 Domain architecture and what it implies for function

1.3 Photochemistry terminology and redox states

2) Recent developments and latest research (prioritizing 2023–2024)

2.1 2023: Mechanistic consolidation of plant CRY photochemistry and coupling to signaling

2.2 2024: Structural framework for cryptochrome signaling specificity

2.3 2024: Translational framing—light control of metabolism and stress-protective compounds

3) Molecular function and pathways (functional annotation focus)

3.1 Primary molecular function: light-sensing flavoprotein switch

3.2 Canonical signaling axis: CRY1 → COP1/SPA → HY5 (proteasome-linked)

3.3 Additional signaling branch: CRY1 → ATG8 → HY5 (selective autophagy)

3.4 Negative regulators and network architecture

4) Subcellular localization and site of action

4.1 Nucleo-cytoplasmic distribution

4.2 Localization dynamics linked to autophagy regulation

5) Current applications and real-world implementations

5.1 Controlled-environment agriculture (CEA) and indoor cultivation

5.2 Crop and trait engineering relevance (mechanistic rationale)

6) Expert opinions and authoritative synthesis

7) Relevant statistics and data points (from recent literature)

8) Concise functional annotation statement (recommended)

Summary table

Key sources (publication date; URL)

Citations

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