Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005634 nucleus	IBA GO_REF:0000033	ACCEPT	Summary: CRY2 localizes to the nucleus where it functions as a transcriptional repressor. UniProt curated location confirms nuclear localization (PMID:9801304, PMID:22798407). IBA annotation is phylogenetically well-supported across cryptochromes. Reason: Nuclear localization is well-established for CRY2 and is essential for its transcriptional repressor function in the TTFL. Supporting Evidence: UniProtKB:Q49AN0 Nucleus {ECO:0000269\|PubMed:22798407, ECO:0000269\|PubMed:9801304}
GO:0005737 cytoplasm	IBA GO_REF:0000033	ACCEPT	Summary: CRY2 localizes to the cytoplasm before nuclear translocation as part of the PER-CRY complex. UniProt curated location confirms cytoplasmic localization (PMID:9801304). Reason: Cytoplasmic localization is well-established; CRY2 accumulates in the cytoplasm and translocates to the nucleus through interaction with PER2 or BMAL1. Supporting Evidence: UniProtKB:Q49AN0 Cytoplasm {ECO:0000269\|PubMed:9801304}
GO:0045892 negative regulation of DNA-templated transcription	IBA GO_REF:0000033	ACCEPT	Summary: CRY2 is a core transcriptional repressor in the mammalian circadian clock. It suppresses CLOCK:BMAL1-driven transcription of Per, Cry, Dec1, Dec2, and other E-box-containing genes (PMID:12397359, PMID:14672706, PMID:15147242). Reason: Transcriptional repression is the primary molecular function of CRY2. Multiple independent studies demonstrate CRY2 suppresses CLOCK:BMAL1-induced transcription. Supporting Evidence: PMID:12397359 Cry proteins to inhibit Per transcription PMID:14672706 PERs and CRYs suppressed the induced expression
GO:0003677 DNA binding	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Purified hCRY2 binds dsDNA weakly and ssDNA with higher affinity (PMID:12627958). However, CRY2 represses transcription primarily through protein-protein interactions with CLOCK:BMAL1 rather than direct DNA binding. DNA binding is a vestigial property from the photolyase ancestor. Reason: DNA binding is experimentally demonstrated but is not the primary mechanism by which CRY2 functions in transcriptional repression. It is a retained ancestral property from the photolyase family. Supporting Evidence: PMID:12627958 binds to double-stranded DNA weakly and to single-stranded DNA with higher affinity
GO:0032922 circadian regulation of gene expression	IBA GO_REF:0000033	ACCEPT	Summary: CRY2 is a core component of the circadian TTFL that regulates rhythmic gene expression through repression of CLOCK:BMAL1 transcriptional activity (PMID:10531061, PMID:20840750). Reason: Circadian regulation of gene expression is the primary biological process in which CRY2 functions. This is well-supported by multiple lines of evidence. Supporting Evidence: PMID:20840750 negatively regulate the transcription of Per and Cry core clock genes UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0043153 entrainment of circadian clock by photoperiod	IBA GO_REF:0000033	REMOVE	Summary: Mammalian CRY proteins function as light-independent transcriptional repressors, not as photoreceptors for entrainment. Unlike Drosophila and plant cryptochromes, mammalian CRYs do not serve as circadian photoreceptors (PMID:10531061). The IBA annotation may reflect ancestral function in non-mammalian family members. Reason: Griffin et al. 1999 (PMID:10531061) demonstrated a light-independent role of CRY1 and CRY2 in the mammalian circadian clock. Mammalian CRY2 is not involved in photic entrainment; this function is mediated by retinal photoreceptors signaling to the SCN. Supporting Evidence: UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0071949 FAD binding	IBA GO_REF:0000033	ACCEPT	Summary: CRY2 binds FAD, confirmed by purification studies showing FAD and pterin cofactors (PMID:8909283). However, FAD binding is weak in mammalian CRYs and the FAD pocket primarily serves as a regulatory hub for FBXL3 recognition and small-molecule binding rather than for catalytic or photochemical function. Reason: FAD binding is experimentally demonstrated and the FAD pocket is functionally important for CRY2 regulation, even though FAD occupancy is low. Supporting Evidence: PMID:8909283 were found to contain FAD and a pterin cofactor
GO:0000166 nucleotide binding	IEA GO_REF:0000043	ACCEPT	Summary: CRY2 binds FAD, which is a dinucleotide cofactor. The nucleotide binding annotation is a broader parent of the more informative FAD binding term. Reason: This is a valid broader term that follows from the FAD binding annotation. As an IEA mapped from the UniProt nucleotide-binding keyword, it is appropriately general. Supporting Evidence: UniProtKB:Q49AN0 Binds 1 FAD per subunit
GO:0005634 nucleus	IEA GO_REF:0000120	ACCEPT	Summary: Duplicate IEA annotation for nucleus. Consistent with IBA and ISS annotations and UniProt curated localization. Reason: Nuclear localization is well-established for CRY2. Supporting Evidence: UniProtKB:Q49AN0 Nucleus {ECO:0000269\|PubMed:22798407, ECO:0000269\|PubMed:9801304}
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: Duplicate IEA annotation for cytoplasm. Consistent with IBA annotation and UniProt curated localization. Reason: Cytoplasmic localization is well-established for CRY2. Supporting Evidence: UniProtKB:Q49AN0 Cytoplasm {ECO:0000269\|PubMed:9801304}
GO:0009881 photoreceptor activity	IEA GO_REF:0000043	REMOVE	Summary: Mammalian CRY2 does not function as a photoreceptor. This IEA annotation derives from the UniProt keyword "Photoreceptor protein" which is a legacy designation based on the photolyase family membership. Griffin et al. 1999 (PMID:10531061) established the light-independent function of mammalian CRYs. Reason: Mammalian CRY2 functions as a light-independent transcriptional repressor. There is no evidence that human CRY2 has photoreceptor activity. The UniProt keyword is misleading for the mammalian protein. Supporting Evidence: PMID:8909283 may function as blue-light photoreceptors in humans UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0019902 phosphatase binding	IEA GO_REF:0000117	ACCEPT	Summary: hCRY2 specifically interacts with protein serine/threonine phosphatase 5 (PP5) via yeast two-hybrid and inhibits its phosphatase activity (PMID:9383998). This is a well-characterized direct interaction. Reason: Direct phosphatase binding is experimentally demonstrated for CRY2 with PP5 (PMID:9383998). The IEA annotation is consistent with the experimental evidence. Supporting Evidence: PMID:9383998 protein serine/threonine phosphatase 5 (PP5) that contains the TPR motif specifically interacted with hCRY2
GO:0048511 rhythmic process	IEA GO_REF:0000043	ACCEPT	Summary: CRY2 is a core circadian clock component. The rhythmic process annotation is a valid broader term encompassing its role in circadian rhythms. Reason: CRY2 is a core component of the circadian clock and participates in generating approximately 24-hour rhythms in gene expression and physiology. Supporting Evidence: UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0005515 protein binding	IPI PMID:16790549 Posttranslational regulation of the mammalian circadian cloc...	MARK AS OVER ANNOTATED	Summary: PMID:16790549 demonstrates CRY2 interacts with PP5 (PPP5C) to modulate CKIepsilon phosphorylation. The specific interaction is better captured by the phosphatase binding (GO:0019902) and protein phosphatase inhibitor activity (GO:0004864) annotations already present. Reason: Generic protein binding does not convey the specific functional interaction between CRY2 and PP5. More informative terms (phosphatase binding, protein phosphatase inhibitor activity) are already annotated. Supporting Evidence: PMID:16790549 cryptochrome regulates clock protein phosphorylation by modulating the effect of PP5 on CKIepsilon
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	MARK AS OVER ANNOTATED	Summary: Large-scale proteome interactome mapping study. Generic protein binding from high-throughput screens is uninformative. Reason: High-throughput interactome mapping does not provide functional insight beyond generic protein binding. More specific interaction terms should be used where validated. Supporting Evidence: PMID:25416956 A proteome-scale map of the human interactome network
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	MARK AS OVER ANNOTATED	Summary: Binary interactome reference map study. This is a high-throughput screen reporting many interaction partners. Generic protein binding from such studies is uninformative. Reason: High-throughput binary interactome mapping provides no functional specificity for CRY2 interactions. Many of the reported partners (keratin associated proteins, etc.) may represent false positives or indirect interactions. Supporting Evidence: PMID:32296183 A reference map of the human binary protein interactome
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	MARK AS OVER ANNOTATED	Summary: Neurodegenerative disease interactome mapping study. Generic protein binding annotation from a high-throughput screen. Reason: High-throughput interactome mapping does not provide functional specificity for CRY2 interactions. Supporting Evidence: PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins
GO:0000976 transcription cis-regulatory region binding	IEA GO_REF:0000107	MODIFY	Summary: This annotation is transferred from mouse CRY2 (Q9R194). CRY2 does not bind cis-regulatory regions specifically; its DNA binding is non-specific and weak (PMID:12627958). CRY2 represses transcription through protein-protein interactions with CLOCK:BMAL1 rather than through direct cis-regulatory element binding. Reason: CRY2 binds DNA non-specifically and weakly. The term "transcription cis-regulatory region binding" implies sequence-specific DNA binding which is not demonstrated for CRY2. A general DNA binding term is more appropriate. Proposed replacements: DNA binding Supporting Evidence: PMID:12627958 binds to double-stranded DNA weakly and to single-stranded DNA with higher affinity
GO:0005739 mitochondrion	IEA GO_REF:0000107	REMOVE	Summary: CRY2 is well-characterized as a cytoplasmic/nuclear protein. Mitochondrial localization is not supported by any direct evidence for CRY2. UniProt curated localization reports only cytoplasm and nucleus. Reason: No evidence supports mitochondrial localization of CRY2. UniProt curated location indicates only cytoplasm and nucleus. Supporting Evidence: UniProtKB:Q49AN0 Cytoplasm {ECO:0000269\|PubMed:9801304}. Nucleus {ECO:0000269\|PubMed:22798407, ECO:0000269\|PubMed:9801304}
GO:0009416 response to light stimulus	IEA GO_REF:0000107	REMOVE	Summary: Transferred from mouse CRY2. Mammalian CRY2 functions as a light-independent transcriptional repressor (PMID:10531061). While CRY2 retains a photolyase-like fold with FAD binding, it does not function as a light sensor in mammals. Reason: Mammalian CRY2 has a well-established light-independent role in the circadian clock. The response to light stimulus annotation is based on ancestral function from the photolyase family that is not retained in mammalian cryptochromes. Supporting Evidence: UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0014823 response to activity	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Transferred from mouse CRY2. UniProt mentions CRY2 represses PPARD and limits exercise capacity (by similarity). This would be a downstream pleiotropic effect of circadian clock function rather than a core function of CRY2. Reason: CRY2 may indirectly affect exercise-related physiology through transcriptional repression of PPARD in skeletal muscle. This is a secondary downstream effect of circadian regulation, not a core function. Supporting Evidence: UniProtKB:Q49AN0 Represses PPARD and its target genes in the skeletal muscle and limits exercise capacity (By similarity)
GO:0016922 nuclear receptor binding	IEA GO_REF:0000107	ACCEPT	Summary: CRY2 interacts with the glucocorticoid receptor (NR3C1/GR) in a ligand-dependent manner (PMID:22170608) and with HNF4A (PMID:30530698). UniProt also reports interactions with AR, PPARA, PPARD, PPARG, NR1I2, NR1I3, and VDR. Reason: Nuclear receptor binding is well-supported by multiple studies demonstrating direct ligand-dependent interactions between CRY2 and various nuclear receptors including GR, HNF4A, and others. Supporting Evidence: PMID:22170608 cryptochromes 1 and 2, interact with the glucocorticoid receptor in a ligand-dependent fashion PMID:30530698 HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer
GO:0019900 kinase binding	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: CRY2 modulates CKIepsilon (CSNK1E) activity through PP5 interaction (PMID:16790549). UniProt reports phosphorylation by CSNK1E requires interaction with PER1 or PER2, suggesting indirect rather than direct kinase binding. However, the circadian core oscillator complex includes CSNK1D/CSNK1E as components. Reason: CRY2 interacts with kinases as part of the circadian repressor complex but direct kinase binding has not been definitively demonstrated independent of complex partners. The interaction may be mediated through PER proteins. Supporting Evidence: PMID:16790549 cryptochrome regulates clock protein phosphorylation by modulating the effect of PP5 on CKIepsilon UniProtKB:Q49AN0 Phosphorylation by CSKNE requires interaction with PER1 or PER2
GO:0019901 protein kinase binding	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Similar to kinase binding above. CRY2 is part of a complex with CSNK1D/CSNK1E but direct protein kinase binding independent of PER proteins is not well-demonstrated. Reason: CRY2 functions in a complex containing protein kinases (CSNK1D/CSNK1E) but direct binding may be mediated through PER protein intermediaries. Supporting Evidence: UniProtKB:Q49AN0 Component of the circadian core oscillator, which includes the CRY proteins, CLOCK or NPAS2, BMAL1 or BMAL2, CSNK1D and/or CSNK1E
GO:0019915 lipid storage	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: UniProt notes CRY2 plays a key role in lipid metabolism modulation through transcriptional regulation of genes like ACSL4. CRY2 repression via PER2 promotes adipogenesis through circadian control of Wnt signaling. However, lipid storage per se is a downstream pleiotropic consequence of circadian regulation. Reason: CRY2 contributes to lipid metabolism modulation through transcriptional regulation, which is a downstream effect of its circadian clock function rather than a direct role in lipid storage. Supporting Evidence: UniProtKB:Q49AN0 Plays a key role in glucose and lipid metabolism modulation, in part, through the transcriptional regulation of genes involved in these pathways, such as LEP or ACSL4
GO:0032868 response to insulin	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Loss of cryptochromes causes glucose intolerance (PMID:22170608), which relates to insulin responsiveness. However, this is a downstream metabolic consequence of cryptochrome deficiency affecting glucocorticoid signaling and glucose homeostasis rather than a direct insulin response function. Reason: CRY2 affects insulin sensitivity indirectly through its role in circadian regulation of glucocorticoid signaling and glucose metabolism. This is a pleiotropic downstream effect rather than a core function. Supporting Evidence: PMID:22170608 genetic loss of cryptochrome 1 and/or 2 results in glucose intolerance and constitutively high levels of circulating corticosterone
GO:0032922 circadian regulation of gene expression	IEA GO_REF:0000107	ACCEPT	Summary: Duplicate IEA annotation for circadian regulation of gene expression. Consistent with IBA and other annotations. Reason: Circadian regulation of gene expression is a core function of CRY2, well-supported across multiple evidence types. Supporting Evidence: PMID:20840750 negatively regulate the transcription of Per and Cry core clock genes
GO:0042593 glucose homeostasis	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Cryptochrome deficiency causes glucose intolerance and elevated corticosterone (PMID:22170608). CRY2 may mediate circadian regulation of cAMP signaling and gluconeogenesis. This is a downstream metabolic effect of circadian clock function. Reason: Glucose homeostasis is affected by CRY2 through its circadian regulation of glucocorticoid signaling and gluconeogenesis, but this is a pleiotropic downstream effect rather than a core molecular function. Supporting Evidence: PMID:22170608 genetic loss of cryptochrome 1 and/or 2 results in glucose intolerance and constitutively high levels of circulating corticosterone
GO:0042752 regulation of circadian rhythm	IEA GO_REF:0000107	ACCEPT	Summary: CRY2 is a core circadian clock component. CRY1 and CRY2 encode inhibitors of the CLOCK:BMAL1 complex and their degradation by SCF(FBXL3) is essential for clock oscillation (PMID:17463251). Reason: CRY2 is a core component of the circadian clock regulatory mechanism. Supporting Evidence: PMID:17463251 Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex that establish a negative-feedback loop
GO:0042754 negative regulation of circadian rhythm	IEA GO_REF:0000107	ACCEPT	Summary: CRY2 functions as part of the negative limb of the circadian TTFL, inhibiting CLOCK:BMAL1 activity (PMID:17463251, PMID:10531061). Reason: CRY2 is a negative regulator in the circadian feedback loop, directly inhibiting the positive limb (CLOCK:BMAL1) of the clock. Supporting Evidence: PMID:17463251 Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex that establish a negative-feedback loop
GO:0043153 entrainment of circadian clock by photoperiod	IEA GO_REF:0000107	REMOVE	Summary: Duplicate IEA annotation. Mammalian CRY2 is not involved in photic entrainment of the circadian clock. Reason: Mammalian CRY2 functions as a light-independent transcriptional repressor (PMID:10531061). Photic entrainment in mammals is mediated by retinal photoreceptors, not by cryptochromes. Supporting Evidence: UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0045892 negative regulation of DNA-templated transcription	IEA GO_REF:0000107	ACCEPT	Summary: Duplicate IEA annotation. Consistent with IBA and IDA annotations for transcriptional repression. Reason: Negative regulation of transcription is the primary molecular function of CRY2. Supporting Evidence: PMID:12397359 Cry proteins to inhibit Per transcription
GO:0071949 FAD binding	IEA GO_REF:0000107	ACCEPT	Summary: Duplicate IEA annotation for FAD binding. Consistent with IBA and ISS annotations. Reason: FAD binding is experimentally demonstrated for CRY2. Supporting Evidence: PMID:8909283 were found to contain FAD and a pterin cofactor
GO:2000323 negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Cryptochromes interact with the glucocorticoid receptor and broadly oppose GR activation while promoting GR-mediated repression (PMID:22170608). CRY deficiency vastly decreases gene repression and approximately doubles dexamethasone-induced genes. Reason: While well-supported by PMID:22170608, regulation of glucocorticoid signaling is a downstream function of CRY2 nuclear receptor binding rather than a core clock function. It represents an important secondary output of the circadian clock. Supporting Evidence: PMID:22170608 cryptochrome deficiency vastly decreases gene repression and approximately doubles the number of dexamethasone-induced genes, suggesting that cryptochromes broadly oppose glucocorticoid receptor activation and promote repression
GO:2000850 negative regulation of glucocorticoid secretion	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Loss of cryptochromes leads to constitutively high circulating corticosterone levels, suggesting reduced suppression of the hypothalamic-pituitary-adrenal axis (PMID:22170608). Reason: While well-supported, regulation of glucocorticoid secretion is a downstream physiological consequence of CRY2 function in the circadian clock and its interaction with the glucocorticoid receptor. This is a secondary output rather than a core molecular function. Supporting Evidence: PMID:22170608 genetic loss of cryptochrome 1 and/or 2 results in glucose intolerance and constitutively high levels of circulating corticosterone, suggesting reduced suppression of the hypothalamic-pituitary-adrenal axis
GO:0005829 cytosol	IDA GO_REF:0000052	ACCEPT	Summary: HPA immunofluorescence data supports cytosolic localization of CRY2. This is consistent with the broader cytoplasm annotation. Reason: Cytosolic localization is consistent with the established cytoplasmic/nuclear distribution of CRY2. HPA provides IDA-level evidence from immunofluorescence. Supporting Evidence: UniProtKB:Q49AN0 Cytoplasm {ECO:0000269\|PubMed:9801304}
GO:0016607 nuclear speck	IDA GO_REF:0000052	UNDECIDED	Summary: HPA immunofluorescence data indicates nuclear speck localization. This is IDA evidence from the Human Protein Atlas. Nuclear specks are subnuclear structures enriched in RNA splicing factors. While the HPA staining pattern may show punctate nuclear signal, nuclear speck localization has not been independently confirmed for CRY2 in the literature. Reason: The HPA immunofluorescence data may show punctate nuclear staining consistent with nuclear specks, but this has not been validated by independent studies. Without access to the specific HPA images and co-localization data with speck markers, it is difficult to confirm this specific subnuclear localization. Supporting Evidence: UniProtKB:Q49AN0 Nucleus {ECO:0000269\|PubMed:22798407, ECO:0000269\|PubMed:9801304}
GO:0032922 circadian regulation of gene expression	NAS PMID:20840750 Identification of two amino acids in the C-terminal domain o...	ACCEPT	Summary: PMID:20840750 identifies CRY2 residues essential for PER2 interaction in the negative arm of the circadian feedback loop (PMID:20840750). Reason: The study provides direct evidence that CRY2-PER2 interaction is essential for the circadian transcriptional repression mechanism. Supporting Evidence: PMID:20840750 negatively regulate the transcription of Per and Cry core clock genes
GO:0042754 negative regulation of circadian rhythm	NAS PMID:20840750 Identification of two amino acids in the C-terminal domain o...	ACCEPT	Summary: CRY2 represses CLOCK:BMAL1 as part of the negative limb of the circadian clock. PMID:20840750 characterizes the CRY2-PER2 interaction interface essential for this repression. Reason: CRY2 is a well-established negative regulator in the circadian feedback loop. Supporting Evidence: PMID:17463251 Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex that establish a negative-feedback loop
GO:0004864 protein phosphatase inhibitor activity	IDA PMID:9383998 Human blue-light photoreceptor hCRY2 specifically interacts ...	ACCEPT	Summary: hCRY2 inhibits the phosphatase activity of PP5. Zhao and Sancar 1997 demonstrated that hCRY2, but not the highly homologous (6-4) photolyase, specifically inhibits PP5 phosphatase activity (PMID:9383998). Reason: This is a well-characterized direct enzymatic inhibition demonstrated by direct assay. CRY2 specifically inhibits PP5, and this interaction is relevant to circadian clock regulation through modulation of CKIepsilon phosphorylation. Supporting Evidence: PMID:9383998 hCRY2, but not the highly homologous (6-4) photolyase, inhibits the phosphatase activity of PP5
GO:0009416 response to light stimulus	ISS GO_REF:0000024	REMOVE	Summary: ISS annotation transferred from mouse CRY2 (Q9R194). Mammalian CRY2 functions as a light-independent transcriptional repressor (PMID:10531061). Reason: Mammalian CRY2 has a light-independent role in the circadian clock. Response to light stimulus is not a function of human CRY2. Supporting Evidence: UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0014823 response to activity	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS annotation transferred from mouse CRY2. UniProt notes CRY2 represses PPARD in skeletal muscle and limits exercise capacity (by similarity). This is a downstream pleiotropic effect. Reason: CRY2 may indirectly affect exercise-related physiology through transcriptional repression of PPARD, but this is a secondary downstream effect of circadian regulation. Supporting Evidence: UniProtKB:Q49AN0 Represses PPARD and its target genes in the skeletal muscle and limits exercise capacity (By similarity)
GO:0005515 protein binding	IPI PMID:30530698 Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modula...	MODIFY	Summary: PMID:30530698 demonstrates CRY2 interacts with HNF4A, a nuclear receptor. The specific interaction is better captured by the nuclear receptor binding annotation (GO:0016922). Reason: The interaction between CRY2 and HNF4A is a specific nuclear receptor binding interaction. Generic protein binding does not convey the functional specificity of this interaction. Proposed replacements: nuclear receptor binding Supporting Evidence: PMID:30530698 HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer
GO:0009416 response to light stimulus	IMP PMID:15751956 Role of structural plasticity in signal transduction by the ...	REMOVE	Summary: PMID:15751956 (Partch et al. 2005) demonstrates a light-dependent conformational change in the C-terminal domain of Arabidopsis Cry1, not human CRY2. The paper also characterizes the CRY2 photolyase homology region structure but does not demonstrate a light response for human CRY2. This IMP annotation from CAFA appears to be a misannotation. Reason: The paper primarily characterizes Arabidopsis Cry1 light-dependent conformational changes. It does not demonstrate a light response function for human CRY2. The IMP evidence code is inappropriate for this reference. Supporting Evidence: PMID:15751956 we demonstrate a light-dependent conformational change in the C-terminal domain of Arabidopsis Cry1
GO:0042752 regulation of circadian rhythm	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation from mouse CRY2. CRY2 is a core circadian clock component, well-established as a regulator of circadian rhythm. Reason: CRY2 is a core component of the circadian clock mechanism. Supporting Evidence: PMID:17463251 Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex that establish a negative-feedback loop
GO:0043153 entrainment of circadian clock by photoperiod	ISS GO_REF:0000024	REMOVE	Summary: ISS annotation from mouse CRY2. Mammalian CRY2 is not involved in photic entrainment. Reason: Mammalian CRY2 functions as a light-independent transcriptional repressor (PMID:10531061). Photic entrainment is not a function of mammalian CRY. Supporting Evidence: UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0045892 negative regulation of DNA-templated transcription	IDA PMID:12397359 Dec1 and Dec2 are regulators of the mammalian molecular cloc...	ACCEPT	Summary: Dec1 and Dec2 study (Honma et al. 2002) shows Cry proteins together with Per proteins inhibit Per transcription by closing the autoregulatory feedback loop. Reason: Direct experimental evidence that Cry proteins inhibit Per transcription, a core function of CRY2. Supporting Evidence: PMID:12397359 Protein products of Per act together with Cry proteins to inhibit Per transcription, thus closing the autoregulatory feedback loop
GO:0032922 circadian regulation of gene expression	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation from mouse CRY2. Consistent with the well-established role of CRY2 in circadian gene regulation. Reason: Circadian regulation of gene expression is a core function of CRY2. Supporting Evidence: PMID:20840750 negatively regulate the transcription of Per and Cry core clock genes
GO:0042593 glucose homeostasis	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS annotation from mouse CRY2. Cryptochrome deficiency causes glucose intolerance (PMID:22170608). This is a downstream metabolic effect. Reason: Glucose homeostasis is affected by CRY2 through its circadian regulation of glucocorticoid signaling, but this is a pleiotropic downstream effect. Supporting Evidence: PMID:22170608 genetic loss of cryptochrome 1 and/or 2 results in glucose intolerance
GO:2000323 negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS annotation from mouse CRY2. Cryptochromes broadly oppose GR activation (PMID:22170608). This is a well-supported secondary function. Reason: Regulation of glucocorticoid signaling is a downstream output of CRY2 nuclear receptor binding, not a core clock function. Supporting Evidence: PMID:22170608 cryptochromes broadly oppose glucocorticoid receptor activation and promote repression
GO:0000976 transcription cis-regulatory region binding	ISS GO_REF:0000024	MODIFY	Summary: ISS annotation from mouse CRY2. CRY2 binds DNA non-specifically rather than at specific cis-regulatory regions. Reason: CRY2 does not specifically bind cis-regulatory regions. Its DNA binding is non-specific and weak. A general DNA binding term is more appropriate. Proposed replacements: DNA binding Supporting Evidence: PMID:12627958 binds to double-stranded DNA weakly and to single-stranded DNA with higher affinity
GO:0042754 negative regulation of circadian rhythm	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation from mouse CRY2. CRY2 functions as a negative regulator in the circadian feedback loop. Reason: CRY2 inhibits CLOCK:BMAL1 in the negative arm of the circadian clock. Supporting Evidence: PMID:17463251 Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex that establish a negative-feedback loop
GO:0045892 negative regulation of DNA-templated transcription	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation from mouse CRY2. Consistent with the core transcriptional repressor function of CRY2. Reason: Negative regulation of transcription is the primary molecular function of CRY2. Supporting Evidence: PMID:20840750 negatively regulate the transcription of Per and Cry core clock genes
GO:0071949 FAD binding	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation from mouse CRY2. FAD binding is experimentally confirmed for human CRY2. Reason: FAD binding is directly demonstrated for purified human CRY2. Supporting Evidence: PMID:8909283 were found to contain FAD and a pterin cofactor
GO:0007623 circadian rhythm	ISS GO_REF:0000024	ACCEPT	Summary: CRY2 is a core component of the mammalian circadian clock, essential for generating approximately 24-hour rhythms. Reason: CRY2 is a well-established core circadian clock component. Mice lacking both CRY1 and CRY2 are completely arrhythmic. Supporting Evidence: UniProtKB:Q49AN0 Transcriptional repressor which forms a core component of the circadian clock
GO:0005515 protein binding	IPI PMID:9383998 Human blue-light photoreceptor hCRY2 specifically interacts ...	MARK AS OVER ANNOTATED	Summary: PMID:9383998 demonstrates CRY2 specifically interacts with PP5. More informative terms (phosphatase binding, protein phosphatase inhibitor activity) are already annotated for this interaction. Reason: Generic protein binding does not convey the specific functional interaction. Phosphatase binding (GO:0019902) and protein phosphatase inhibitor activity (GO:0004864) from the same reference are more informative. Supporting Evidence: PMID:9383998 protein serine/threonine phosphatase 5 (PP5) that contains the TPR motif specifically interacted with hCRY2
GO:0019902 phosphatase binding	IPI PMID:9383998 Human blue-light photoreceptor hCRY2 specifically interacts ...	ACCEPT	Summary: Zhao and Sancar 1997 demonstrated by yeast two-hybrid that PP5 specifically interacts with hCRY2 (PMID:9383998). This is a well-characterized direct interaction. Reason: Direct experimental evidence for CRY2-PP5 interaction by yeast two-hybrid assay. Supporting Evidence: PMID:9383998 protein serine/threonine phosphatase 5 (PP5) that contains the TPR motif specifically interacted with hCRY2
GO:0005576 extracellular region	IDA PMID:9753616 Molecular cloning of a second human stanniocalcin homologue ...	REMOVE	Summary: PMID:9753616 (Ishibashi et al. 1998) describes the cloning of stanniocalcin-2 (STC2), an unrelated protein. This appears to be a misannotation where the wrong gene was associated with this reference. CRY2 is not an extracellular protein. Reason: The cited reference is about STC2 (stanniocalcin-2), not CRY2. This is a clear misannotation. CRY2 is an intracellular protein localized to cytoplasm and nucleus. Supporting Evidence: PMID:9753616 Molecular cloning of a second human stanniocalcin homologue (STC2)
GO:2000118 regulation of sodium-dependent phosphate transport	IDA PMID:9753616 Molecular cloning of a second human stanniocalcin homologue ...	REMOVE	Summary: PMID:9753616 describes STC2-mediated inhibition of sodium-phosphate cotransporter. This is unrelated to CRY2. This is a clear misannotation. Reason: The cited reference concerns STC2 (stanniocalcin-2) biology, not CRY2. CRY2 has no demonstrated role in phosphate transport regulation. Supporting Evidence: PMID:9753616 STC2-transfected CHO cells inhibited the promoter activity of Na-phosphate cotransporter
GO:0000122 negative regulation of transcription by RNA polymerase II	IDA PMID:12397359 Dec1 and Dec2 are regulators of the mammalian molecular cloc...	ACCEPT	Summary: Honma et al. 2002 demonstrated that Cry proteins act together with Per proteins to inhibit CLOCK:BMAL1-driven transcription from E-box elements in the Per1 promoter (PMID:12397359). This is RNA Pol II-dependent transcription. Reason: CRY2 inhibits CLOCK:BMAL1-driven transcription from E-box elements, which are RNA polymerase II promoter elements. Supporting Evidence: PMID:12397359 Protein products of Per act together with Cry proteins to inhibit Per transcription, thus closing the autoregulatory feedback loop
GO:0000122 negative regulation of transcription by RNA polymerase II	IDA PMID:14672706 A novel autofeedback loop of Dec1 transcription involved in ...	ACCEPT	Summary: Kawamoto et al. 2004 showed PERs and CRYs suppressed CLOCK/BMAL-induced expression of Dec1 through E-box elements (PMID:14672706). Reason: Direct experimental evidence that CRY proteins suppress CLOCK/BMAL-induced transcription from E-box-containing promoters. Supporting Evidence: PMID:14672706 PERs and CRYs suppressed the induced expression
GO:0000122 negative regulation of transcription by RNA polymerase II	IDA PMID:15147242 Expression of the gene for Dec2, a basic helix-loop-helix tr...	ACCEPT	Summary: Hamaguchi et al. 2004 showed Cry suppressed Clock/Bmal-induced transcription from the Dec2 promoter (PMID:15147242). Reason: Direct experimental evidence that Cry proteins suppress CLOCK/BMAL-induced transcription of Dec2. Supporting Evidence: PMID:15147242 Like Dec, Cry and Per also suppressed Clock/Bmal-induced transcription from the Dec2 promoter
GO:0005634 nucleus	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation from mouse CRY2 for nuclear localization. Consistent with direct evidence from human cells. Reason: Nuclear localization is well-established for CRY2 by multiple lines of evidence. Supporting Evidence: UniProtKB:Q49AN0 Nucleus {ECO:0000269\|PubMed:22798407, ECO:0000269\|PubMed:9801304}
GO:0009785 blue light signaling pathway	NAS PMID:8909283 Putative human blue-light photoreceptors hCRY1 and hCRY2 are...	REMOVE	Summary: Hsu et al. 1996 initially hypothesized human CRY proteins may function as blue-light photoreceptors (PMID:8909283). However, subsequent work by Griffin et al. 1999 (PMID:10531061) established that mammalian CRYs function as light-independent transcriptional repressors. There is no evidence for blue light signaling by human CRY2. Reason: The original NAS annotation was based on a hypothesis that has been superseded by definitive evidence that mammalian CRY2 functions as a light-independent repressor. Human CRY2 does not participate in blue light signaling. Supporting Evidence: PMID:8909283 may function as blue-light photoreceptors in humans
GO:0009882 blue light photoreceptor activity	NAS PMID:8909283 Putative human blue-light photoreceptors hCRY1 and hCRY2 are...	REMOVE	Summary: Hsu et al. 1996 speculated CRY proteins may be blue-light photoreceptors (PMID:8909283), but Griffin et al. 1999 (PMID:10531061) demonstrated a light-independent role for mammalian CRYs. Human CRY2 has no demonstrated photoreceptor activity. Reason: The original NAS annotation was speculative. Mammalian CRY2 does not function as a blue light photoreceptor. The annotation should be removed rather than merely marked as over-annotated because the function is not supported by any evidence. Supporting Evidence: PMID:8909283 may function as blue-light photoreceptors in humans
GO:0000719 photoreactive repair	IDA NOT PMID:12627958 Purification and properties of human blue-light photorecepto...	ACCEPT	Summary: Ozgur and Sancar 2003 confirmed that hCRY2 lacks photorepair activity (PMID:12627958). This is a correctly negated annotation documenting the absence of photolyase function. Reason: The negated annotation is correct and well-supported. CRY2 lacks photorepair activity despite its structural similarity to photolyases. Supporting Evidence: PMID:12627958 appear to lack photorepair activity
GO:0003677 DNA binding	IDA PMID:12627958 Purification and properties of human blue-light photorecepto...	KEEP AS NON CORE	Summary: Ozgur and Sancar 2003 demonstrated that purified hCRY2 binds dsDNA weakly and ssDNA with higher affinity (PMID:12627958). This is a residual property from the photolyase ancestor rather than a core functional activity. Reason: DNA binding is experimentally demonstrated but is not the primary mechanism of CRY2 function. CRY2 represses transcription through protein-protein interactions with CLOCK:BMAL1, not through direct DNA binding. Supporting Evidence: PMID:12627958 binds to double-stranded DNA weakly and to single-stranded DNA with higher affinity
GO:0003684 damaged DNA binding	IDA PMID:12627958 Purification and properties of human blue-light photorecepto...	KEEP AS NON CORE	Summary: CRY2 DNA binding is stimulated by the presence of a (6-4) photoproduct (PMID:12627958). This reflects the ancestral photolyase substrate recognition capability retained in the protein structure but without associated repair activity. Reason: Damaged DNA binding is experimentally demonstrated but is a vestigial property from the photolyase ancestor. CRY2 lacks photolyase activity and damaged DNA binding is not its primary function. Supporting Evidence: PMID:12627958 this binding is further stimulated by the presence of a (6-4) photoproduct
GO:0003697 single-stranded DNA binding	IDA PMID:12627958 Purification and properties of human blue-light photorecepto...	KEEP AS NON CORE	Summary: Ozgur and Sancar 2003 showed hCRY2 binds ssDNA with higher affinity than dsDNA (PMID:12627958). This is a vestigial property from the photolyase ancestor. Reason: Single-stranded DNA binding is experimentally demonstrated but is not the primary mechanism of CRY2 function. It represents a retained ancestral property. Supporting Evidence: PMID:12627958 single-stranded DNA with higher affinity
GO:0003904 deoxyribodipyrimidine photo-lyase activity	IDA NOT PMID:8909283 Putative human blue-light photoreceptors hCRY1 and hCRY2 are...	ACCEPT	Summary: Hsu et al. 1996 demonstrated that purified hCRY2 lacks photolyase activity on cyclobutane pyrimidine dimers (PMID:8909283). Correctly negated annotation. Reason: The negated annotation is correct. CRY2 lacks CPD photolyase activity despite its structural similarity to DNA photolyases. Supporting Evidence: PMID:8909283 lacked photolyase activity on the cyclobutane pyrimidine dimer and the (6-4) photoproduct
GO:0003914 DNA (6-4) photolyase activity	IDA NOT PMID:8909283 Putative human blue-light photoreceptors hCRY1 and hCRY2 are...	ACCEPT	Summary: Hsu et al. 1996 demonstrated that purified hCRY2 lacks (6-4) photolyase activity (PMID:8909283). Correctly negated annotation. Reason: The negated annotation is correct. CRY2 lacks (6-4) photolyase activity despite its homology to the Drosophila (6-4) photolyase. Supporting Evidence: PMID:8909283 lacked photolyase activity on the cyclobutane pyrimidine dimer and the (6-4) photoproduct
GO:0005515 protein binding	IPI PMID:17463251 SCFFbxl3 controls the oscillation of the circadian clock by ...	MARK AS OVER ANNOTATED	Summary: Busino et al. 2007 identified CRY2 interaction with FBXL3 as part of the SCF(FBXL3) ubiquitin ligase complex that targets CRY proteins for degradation (PMID:17463251). The specific ubiquitin ligase interaction is functionally important but annotated as generic protein binding. Reason: The CRY2-FBXL3 interaction is a specific ubiquitin ligase substrate recognition event. Generic protein binding does not convey the functional significance of this interaction. Supporting Evidence: PMID:17463251 both Cry1 and Cry2 proteins are ubiquitinated and degraded via the SCF(Fbxl3) ubiquitin ligase complex

Core Functions

CRY2 functions as a transcriptional corepressor in the mammalian circadian clock. It partners with PER proteins (PER1/2/3) to form nuclear repressor complexes that inhibit CLOCK:BMAL1-driven transcription of E-box containing genes including Per, Cry, Dec1, Dec2, and other clock-controlled genes. CRY2 also inhibits PP5 phosphatase activity, modulating CKIepsilon-dependent phosphorylation of clock proteins. CRY2 repression and stability are regulated through the FAD pocket, which mediates FBXL3-dependent ubiquitination and degradation.

Molecular Function:

protein phosphatase inhibitor activity

Directly Involved In:

circadian regulation of gene expression negative regulation of transcription by RNA polymerase II negative regulation of circadian rhythm

Cellular Locations:

nucleus

Supporting Evidence:

PMID:12397359
Protein products of Per act together with Cry proteins to inhibit Per transcription, thus closing the autoregulatory feedback loop
PMID:17463251
Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex that establish a negative-feedback loop
PMID:9383998
hCRY2, but not the highly homologous (6-4) photolyase, inhibits the phosphatase activity of PP5

CRY2 binds FAD as a cofactor in its photolyase homology region. Although FAD occupancy is low in mammalian CRYs, the FAD-binding pocket is functionally critical as a regulatory hub for ubiquitin ligase (FBXL3) recognition, PER2 competitive binding, and small-molecule stabilizer binding.

Molecular Function:

FAD binding

Supporting Evidence:

PMID:8909283
were found to contain FAD and a pterin cofactor

CRY2 interacts with nuclear receptors including the glucocorticoid receptor (NR3C1/GR), androgen receptor (AR), HNF4A, PPARA, PPARD, PPARG, NR1I2, NR1I3, and VDR in a ligand-dependent manner. Through these interactions, CRY2 mediates circadian modulation of nuclear receptor target gene expression, including rhythmic repression of glucocorticoid-responsive genes.

Molecular Function:

nuclear receptor binding

Directly Involved In:

negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway

Cellular Locations:

nucleus

Supporting Evidence:

PMID:22170608
cryptochromes 1 and 2, interact with the glucocorticoid receptor in a ligand-dependent fashion and globally alter the transcriptional response to glucocorticoids
PMID:30530698
HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer

References

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:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

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:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:8909283

Putative human blue-light photoreceptors hCRY1 and hCRY2 are flavoproteins.

hCRY1 and hCRY2 contain FAD and pterin cofactors but lack photolyase activity on cyclobutane pyrimidine dimers and (6-4) photoproducts.

"were found to contain FAD and a pterin cofactor. Like the plant blue-light photoreceptors, both hCRY1 and hCRY2 lacked photolyase activity on the cyclobutane pyrimidine dimer and the (6-4) photoproduct"

PMID:9383998

Human blue-light photoreceptor hCRY2 specifically interacts with protein serine/threonine phosphatase 5 and modulates its activity.

hCRY2 specifically interacts with PP5 and inhibits its phosphatase activity.

"protein serine/threonine phosphatase 5 (PP5) that contains the TPR motif specifically interacted with hCRY2"

PMID:9753616

Molecular cloning of a second human stanniocalcin homologue (STC2).

This paper is about STC2, not CRY2. Annotations citing this reference for CRY2 are misannotations.

PMID:10531061

Light-independent role of CRY1 and CRY2 in the mammalian circadian clock.

CRY1 and CRY2 function as light-independent components of the mammalian circadian clock, inhibiting CLOCK:BMAL1-mediated transcription.

PMID:12397359

Dec1 and Dec2 are regulators of the mammalian molecular clock.

Cry proteins act together with Per proteins to inhibit Per transcription and close the autoregulatory feedback loop.

"Protein products of Per act together with Cry proteins to inhibit Per transcription, thus closing the autoregulatory feedback loop"

PMID:12627958

Purification and properties of human blue-light photoreceptor cryptochrome 2.

Purified hCRY2 binds dsDNA weakly and ssDNA with higher affinity, stimulated by (6-4) photoproducts. CRY2 lacks photorepair activity.

"binds to double-stranded DNA weakly and to single-stranded DNA with higher affinity, and this binding is further stimulated by the presence of a (6-4) photoproduct"

PMID:14672706

A novel autofeedback loop of Dec1 transcription involved in circadian rhythm regulation.

PERs and CRYs suppress CLOCK/BMAL-induced Dec1 expression through E-box elements.

"PERs and CRYs suppressed the induced expression"

PMID:15147242

Expression of the gene for Dec2, a basic helix-loop-helix transcription factor, is regulated by a molecular clock system.

Cry and Per proteins suppress Clock/Bmal-induced transcription from the Dec2 promoter.

PMID:15751956

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

Light-dependent conformational change demonstrated for Arabidopsis Cry1, not human CRY2. The paper characterizes CRY structure but does not demonstrate light response function for human CRY2.

"we demonstrate a light-dependent conformational change in the C-terminal domain of Arabidopsis Cry1"

PMID:16790549

Posttranslational regulation of the mammalian circadian clock by cryptochrome and protein phosphatase 5.

Cryptochrome regulates clock protein phosphorylation by modulating the effect of PP5 on CKIepsilon.

"cryptochrome regulates clock protein phosphorylation by modulating the effect of PP5 on CKIepsilon"

PMID:17463251

SCFFbxl3 controls the oscillation of the circadian clock by directing the degradation of cryptochrome proteins.

CRY1 and CRY2 are ubiquitinated and degraded by SCF(FBXL3), which is essential for clock oscillation.

"both Cry1 and Cry2 proteins are ubiquitinated and degraded via the SCF(Fbxl3) ubiquitin ligase complex"

PMID:20840750

Identification of two amino acids in the C-terminal domain of mouse CRY2 essential for PER2 interaction.

CRY2 residues R501 and K503 are essential for PER2 interaction and circadian transcriptional repression.

"negatively regulate the transcription of Per and Cry core clock genes"

PMID:22170608

Cryptochromes mediate rhythmic repression of the glucocorticoid receptor.

CRY1 and CRY2 interact with the glucocorticoid receptor in a ligand-dependent manner, globally altering glucocorticoid transcriptional response. Cryptochrome deficiency causes glucose intolerance and constitutively high corticosterone.

"cryptochromes 1 and 2, interact with the glucocorticoid receptor in a ligand-dependent fashion and globally alter the transcriptional response to glucocorticoids"

PMID:25416956

A proteome-scale map of the human interactome network.

PMID:30530698

Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks.

HNF4A interacts with CRY2 and modulates tissue-specific circadian networks.

"HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer"

PMID:32296183

A reference map of the human binary protein interactome.

PMID:32814053

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.

📚 Additional Documentation

Deep Research Falcon

(CRY2-deep-research-falcon.md)

provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2026-03-06T03:10:28.657460'
end_time: '2026-03-06T03:25:23.814516'
duration_seconds: 895.16
template_file: templates/gene_research_go_focused.md
template_variables:
organism: human
gene_id: CRY2
gene_symbol: CRY2
uniprot_accession: Q49AN0
protein_description: 'RecName: Full=Cryptochrome-2;'
gene_info: Name=CRY2; Synonyms=KIAA0658;
organism_full: Homo sapiens (Human).
protein_family: Belongs to the DNA photolyase class-1 family.
protein_domains: Crypto/Photolyase_FAD-like_sf. (IPR036134); Crypto/Photolyase_N_sf.
(IPR036155); Cryptochr/Photolyase_FAD-bd. (IPR005101); Cryptochrome/DNA_photolyase_1.
(IPR002081); DNA_photolyase_N. (IPR006050)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 25

Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: Q49AN0
Protein Description: RecName: Full=Cryptochrome-2;
Gene Information: Name=CRY2; Synonyms=KIAA0658;
Organism (full): Homo sapiens (Human).
Protein Family: Belongs to the DNA photolyase class-1 family.
Key Domains: Crypto/Photolyase_FAD-like_sf. (IPR036134); Crypto/Photolyase_N_sf. (IPR036155); Cryptochr/Photolyase_FAD-bd. (IPR005101); Cryptochrome/DNA_photolyase_1. (IPR002081); DNA_photolyase_N. (IPR006050)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "CRY2" matches the protein description above
Verify the organism is correct: Homo sapiens (Human).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'CRY2' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene CRY2 (gene ID: CRY2, UniProt: Q49AN0) in human.

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.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: Q49AN0
Protein Description: RecName: Full=Cryptochrome-2;
Gene Information: Name=CRY2; Synonyms=KIAA0658;
Organism (full): Homo sapiens (Human).
Protein Family: Belongs to the DNA photolyase class-1 family.
Key Domains: Crypto/Photolyase_FAD-like_sf. (IPR036134); Crypto/Photolyase_N_sf. (IPR036155); Cryptochr/Photolyase_FAD-bd. (IPR005101); Cryptochrome/DNA_photolyase_1. (IPR002081); DNA_photolyase_N. (IPR006050)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "CRY2" matches the protein description above
Verify the organism is correct: Homo sapiens (Human).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Please provide a comprehensive research report on the gene CRY2 (gene ID: CRY2, UniProt: Q49AN0) in human.

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.

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.

Research Report: Human CRY2 (Cryptochrome-2; UniProt Q49AN0, gene CRY2/KIAA0658)

Executive summary

Human CRY2 is a flavoprotein of the cryptochrome/photolyase family that acts primarily as a light-independent transcriptional repressor in the mammalian circadian clock transcription–translation feedback loop (TTFL). Its core biochemical role is to assemble with PER proteins, enter the nucleus, and inhibit CLOCK:BMAL1-driven transcription, with CRY2 stability and repression strength governed by FAD-pocket–centered protein interactions with ubiquitin ligases (notably FBXL3/FBXL21) and by PER2-dependent protection from degradation. Recent work (2023–2024) adds mechanistic detail on (i) how specific CRY2 residues enable PER2-mediated repression and adipogenic output programs, (ii) how human CRY2 can undergo noncanonical/lysosomal degradation, and (iii) translational progress of CRY2-selective stabilizers/activators into early clinical testing (Phase I) for glioblastoma as a clock-targeting therapeutic strategy. (li2023transcriptionrepressionof pages 13-15, calloni2023thestructuraland pages 1-2, parlak2023functionalcharacterizationof pages 4-5, chan2024advancingclinicalresponse pages 8-11)

1) Key concepts and definitions (current understanding)

1.1 Cryptochrome-2 (CRY2) and the mammalian TTFL

In mammals, CRY1 and CRY2 are essential negative-limb components of the TTFL: CLOCK:BMAL1 activates transcription of PER and CRY genes, and PER/CRY proteins accumulate and form repressive complexes that suppress CLOCK:BMAL1 activity to close the feedback loop. Mammalian cryptochromes are direct suppressors of circadian transcription and act independently of light, in contrast to many insect/plant cryptochromes that function as photoreceptors. (calloni2023thestructuraland pages 1-2, conrady2024identificationandevolution pages 34-37)

1.2 Domain architecture and family context

CRY2 is a member of the cryptochrome/photolyase (CRY/PL) family, derived from ancestral DNA photolyases. It contains a conserved photolyase homology region (PHR) plus a regulatory C-terminal extension/tail (often called CCT/CCE). The PHR contains a primary pocket homologous to the photolyase FAD/lesion pocket and also a secondary pocket used for regulatory interactions. (khan2025aninsilico pages 1-2, conrady2024identificationandevolution pages 34-37)

1.3 FAD binding in mammalian cryptochromes: weak but functionally central

A key concept in mammalian cryptochromes is that they often show weak FAD association in vitro, raising the question of whether FAD is essential as a cofactor. However, the FAD-binding pocket remains functionally critical because it is directly tied to ubiquitin-ligase recognition (e.g., FBXL3) and is the binding site for small molecules that stabilize CRYs (e.g., KL001-class compounds). Thus, the “FAD pocket” is best viewed as a regulatory hub, even when FAD occupancy is low. (calloni2023thestructuraland pages 1-2, calloni2023thestructuraland pages 2-3)

2) Molecular function, pathways, and cellular localization

2.1 Primary molecular function: transcriptional repression of CLOCK:BMAL1

CRY2 represses CLOCK:BMAL1-induced transcription as part of a PER–CRY repressor complex that accumulates and translocates to the nucleus. A 2023 review summarizes that CRY and PER proteins form a large nuclear repressor complex with CLOCK:BMAL1 to inhibit transcription, framing CRY2 as a direct transcriptional suppressor rather than a DNA repair enzyme. (calloni2023thestructuraland pages 1-2, calloni2023thestructuraland pages 2-3)

2.2 Key protein interactions that implement CRY2 function

PER2 interaction is central to CRY2 repression and stability. A 2023 mechanistic study identified a conserved CRY2 cysteine (C432) in a loop interfacing with PER2 as critical for PER2 association; mutation of this residue disrupts PER2 binding and is linked to loss of repression while preserving BMAL1 binding, highlighting separable binding determinants for repression complex assembly. (li2023transcriptionrepressionof pages 13-15)

Ubiquitin ligases via the FAD pocket: Reviews emphasize that the cofactor/FAD pocket is a recognition site for the SCF ubiquitin ligase FBXL3, and that related ligases (including FBXL21 discussed in reviews) modulate CRY stability and oscillation properties by competition at this site. (calloni2023thestructuraland pages 2-3, conrady2024identificationandevolution pages 136-139)

2.3 Post-translational regulation and proteostasis

CRY2 abundance is tightly regulated by post-translational mechanisms.

PER2-dependent stabilization and half-life control (quantitative): In a 2023 Journal of Biological Chemistry study of human CRY2, PER2 overexpression increased wild-type CRY2 half-life from ~7.9 h to ~12 h, supporting the model that PER2 binding protects CRY2 from degradation and supports repression. (parlak2023functionalcharacterizationof pages 4-5)

Noncanonical degradation pathways (2023 finding): The same 2023 study reports that a human CRY2 variant (p.Ser420Phe) shows markedly reduced stability (half-life ~2 h without PER2), reduced abundance in cytosolic and nuclear fractions, and impaired repression of CLOCK:BMAL1. Notably, proteasome inhibition stabilized wild-type CRY2 but did not stabilize the p.Ser420Phe variant, and the authors provide evidence consistent with lysosomal degradation contributing to CRY2 turnover (e.g., inhibition by lysosomal protease inhibitors). This indicates that human CRY2 turnover can involve proteasomal and lysosomal routes, depending on context/variant. (parlak2023functionalcharacterizationof pages 4-5)

2.4 Subcellular localization

CRY2 function requires dynamic cytosol-to-nucleus shuttling as part of PER:CRY complexes; nuclear accumulation is integral to repression. Impaired nuclear abundance (e.g., destabilizing variants) is associated with impaired repression capacity. (calloni2023thestructuraland pages 1-2, parlak2023functionalcharacterizationof pages 4-5)

3) Recent developments and latest research (emphasis 2023–2024)

3.1 2023: Clarifying the regulatory role of the FAD pocket

A 2023 review synthesizes evidence that mammalian CRYs are light-independent repressors yet retain a photolyase-like pocket that is directly related to ubiquitylation by FBXL3 and is the target for protein-stabilizing small molecules; it also notes that altering cellular FAD supply can stabilize cryptochromes and affect circadian gene expression, reinforcing metabolic coupling to clock protein stability. (Publication date: Jan 2023; https://doi.org/10.3389/fmolb.2022.1081661) (calloni2023thestructuraland pages 1-2, calloni2023thestructuraland pages 2-3)

3.2 2023: CRY2–PER2 interface determinants and functional output (adipogenesis)

A 2023 Molecular and Cellular Biology study links CRY2 repression mechanisms to adipocyte biology. It identifies C432 as a PER2-interaction determinant required for repression and reports that CRY2 repression modulates circadian control of Wnt signaling to promote adipogenesis, tying TTFL repression mechanisms to a defined downstream output program. (Publication date: Sep 2023; https://doi.org/10.1080/10985549.2023.2253710) (li2023transcriptionrepressionof pages 13-15)

3.3 2023: Human variant p.Ser420Phe reveals a “new” degradation pathway

The 2023 JBC paper on p.Ser420Phe provides mechanistic insight into how specific CRY2 residues can disrupt PER2 interactions, nuclear localization/abundance, and degradation routing, with quantitative half-life measurements demonstrating strong PER2-dependent stabilization and variant-dependent turnover. (Publication date: Dec 2023; https://doi.org/10.1016/j.jbc.2023.105451) (parlak2023functionalcharacterizationof pages 4-5)

3.4 2024: Translational advance—CRY2-targeting compounds in glioblastoma and Phase I safety

A 2024 bioRxiv preprint reports development of SHP1705, described as a CRY2-selective activator intended to inhibit BMAL1–CLOCK transcriptional activity in glioblastoma stem cell (GSC) contexts. It reports a randomized, double-blind Phase I study in healthy volunteers with explicit cohort sizes (see statistics below) and states both single and multiple dosing were well tolerated. (Publication date: Sep 2024; https://doi.org/10.1101/2024.09.17.613520) (chan2024advancingclinicalresponse pages 8-11)

4) Current applications and real-world implementations

4.1 Chemical biology tool compounds targeting CRY2 stability

Multiple small molecules target the cryptochrome FAD-pocket region to modulate stability and circadian outputs. A 2025 translational review summarizes that KL001-class compounds bind in the CRY pocket to stabilize CRYs, with derivatives that show CRY2 selectivity (e.g., SHP656/SHP1705, TH301-class) and are being studied across cancer and metabolic indications. (Publication date: Sep 2025; https://doi.org/10.1002/cbin.70087) (toda2025targetingcryptochromesin pages 2-3)

4.2 Glioblastoma: from mechanism to early clinical testing

SHP1705 is reported as the first circadian clock–modulating compound in this class to be found safe and well tolerated in Phase I clinical trials (healthy volunteers), and it is positioned for use against GSC-driven glioblastoma based on preclinical efficacy and combination strategies (e.g., with a REV-ERB agonist). (chan2024advancingclinicalresponse pages 1-4, chan2024advancingclinicalresponse pages 8-11)

Visual evidence: The Chan et al. 2024 study includes a TTFL schematic highlighting how CRY stabilizers are proposed to block SCF-FBXL3-mediated degradation of CRY proteins in the repression loop, and a separate schematic of the in vivo experimental timeline in xenograft models. (chan2024advancingclinicalresponse media 0254a939, chan2024advancingclinicalresponse media bc968ea3)

5) Expert opinions and analysis (authoritative sources)

5.1 FAD pocket as a druggable control node

Authoritative reviews emphasize that even with weak FAD binding in vitro, the FAD pocket is a central structural feature because it mediates E3 ligase recognition and provides a binding site for small-molecule stabilizers, making it a practical “handle” for manipulating clock function pharmacologically. This is a prominent theme in 2023 and later syntheses of the field. (calloni2023thestructuraland pages 1-2, calloni2023thestructuraland pages 2-3)

5.2 Proteostasis complexity: multiple turnover routes

The p.Ser420Phe work illustrates an expert-level caution: CRY2 turnover cannot be treated as exclusively proteasome-mediated. Variant- and context-dependent routing to lysosomal degradation suggests that “degradation pathway” is itself a regulated phenotype, potentially affecting how CRY2-targeting drugs perform across tissues/diseases. (parlak2023functionalcharacterizationof pages 4-5)

6) Relevant statistics and quantitative data (recent studies)

6.1 CRY2 stability (human cells) and PER2 protection

Study: Parlak et al., JBC, Dec 2023 (https://doi.org/10.1016/j.jbc.2023.105451)
- WT CRY2 half-life: ~7.9 h (no PER2) vs ~12 h (with PER2 overexpression). (parlak2023functionalcharacterizationof pages 4-5)
- CRY2 p.Ser420Phe half-life: ~2 h (no PER2) and “comparable to WT” when PER2 is overexpressed (indicating rescue via PER2 protection). (parlak2023functionalcharacterizationof pages 4-5)

6.2 SHP1705 Phase I trial design and adverse events (2024)

Study: Chan et al., bioRxiv, Sep 2024 (https://doi.org/10.1101/2024.09.17.613520)
- Randomized, double-blind, placebo-controlled Phase I with SAD and MAD stages. (chan2024advancingclinicalresponse pages 8-11)
- SAD: 56 treated (42 SHP1705; 14 placebo). (chan2024advancingclinicalresponse pages 8-11)
- MAD: 16 treated (12 SHP1705; 4 placebo). (chan2024advancingclinicalresponse pages 8-11)
- Most frequent TEAE: headache (5 SHP1705 vs 2 placebo); diarrhea and nausea each reported in 3 SHP1705 subjects. One discontinuation (ventricular extrasystoles) judged unrelated. (chan2024advancingclinicalresponse pages 8-11)

Functional annotation snapshot (table)

Functional Aspect	Key Mechanism / Role	Experimental Evidence & Quantitative Data	Key Sources (2023\u20132025)
Core Clock Function (TTFL)	Transcriptional Repressor: Essential component of the negative limb; heterodimerizes with PER proteins to repress CLOCK:BMAL1-mediated transcription.	Forms a ~1.9 MDa repressor complex in the nucleus. Acts via "displacement" or "blocking" of CLOCK:BMAL1.	Li et al. 2023 Mol Cell Biol (li2023transcriptionrepressionof pages 13-15); Calloni & Vabulas 2023 Front Mol Biosci (calloni2023thestructuraland pages 1-2)
Protein Interactions	Key Partners: PER2, CLOCK, BMAL1, FBXL3 (E3 ligase). Specific Interfaces: Cysteine-432 (C432) in CRY2 loop is critical for PER2 binding.	Quantitative: Mutation of C432 disrupts PER2 binding (without affecting BMAL1 binding) and abolishes repression. Structure: FBXL3 binds the FAD pocket via a C-terminal tryptophan.	Li et al. 2023 (li2023transcriptionrepressionof pages 13-15); Conrady 2024 (conrady2024identificationandevolution pages 34-37)
FAD Binding Pocket	Repurposed Domain: Mammalian CRY2 retains the ancestral photolyase FAD pocket but uses it for E3 ligase (FBXL3) recognition and small-molecule binding rather than light sensing.	Binding: Associates with FAD only weakly in vitro (often purifies empty). Cellular FAD levels can still influence stability. Targeted by stabilizers like KL001.	Calloni & Vabulas 2023 (calloni2023thestructuraland pages 2-3); Toda & Hirota 2025 Cell Biol Int (toda2025targetingcryptochromesin pages 12-12)
Stability & Degradation	Regulation: Controlled by SCFFBXL3 (degradation) and SCFFBXL21 (stabilization). Stabilization by PER2 is critical. New Pathway: Lysosomal degradation (via LIR motifs).	Half-life Data: Basal half-life ~7.9 h; extended to ~12 h with PER2. p.Ser420Phe variant is unstable (t1/2 ~2 h) due to loss of PER2 protection.	Parlak et al. 2023 JBC (parlak2023functionalcharacterizationof pages 4-5); Conrady 2024 (conrady2024identificationandevolution pages 136-139)
Small Molecule Modulation	Therapeutic Targets: CRY2 stabilizers (KL001 derivatives) mimic FAD/FBXL3 tail to block degradation.	Compounds: SHP1705 (CRY2-selective, Phase I safe/well-tolerated, effective in GBM xenografts). TH301 (CRY2 stabilizer, induces p21/arrest in pancreatic cancer).	Chan et al. 2025 Neuro-Oncology (chan2025advancingclinicalresponse pages 1-2); Toda & Hirota 2025 (toda2025targetingcryptochromesin pages 2-3); Farmakis et al. 2024 (farmakis2024th301emergesas pages 1-2)
Physiological Outputs	Adipogenesis: Promotes adipocyte differentiation by repressing Wnt signaling. Cancer: Tumor suppressor or oncogene context-dependently (e.g., low in GBM).	Mechanism: CRY2 repression of Wnt is required for adipogenesis; C432 mutants fail to support differentiation. KL001 treatment augments adipocyte maturation.	Li et al. 2023 (li2023transcriptionrepressionof pages 13-15); Chan et al. 2024 bioRxiv (chan2024advancingclinicalresponse pages 1-4)

Table: Overview of human CRY2 molecular functions, interactions, and therapeutic targeting potential based on 2023–2025 research literature.

Limitations of this report

Several mechanistic points about FBXL21 and certain structural interfaces are presented in reviews and may not be CRY2-isoform-specific in the evidence snippets available here; isoform-specific quantitative binding constants (e.g., Kd values) were not present in the retrieved excerpts. (conrady2024identificationandevolution pages 136-139)
ClinicalTrials.gov tool searches did not return structured trial registry records in the available tool output, so Phase I details are taken from the primary manuscript text rather than a registry entry. (chan2024advancingclinicalresponse pages 8-11)

Key references (with dates and URLs)

Calloni G, Vabulas RM. Frontiers in Molecular Biosciences (Jan 2023). “The structural and functional roles of the flavin cofactor FAD in mammalian cryptochromes.” https://doi.org/10.3389/fmolb.2022.1081661 (calloni2023thestructuraland pages 1-2)
Li W et al. Molecular and Cellular Biology (Sep 2023). “Transcription repression of CRY2 via PER2 interaction promotes adipogenesis.” https://doi.org/10.1080/10985549.2023.2253710 (li2023transcriptionrepressionof pages 13-15)
Parlak GC et al. Journal of Biological Chemistry (Dec 2023). “Functional characterization of the CRY2 circadian clock component variant p.Ser420Phe revealed a new degradation pathway for CRY2.” https://doi.org/10.1016/j.jbc.2023.105451 (parlak2023functionalcharacterizationof pages 4-5)
Chan P et al. bioRxiv (Sep 2024). “Advancing Clinical Response Against Glioblastoma: Evaluating SHP1705 CRY2 Activator Efficacy in Preclinical Models and Safety in Phase I Trials.” https://doi.org/10.1101/2024.09.17.613520 (chan2024advancingclinicalresponse pages 8-11)
Toda T, Hirota T. Cell Biology International (Sep 2025). “Targeting Cryptochromes in Chronic Diseases.” https://doi.org/10.1002/cbin.70087 (toda2025targetingcryptochromesin pages 2-3)

References

(li2023transcriptionrepressionof pages 13-15): Weini Li, Xuekai Xiong, Tali Kiperman, and Ke Ma. Transcription repression of cry2 via per2 interaction promotes adipogenesis. Molecular and Cellular Biology, 43:500-514, Sep 2023. URL: https://doi.org/10.1080/10985549.2023.2253710, doi:10.1080/10985549.2023.2253710. This article has 8 citations and is from a domain leading peer-reviewed journal.
(calloni2023thestructuraland pages 1-2): Giulia Calloni and R. Martin Vabulas. The structural and functional roles of the flavin cofactor fad in mammalian cryptochromes. Frontiers in Molecular Biosciences, Jan 2023. URL: https://doi.org/10.3389/fmolb.2022.1081661, doi:10.3389/fmolb.2022.1081661. This article has 7 citations.
(parlak2023functionalcharacterizationof pages 4-5): Gizem Cagla Parlak, Ibrahim Baris, Seref Gul, and Ibrahim Halil Kavakli. Functional characterization of the cry2 circadian clock component variant p.ser420phe revealed a new degradation pathway for cry2. Journal of Biological Chemistry, 299:105451, Dec 2023. URL: https://doi.org/10.1016/j.jbc.2023.105451, doi:10.1016/j.jbc.2023.105451. This article has 5 citations and is from a domain leading peer-reviewed journal.
(chan2024advancingclinicalresponse pages 8-11): Priscilla Chan, Yoshiko Nagai, Qiulian Wu, Anahit Hovsepyan, Seda Mkhitaryan, Jiarui Wang, Gevorg Karapetyan, Theodore Kamenecka, Laura A. Solt, Jamie Cope, Rex A. Moats, Tsuyoshi Hirota, Jeremy N. Rich, and Steve A. Kay. Advancing clinical response against glioblastoma: evaluating shp1705 cry2 activator efficacy in preclinical models and safety in phase i trials. bioRxiv, Sep 2024. URL: https://doi.org/10.1101/2024.09.17.613520, doi:10.1101/2024.09.17.613520. This article has 1 citations.
(conrady2024identificationandevolution pages 34-37): MC Conrady. Identification and evolution of protein-protein interactions in circadian gene regulation. Unknown journal, 2024.
(khan2025aninsilico pages 1-2): Auroni Semonti Khan, Mahmuda Akter, Mansura Akter Enni, and Sumaiya Farah Khan. An in silico approach for the identification of detrimental missense snps and their potential impacts on human cry2 protein. Journal of Bangladesh Academy of Sciences, Jun 2025. URL: https://doi.org/10.3329/jbas.v49i1.71914, doi:10.3329/jbas.v49i1.71914. This article has 11 citations.
(calloni2023thestructuraland pages 2-3): Giulia Calloni and R. Martin Vabulas. The structural and functional roles of the flavin cofactor fad in mammalian cryptochromes. Frontiers in Molecular Biosciences, Jan 2023. URL: https://doi.org/10.3389/fmolb.2022.1081661, doi:10.3389/fmolb.2022.1081661. This article has 7 citations.
(conrady2024identificationandevolution pages 136-139): MC Conrady. Identification and evolution of protein-protein interactions in circadian gene regulation. Unknown journal, 2024.
(toda2025targetingcryptochromesin pages 2-3): Takuro Toda and Tsuyoshi Hirota. Targeting cryptochromes in chronic diseases. Cell Biology International, 49(12):1579-1590, Sep 2025. URL: https://doi.org/10.1002/cbin.70087, doi:10.1002/cbin.70087. This article has 0 citations and is from a peer-reviewed journal.
(chan2024advancingclinicalresponse pages 1-4): Priscilla Chan, Yoshiko Nagai, Qiulian Wu, Anahit Hovsepyan, Seda Mkhitaryan, Jiarui Wang, Gevorg Karapetyan, Theodore Kamenecka, Laura A. Solt, Jamie Cope, Rex A. Moats, Tsuyoshi Hirota, Jeremy N. Rich, and Steve A. Kay. Advancing clinical response against glioblastoma: evaluating shp1705 cry2 activator efficacy in preclinical models and safety in phase i trials. bioRxiv, Sep 2024. URL: https://doi.org/10.1101/2024.09.17.613520, doi:10.1101/2024.09.17.613520. This article has 1 citations.
(chan2024advancingclinicalresponse media 0254a939): Priscilla Chan, Yoshiko Nagai, Qiulian Wu, Anahit Hovsepyan, Seda Mkhitaryan, Jiarui Wang, Gevorg Karapetyan, Theodore Kamenecka, Laura A. Solt, Jamie Cope, Rex A. Moats, Tsuyoshi Hirota, Jeremy N. Rich, and Steve A. Kay. Advancing clinical response against glioblastoma: evaluating shp1705 cry2 activator efficacy in preclinical models and safety in phase i trials. bioRxiv, Sep 2024. URL: https://doi.org/10.1101/2024.09.17.613520, doi:10.1101/2024.09.17.613520. This article has 1 citations.
(chan2024advancingclinicalresponse media bc968ea3): Priscilla Chan, Yoshiko Nagai, Qiulian Wu, Anahit Hovsepyan, Seda Mkhitaryan, Jiarui Wang, Gevorg Karapetyan, Theodore Kamenecka, Laura A. Solt, Jamie Cope, Rex A. Moats, Tsuyoshi Hirota, Jeremy N. Rich, and Steve A. Kay. Advancing clinical response against glioblastoma: evaluating shp1705 cry2 activator efficacy in preclinical models and safety in phase i trials. bioRxiv, Sep 2024. URL: https://doi.org/10.1101/2024.09.17.613520, doi:10.1101/2024.09.17.613520. This article has 1 citations.
(toda2025targetingcryptochromesin pages 12-12): Takuro Toda and Tsuyoshi Hirota. Targeting cryptochromes in chronic diseases. Cell Biology International, 49(12):1579-1590, Sep 2025. URL: https://doi.org/10.1002/cbin.70087, doi:10.1002/cbin.70087. This article has 0 citations and is from a peer-reviewed journal.
(chan2025advancingclinicalresponse pages 1-2): Priscilla Chan, Yoshiko Nagai, Qiulian Wu, Anahit Hovsepyan, Seda Mkhitaryan, Jiarui Wang, Gevorg Karapetyan, Theodore Kamenecka, Laura A. Solt, Jamie Cope, Rex A. Moats, Tsuyoshi Hirota, Jeremy N. Rich, and Steve A. Kay. Advancing clinical response against glioblastoma: evaluating shp1705 cry2 activator efficacy in preclinical models and safety in phase i trials. Neuro-oncology, Apr 2025. URL: https://doi.org/10.1093/neuonc/noaf089, doi:10.1093/neuonc/noaf089. This article has 10 citations and is from a domain leading peer-reviewed journal.
(farmakis2024th301emergesas pages 1-2): Danae Farmakis, Dimitrios J. Stravopodis, and Anastasia Prombona. Th301 emerges as a novel anti-oncogenic agent for human pancreatic cancer cells: the dispensable roles of p53, cry2 and bmal1 in th301-induced cdkn1a/p21cip1/waf1 upregulation. International Journal of Molecular Sciences, 26:178, Dec 2024. URL: https://doi.org/10.3390/ijms26010178, doi:10.3390/ijms26010178. This article has 1 citations.

Citations

li2023transcriptionrepressionof pages 13-15
parlak2023functionalcharacterizationof pages 4-5
chan2024advancingclinicalresponse pages 8-11
toda2025targetingcryptochromesin pages 2-3
calloni2023thestructuraland pages 1-2
conrady2024identificationandevolution pages 34-37
calloni2023thestructuraland pages 2-3
toda2025targetingcryptochromesin pages 12-12
conrady2024identificationandevolution pages 136-139
chan2025advancingclinicalresponse pages 1-2
chan2024advancingclinicalresponse pages 1-4
khan2025aninsilico pages 1-2
https://doi.org/10.3389/fmolb.2022.1081661
https://doi.org/10.1080/10985549.2023.2253710
https://doi.org/10.1016/j.jbc.2023.105451
https://doi.org/10.1101/2024.09.17.613520
https://doi.org/10.1002/cbin.70087
https://doi.org/10.1080/10985549.2023.2253710,
https://doi.org/10.3389/fmolb.2022.1081661,
https://doi.org/10.1016/j.jbc.2023.105451,
https://doi.org/10.1101/2024.09.17.613520,
https://doi.org/10.3329/jbas.v49i1.71914,
https://doi.org/10.1002/cbin.70087,
https://doi.org/10.1093/neuonc/noaf089,
https://doi.org/10.3390/ijms26010178,

📄 View Raw YAML

---
id: Q49AN0
gene_symbol: CRY2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: Cryptochrome-2 (CRY2) is a flavoprotein member of the cryptochrome/photolyase
  family that functions as a light-independent transcriptional repressor in the mammalian
  circadian clock. CRY2 heterodimerizes with PER proteins (PER1, PER2, PER3) and translocates
  to the nucleus where the PER-CRY complex inhibits CLOCK:BMAL1-driven transcription,
  forming the negative limb of the transcription-translation feedback loop (TTFL).
  CRY2 retains a photolyase homology region with an FAD-binding pocket that serves
  as a regulatory hub for ubiquitin ligase recognition (FBXL3, FBXL21) and small-molecule
  stabilizers rather than for photoreception. CRY2 lacks DNA photolyase activity but
  can bind DNA weakly. CRY2 also inhibits protein phosphatase 5 (PP5) activity, interacts
  with nuclear receptors (glucocorticoid receptor, HNF4A) in a ligand-dependent manner,
  and contributes to glucose and glucocorticoid homeostasis. CRY2 stability is regulated
  by phosphorylation-dependent ubiquitination via SCF(FBXL3) and SCF(FBXL21) complexes,
  and by PER2-mediated protection from degradation.
alternative_products:
  - name: '1'
    id: Q49AN0-1
  - name: '2'
    id: Q49AN0-2
    sequence_note: VSP_038970
existing_annotations:
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CRY2 localizes to the nucleus where it functions as a transcriptional
        repressor. UniProt curated location confirms nuclear localization (PMID:9801304,
        PMID:22798407). IBA annotation is phylogenetically well-supported across cryptochromes.
      action: ACCEPT
      reason: Nuclear localization is well-established for CRY2 and is essential for
        its transcriptional repressor function in the TTFL.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Nucleus {ECO:0000269|PubMed:22798407, ECO:0000269|PubMed:9801304}
  - term:
      id: GO:0005737
      label: cytoplasm
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CRY2 localizes to the cytoplasm before nuclear translocation as part
        of the PER-CRY complex. UniProt curated location confirms cytoplasmic localization
        (PMID:9801304).
      action: ACCEPT
      reason: Cytoplasmic localization is well-established; CRY2 accumulates in the
        cytoplasm and translocates to the nucleus through interaction with PER2 or
        BMAL1.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Cytoplasm {ECO:0000269|PubMed:9801304}
  - term:
      id: GO:0045892
      label: negative regulation of DNA-templated transcription
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CRY2 is a core transcriptional repressor in the mammalian circadian
        clock. It suppresses CLOCK:BMAL1-driven transcription of Per, Cry, Dec1, Dec2,
        and other E-box-containing genes (PMID:12397359, PMID:14672706, PMID:15147242).
      action: ACCEPT
      reason: Transcriptional repression is the primary molecular function of CRY2.
        Multiple independent studies demonstrate CRY2 suppresses CLOCK:BMAL1-induced
        transcription.
      supported_by:
        - reference_id: PMID:12397359
          supporting_text: Cry proteins to inhibit Per transcription
        - reference_id: PMID:14672706
          supporting_text: PERs and CRYs suppressed the induced expression
  - term:
      id: GO:0003677
      label: DNA binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: Purified hCRY2 binds dsDNA weakly and ssDNA with higher affinity (PMID:12627958).
        However, CRY2 represses transcription primarily through protein-protein interactions
        with CLOCK:BMAL1 rather than direct DNA binding. DNA binding is a vestigial
        property from the photolyase ancestor.
      action: KEEP_AS_NON_CORE
      reason: DNA binding is experimentally demonstrated but is not the primary mechanism
        by which CRY2 functions in transcriptional repression. It is a retained ancestral
        property from the photolyase family.
      supported_by:
        - reference_id: PMID:12627958
          supporting_text: binds to double-stranded DNA weakly and to single-stranded
            DNA with higher affinity
  - term:
      id: GO:0032922
      label: circadian regulation of gene expression
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CRY2 is a core component of the circadian TTFL that regulates rhythmic
        gene expression through repression of CLOCK:BMAL1 transcriptional activity
        (PMID:10531061, PMID:20840750).
      action: ACCEPT
      reason: Circadian regulation of gene expression is the primary biological process
        in which CRY2 functions. This is well-supported by multiple lines of evidence.
      supported_by:
        - reference_id: PMID:20840750
          supporting_text: negatively regulate the transcription of Per and Cry core
            clock genes
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0043153
      label: entrainment of circadian clock by photoperiod
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: Mammalian CRY proteins function as light-independent transcriptional
        repressors, not as photoreceptors for entrainment. Unlike Drosophila and plant
        cryptochromes, mammalian CRYs do not serve as circadian photoreceptors (PMID:10531061).
        The IBA annotation may reflect ancestral function in non-mammalian family
        members.
      action: REMOVE
      reason: Griffin et al. 1999 (PMID:10531061) demonstrated a light-independent
        role of CRY1 and CRY2 in the mammalian circadian clock. Mammalian CRY2 is
        not involved in photic entrainment; this function is mediated by retinal photoreceptors
        signaling to the SCN.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0071949
      label: FAD binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: CRY2 binds FAD, confirmed by purification studies showing FAD and pterin
        cofactors (PMID:8909283). However, FAD binding is weak in mammalian CRYs and
        the FAD pocket primarily serves as a regulatory hub for FBXL3 recognition
        and small-molecule binding rather than for catalytic or photochemical function.
      action: ACCEPT
      reason: FAD binding is experimentally demonstrated and the FAD pocket is functionally
        important for CRY2 regulation, even though FAD occupancy is low.
      supported_by:
        - reference_id: PMID:8909283
          supporting_text: were found to contain FAD and a pterin cofactor
  - term:
      id: GO:0000166
      label: nucleotide binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: CRY2 binds FAD, which is a dinucleotide cofactor. The nucleotide binding
        annotation is a broader parent of the more informative FAD binding term.
      action: ACCEPT
      reason: This is a valid broader term that follows from the FAD binding annotation.
        As an IEA mapped from the UniProt nucleotide-binding keyword, it is appropriately
        general.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Binds 1 FAD per subunit
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: Duplicate IEA annotation for nucleus. Consistent with IBA and ISS annotations
        and UniProt curated localization.
      action: ACCEPT
      reason: Nuclear localization is well-established for CRY2.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Nucleus {ECO:0000269|PubMed:22798407, ECO:0000269|PubMed:9801304}
  - term:
      id: GO:0005737
      label: cytoplasm
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: Duplicate IEA annotation for cytoplasm. Consistent with IBA annotation
        and UniProt curated localization.
      action: ACCEPT
      reason: Cytoplasmic localization is well-established for CRY2.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Cytoplasm {ECO:0000269|PubMed:9801304}
  - term:
      id: GO:0009881
      label: photoreceptor activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: Mammalian CRY2 does not function as a photoreceptor. This IEA annotation
        derives from the UniProt keyword "Photoreceptor protein" which is a legacy
        designation based on the photolyase family membership. Griffin et al. 1999
        (PMID:10531061) established the light-independent function of mammalian CRYs.
      action: REMOVE
      reason: Mammalian CRY2 functions as a light-independent transcriptional repressor.
        There is no evidence that human CRY2 has photoreceptor activity. The UniProt
        keyword is misleading for the mammalian protein.
      supported_by:
        - reference_id: PMID:8909283
          supporting_text: may function as blue-light photoreceptors in humans
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0019902
      label: phosphatase binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000117
    review:
      summary: hCRY2 specifically interacts with protein serine/threonine phosphatase
        5 (PP5) via yeast two-hybrid and inhibits its phosphatase activity (PMID:9383998).
        This is a well-characterized direct interaction.
      action: ACCEPT
      reason: Direct phosphatase binding is experimentally demonstrated for CRY2 with
        PP5 (PMID:9383998). The IEA annotation is consistent with the experimental
        evidence.
      supported_by:
        - reference_id: PMID:9383998
          supporting_text: protein serine/threonine phosphatase 5 (PP5) that contains
            the TPR motif specifically interacted with hCRY2
  - term:
      id: GO:0048511
      label: rhythmic process
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: CRY2 is a core circadian clock component. The rhythmic process annotation
        is a valid broader term encompassing its role in circadian rhythms.
      action: ACCEPT
      reason: CRY2 is a core component of the circadian clock and participates in
        generating approximately 24-hour rhythms in gene expression and physiology.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:16790549
    review:
      summary: PMID:16790549 demonstrates CRY2 interacts with PP5 (PPP5C) to modulate
        CKIepsilon phosphorylation. The specific interaction is better captured by
        the phosphatase binding (GO:0019902) and protein phosphatase inhibitor activity
        (GO:0004864) annotations already present.
      action: MARK_AS_OVER_ANNOTATED
      reason: Generic protein binding does not convey the specific functional interaction
        between CRY2 and PP5. More informative terms (phosphatase binding, protein
        phosphatase inhibitor activity) are already annotated.
      supported_by:
        - reference_id: PMID:16790549
          supporting_text: cryptochrome regulates clock protein phosphorylation by
            modulating the effect of PP5 on CKIepsilon
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:25416956
    review:
      summary: Large-scale proteome interactome mapping study. Generic protein binding
        from high-throughput screens is uninformative.
      action: MARK_AS_OVER_ANNOTATED
      reason: High-throughput interactome mapping does not provide functional insight
        beyond generic protein binding. More specific interaction terms should be
        used where validated.
      supported_by:
        - reference_id: PMID:25416956
          supporting_text: A proteome-scale map of the human interactome network
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32296183
    review:
      summary: Binary interactome reference map study. This is a high-throughput screen
        reporting many interaction partners. Generic protein binding from such studies
        is uninformative.
      action: MARK_AS_OVER_ANNOTATED
      reason: High-throughput binary interactome mapping provides no functional specificity
        for CRY2 interactions. Many of the reported partners (keratin associated proteins,
        etc.) may represent false positives or indirect interactions.
      supported_by:
        - reference_id: PMID:32296183
          supporting_text: A reference map of the human binary protein interactome
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32814053
    review:
      summary: Neurodegenerative disease interactome mapping study. Generic protein
        binding annotation from a high-throughput screen.
      action: MARK_AS_OVER_ANNOTATED
      reason: High-throughput interactome mapping does not provide functional specificity
        for CRY2 interactions.
      supported_by:
        - reference_id: PMID:32814053
          supporting_text: Interactome Mapping Provides a Network of Neurodegenerative
            Disease Proteins
  - term:
      id: GO:0000976
      label: transcription cis-regulatory region binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: This annotation is transferred from mouse CRY2 (Q9R194). CRY2 does
        not bind cis-regulatory regions specifically; its DNA binding is non-specific
        and weak (PMID:12627958). CRY2 represses transcription through protein-protein
        interactions with CLOCK:BMAL1 rather than through direct cis-regulatory element
        binding.
      action: MODIFY
      reason: CRY2 binds DNA non-specifically and weakly. The term "transcription
        cis-regulatory region binding" implies sequence-specific DNA binding which
        is not demonstrated for CRY2. A general DNA binding term is more appropriate.
      proposed_replacement_terms:
        - id: GO:0003677
          label: DNA binding
      supported_by:
        - reference_id: PMID:12627958
          supporting_text: binds to double-stranded DNA weakly and to single-stranded
            DNA with higher affinity
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: CRY2 is well-characterized as a cytoplasmic/nuclear protein. Mitochondrial
        localization is not supported by any direct evidence for CRY2. UniProt curated
        localization reports only cytoplasm and nucleus.
      action: REMOVE
      reason: No evidence supports mitochondrial localization of CRY2. UniProt curated
        location indicates only cytoplasm and nucleus.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Cytoplasm {ECO:0000269|PubMed:9801304}. Nucleus {ECO:0000269|PubMed:22798407,
            ECO:0000269|PubMed:9801304}
  - term:
      id: GO:0009416
      label: response to light stimulus
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Transferred from mouse CRY2. Mammalian CRY2 functions as a light-independent
        transcriptional repressor (PMID:10531061). While CRY2 retains a photolyase-like
        fold with FAD binding, it does not function as a light sensor in mammals.
      action: REMOVE
      reason: Mammalian CRY2 has a well-established light-independent role in the
        circadian clock. The response to light stimulus annotation is based on ancestral
        function from the photolyase family that is not retained in mammalian cryptochromes.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0014823
      label: response to activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Transferred from mouse CRY2. UniProt mentions CRY2 represses PPARD
        and limits exercise capacity (by similarity). This would be a downstream pleiotropic
        effect of circadian clock function rather than a core function of CRY2.
      action: KEEP_AS_NON_CORE
      reason: CRY2 may indirectly affect exercise-related physiology through transcriptional
        repression of PPARD in skeletal muscle. This is a secondary downstream effect
        of circadian regulation, not a core function.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Represses PPARD and its target genes in the skeletal muscle
            and limits exercise capacity (By similarity)
  - term:
      id: GO:0016922
      label: nuclear receptor binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: CRY2 interacts with the glucocorticoid receptor (NR3C1/GR) in a ligand-dependent
        manner (PMID:22170608) and with HNF4A (PMID:30530698). UniProt also reports
        interactions with AR, PPARA, PPARD, PPARG, NR1I2, NR1I3, and VDR.
      action: ACCEPT
      reason: Nuclear receptor binding is well-supported by multiple studies demonstrating
        direct ligand-dependent interactions between CRY2 and various nuclear receptors
        including GR, HNF4A, and others.
      supported_by:
        - reference_id: PMID:22170608
          supporting_text: cryptochromes 1 and 2, interact with the glucocorticoid
            receptor in a ligand-dependent fashion
        - reference_id: PMID:30530698
          supporting_text: HNF4A strongly transrepresses the transcriptional activity
            of the CLOCK:BMAL1 heterodimer
  - term:
      id: GO:0019900
      label: kinase binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: CRY2 modulates CKIepsilon (CSNK1E) activity through PP5 interaction
        (PMID:16790549). UniProt reports phosphorylation by CSNK1E requires interaction
        with PER1 or PER2, suggesting indirect rather than direct kinase binding.
        However, the circadian core oscillator complex includes CSNK1D/CSNK1E as components.
      action: KEEP_AS_NON_CORE
      reason: CRY2 interacts with kinases as part of the circadian repressor complex
        but direct kinase binding has not been definitively demonstrated independent
        of complex partners. The interaction may be mediated through PER proteins.
      supported_by:
        - reference_id: PMID:16790549
          supporting_text: cryptochrome regulates clock protein phosphorylation by
            modulating the effect of PP5 on CKIepsilon
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Phosphorylation by CSKNE requires interaction with PER1
            or PER2
  - term:
      id: GO:0019901
      label: protein kinase binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Similar to kinase binding above. CRY2 is part of a complex with CSNK1D/CSNK1E
        but direct protein kinase binding independent of PER proteins is not well-demonstrated.
      action: KEEP_AS_NON_CORE
      reason: CRY2 functions in a complex containing protein kinases (CSNK1D/CSNK1E)
        but direct binding may be mediated through PER protein intermediaries.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Component of the circadian core oscillator, which includes
            the CRY proteins, CLOCK or NPAS2, BMAL1 or BMAL2, CSNK1D and/or CSNK1E
  - term:
      id: GO:0019915
      label: lipid storage
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: UniProt notes CRY2 plays a key role in lipid metabolism modulation
        through transcriptional regulation of genes like ACSL4. CRY2 repression via
        PER2 promotes adipogenesis through circadian control of Wnt signaling. However,
        lipid storage per se is a downstream pleiotropic consequence of circadian
        regulation.
      action: KEEP_AS_NON_CORE
      reason: CRY2 contributes to lipid metabolism modulation through transcriptional
        regulation, which is a downstream effect of its circadian clock function rather
        than a direct role in lipid storage.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Plays a key role in glucose and lipid metabolism modulation,
            in part, through the transcriptional regulation of genes involved in these
            pathways, such as LEP or ACSL4
  - term:
      id: GO:0032868
      label: response to insulin
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Loss of cryptochromes causes glucose intolerance (PMID:22170608), which
        relates to insulin responsiveness. However, this is a downstream metabolic
        consequence of cryptochrome deficiency affecting glucocorticoid signaling
        and glucose homeostasis rather than a direct insulin response function.
      action: KEEP_AS_NON_CORE
      reason: CRY2 affects insulin sensitivity indirectly through its role in circadian
        regulation of glucocorticoid signaling and glucose metabolism. This is a pleiotropic
        downstream effect rather than a core function.
      supported_by:
        - reference_id: PMID:22170608
          supporting_text: genetic loss of cryptochrome 1 and/or 2 results in glucose
            intolerance and constitutively high levels of circulating corticosterone
  - term:
      id: GO:0032922
      label: circadian regulation of gene expression
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Duplicate IEA annotation for circadian regulation of gene expression.
        Consistent with IBA and other annotations.
      action: ACCEPT
      reason: Circadian regulation of gene expression is a core function of CRY2,
        well-supported across multiple evidence types.
      supported_by:
        - reference_id: PMID:20840750
          supporting_text: negatively regulate the transcription of Per and Cry core
            clock genes
  - term:
      id: GO:0042593
      label: glucose homeostasis
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Cryptochrome deficiency causes glucose intolerance and elevated corticosterone
        (PMID:22170608). CRY2 may mediate circadian regulation of cAMP signaling and
        gluconeogenesis. This is a downstream metabolic effect of circadian clock
        function.
      action: KEEP_AS_NON_CORE
      reason: Glucose homeostasis is affected by CRY2 through its circadian regulation
        of glucocorticoid signaling and gluconeogenesis, but this is a pleiotropic
        downstream effect rather than a core molecular function.
      supported_by:
        - reference_id: PMID:22170608
          supporting_text: genetic loss of cryptochrome 1 and/or 2 results in glucose
            intolerance and constitutively high levels of circulating corticosterone
  - term:
      id: GO:0042752
      label: regulation of circadian rhythm
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: CRY2 is a core circadian clock component. CRY1 and CRY2 encode inhibitors
        of the CLOCK:BMAL1 complex and their degradation by SCF(FBXL3) is essential
        for clock oscillation (PMID:17463251).
      action: ACCEPT
      reason: CRY2 is a core component of the circadian clock regulatory mechanism.
      supported_by:
        - reference_id: PMID:17463251
          supporting_text: Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex
            that establish a negative-feedback loop
  - term:
      id: GO:0042754
      label: negative regulation of circadian rhythm
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: CRY2 functions as part of the negative limb of the circadian TTFL,
        inhibiting CLOCK:BMAL1 activity (PMID:17463251, PMID:10531061).
      action: ACCEPT
      reason: CRY2 is a negative regulator in the circadian feedback loop, directly
        inhibiting the positive limb (CLOCK:BMAL1) of the clock.
      supported_by:
        - reference_id: PMID:17463251
          supporting_text: Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex
            that establish a negative-feedback loop
  - term:
      id: GO:0043153
      label: entrainment of circadian clock by photoperiod
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Duplicate IEA annotation. Mammalian CRY2 is not involved in photic
        entrainment of the circadian clock.
      action: REMOVE
      reason: Mammalian CRY2 functions as a light-independent transcriptional repressor
        (PMID:10531061). Photic entrainment in mammals is mediated by retinal photoreceptors,
        not by cryptochromes.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0045892
      label: negative regulation of DNA-templated transcription
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Duplicate IEA annotation. Consistent with IBA and IDA annotations for
        transcriptional repression.
      action: ACCEPT
      reason: Negative regulation of transcription is the primary molecular function
        of CRY2.
      supported_by:
        - reference_id: PMID:12397359
          supporting_text: Cry proteins to inhibit Per transcription
  - term:
      id: GO:0071949
      label: FAD binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Duplicate IEA annotation for FAD binding. Consistent with IBA and ISS
        annotations.
      action: ACCEPT
      reason: FAD binding is experimentally demonstrated for CRY2.
      supported_by:
        - reference_id: PMID:8909283
          supporting_text: were found to contain FAD and a pterin cofactor
  - term:
      id: GO:2000323
      label: negative regulation of nuclear receptor-mediated glucocorticoid signaling
        pathway
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Cryptochromes interact with the glucocorticoid receptor and broadly
        oppose GR activation while promoting GR-mediated repression (PMID:22170608).
        CRY deficiency vastly decreases gene repression and approximately doubles
        dexamethasone-induced genes.
      action: KEEP_AS_NON_CORE
      reason: While well-supported by PMID:22170608, regulation of glucocorticoid
        signaling is a downstream function of CRY2 nuclear receptor binding rather
        than a core clock function. It represents an important secondary output of
        the circadian clock.
      supported_by:
        - reference_id: PMID:22170608
          supporting_text: cryptochrome deficiency vastly decreases gene repression
            and approximately doubles the number of dexamethasone-induced genes, suggesting
            that cryptochromes broadly oppose glucocorticoid receptor activation and
            promote repression
  - term:
      id: GO:2000850
      label: negative regulation of glucocorticoid secretion
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: Loss of cryptochromes leads to constitutively high circulating corticosterone
        levels, suggesting reduced suppression of the hypothalamic-pituitary-adrenal
        axis (PMID:22170608).
      action: KEEP_AS_NON_CORE
      reason: While well-supported, regulation of glucocorticoid secretion is a downstream
        physiological consequence of CRY2 function in the circadian clock and its
        interaction with the glucocorticoid receptor. This is a secondary output rather
        than a core molecular function.
      supported_by:
        - reference_id: PMID:22170608
          supporting_text: genetic loss of cryptochrome 1 and/or 2 results in glucose
            intolerance and constitutively high levels of circulating corticosterone,
            suggesting reduced suppression of the hypothalamic-pituitary-adrenal axis
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: IDA
    original_reference_id: GO_REF:0000052
    review:
      summary: HPA immunofluorescence data supports cytosolic localization of CRY2.
        This is consistent with the broader cytoplasm annotation.
      action: ACCEPT
      reason: Cytosolic localization is consistent with the established cytoplasmic/nuclear
        distribution of CRY2. HPA provides IDA-level evidence from immunofluorescence.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Cytoplasm {ECO:0000269|PubMed:9801304}
  - term:
      id: GO:0016607
      label: nuclear speck
    evidence_type: IDA
    original_reference_id: GO_REF:0000052
    review:
      summary: HPA immunofluorescence data indicates nuclear speck localization. This
        is IDA evidence from the Human Protein Atlas. Nuclear specks are subnuclear
        structures enriched in RNA splicing factors. While the HPA staining pattern
        may show punctate nuclear signal, nuclear speck localization has not been
        independently confirmed for CRY2 in the literature.
      action: UNDECIDED
      reason: The HPA immunofluorescence data may show punctate nuclear staining consistent
        with nuclear specks, but this has not been validated by independent studies.
        Without access to the specific HPA images and co-localization data with speck
        markers, it is difficult to confirm this specific subnuclear localization.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Nucleus {ECO:0000269|PubMed:22798407, ECO:0000269|PubMed:9801304}
  - term:
      id: GO:0032922
      label: circadian regulation of gene expression
    evidence_type: NAS
    original_reference_id: PMID:20840750
    review:
      summary: PMID:20840750 identifies CRY2 residues essential for PER2 interaction
        in the negative arm of the circadian feedback loop (PMID:20840750).
      action: ACCEPT
      reason: The study provides direct evidence that CRY2-PER2 interaction is essential
        for the circadian transcriptional repression mechanism.
      supported_by:
        - reference_id: PMID:20840750
          supporting_text: negatively regulate the transcription of Per and Cry core
            clock genes
  - term:
      id: GO:0042754
      label: negative regulation of circadian rhythm
    evidence_type: NAS
    original_reference_id: PMID:20840750
    review:
      summary: CRY2 represses CLOCK:BMAL1 as part of the negative limb of the circadian
        clock. PMID:20840750 characterizes the CRY2-PER2 interaction interface essential
        for this repression.
      action: ACCEPT
      reason: CRY2 is a well-established negative regulator in the circadian feedback
        loop.
      supported_by:
        - reference_id: PMID:17463251
          supporting_text: Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex
            that establish a negative-feedback loop
  - term:
      id: GO:0004864
      label: protein phosphatase inhibitor activity
    evidence_type: IDA
    original_reference_id: PMID:9383998
    review:
      summary: hCRY2 inhibits the phosphatase activity of PP5. Zhao and Sancar 1997
        demonstrated that hCRY2, but not the highly homologous (6-4) photolyase, specifically
        inhibits PP5 phosphatase activity (PMID:9383998).
      action: ACCEPT
      reason: This is a well-characterized direct enzymatic inhibition demonstrated
        by direct assay. CRY2 specifically inhibits PP5, and this interaction is relevant
        to circadian clock regulation through modulation of CKIepsilon phosphorylation.
      supported_by:
        - reference_id: PMID:9383998
          supporting_text: hCRY2, but not the highly homologous (6-4) photolyase,
            inhibits the phosphatase activity of PP5
  - term:
      id: GO:0009416
      label: response to light stimulus
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation transferred from mouse CRY2 (Q9R194). Mammalian CRY2
        functions as a light-independent transcriptional repressor (PMID:10531061).
      action: REMOVE
      reason: Mammalian CRY2 has a light-independent role in the circadian clock.
        Response to light stimulus is not a function of human CRY2.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0014823
      label: response to activity
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation transferred from mouse CRY2. UniProt notes CRY2 represses
        PPARD in skeletal muscle and limits exercise capacity (by similarity). This
        is a downstream pleiotropic effect.
      action: KEEP_AS_NON_CORE
      reason: CRY2 may indirectly affect exercise-related physiology through transcriptional
        repression of PPARD, but this is a secondary downstream effect of circadian
        regulation.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Represses PPARD and its target genes in the skeletal muscle
            and limits exercise capacity (By similarity)
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:30530698
    review:
      summary: PMID:30530698 demonstrates CRY2 interacts with HNF4A, a nuclear receptor.
        The specific interaction is better captured by the nuclear receptor binding
        annotation (GO:0016922).
      action: MODIFY
      reason: The interaction between CRY2 and HNF4A is a specific nuclear receptor
        binding interaction. Generic protein binding does not convey the functional
        specificity of this interaction.
      proposed_replacement_terms:
        - id: GO:0016922
          label: nuclear receptor binding
      supported_by:
        - reference_id: PMID:30530698
          supporting_text: HNF4A strongly transrepresses the transcriptional activity
            of the CLOCK:BMAL1 heterodimer
  - term:
      id: GO:0009416
      label: response to light stimulus
    evidence_type: IMP
    original_reference_id: PMID:15751956
    review:
      summary: PMID:15751956 (Partch et al. 2005) demonstrates a light-dependent conformational
        change in the C-terminal domain of Arabidopsis Cry1, not human CRY2. The paper
        also characterizes the CRY2 photolyase homology region structure but does
        not demonstrate a light response for human CRY2. This IMP annotation from
        CAFA appears to be a misannotation.
      action: REMOVE
      reason: The paper primarily characterizes Arabidopsis Cry1 light-dependent conformational
        changes. It does not demonstrate a light response function for human CRY2.
        The IMP evidence code is inappropriate for this reference.
      supported_by:
        - reference_id: PMID:15751956
          supporting_text: we demonstrate a light-dependent conformational change
            in the C-terminal domain of Arabidopsis Cry1
  - term:
      id: GO:0042752
      label: regulation of circadian rhythm
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. CRY2 is a core circadian clock component,
        well-established as a regulator of circadian rhythm.
      action: ACCEPT
      reason: CRY2 is a core component of the circadian clock mechanism.
      supported_by:
        - reference_id: PMID:17463251
          supporting_text: Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex
            that establish a negative-feedback loop
  - term:
      id: GO:0043153
      label: entrainment of circadian clock by photoperiod
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. Mammalian CRY2 is not involved in photic
        entrainment.
      action: REMOVE
      reason: Mammalian CRY2 functions as a light-independent transcriptional repressor
        (PMID:10531061). Photic entrainment is not a function of mammalian CRY.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0045892
      label: negative regulation of DNA-templated transcription
    evidence_type: IDA
    original_reference_id: PMID:12397359
    review:
      summary: Dec1 and Dec2 study (Honma et al. 2002) shows Cry proteins together
        with Per proteins inhibit Per transcription by closing the autoregulatory
        feedback loop.
      action: ACCEPT
      reason: Direct experimental evidence that Cry proteins inhibit Per transcription,
        a core function of CRY2.
      supported_by:
        - reference_id: PMID:12397359
          supporting_text: Protein products of Per act together with Cry proteins
            to inhibit Per transcription, thus closing the autoregulatory feedback
            loop
  - term:
      id: GO:0032922
      label: circadian regulation of gene expression
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. Consistent with the well-established
        role of CRY2 in circadian gene regulation.
      action: ACCEPT
      reason: Circadian regulation of gene expression is a core function of CRY2.
      supported_by:
        - reference_id: PMID:20840750
          supporting_text: negatively regulate the transcription of Per and Cry core
            clock genes
  - term:
      id: GO:0042593
      label: glucose homeostasis
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. Cryptochrome deficiency causes glucose
        intolerance (PMID:22170608). This is a downstream metabolic effect.
      action: KEEP_AS_NON_CORE
      reason: Glucose homeostasis is affected by CRY2 through its circadian regulation
        of glucocorticoid signaling, but this is a pleiotropic downstream effect.
      supported_by:
        - reference_id: PMID:22170608
          supporting_text: genetic loss of cryptochrome 1 and/or 2 results in glucose
            intolerance
  - term:
      id: GO:2000323
      label: negative regulation of nuclear receptor-mediated glucocorticoid signaling
        pathway
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. Cryptochromes broadly oppose GR activation
        (PMID:22170608). This is a well-supported secondary function.
      action: KEEP_AS_NON_CORE
      reason: Regulation of glucocorticoid signaling is a downstream output of CRY2
        nuclear receptor binding, not a core clock function.
      supported_by:
        - reference_id: PMID:22170608
          supporting_text: cryptochromes broadly oppose glucocorticoid receptor activation
            and promote repression
  - term:
      id: GO:0000976
      label: transcription cis-regulatory region binding
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. CRY2 binds DNA non-specifically rather
        than at specific cis-regulatory regions.
      action: MODIFY
      reason: CRY2 does not specifically bind cis-regulatory regions. Its DNA binding
        is non-specific and weak. A general DNA binding term is more appropriate.
      proposed_replacement_terms:
        - id: GO:0003677
          label: DNA binding
      supported_by:
        - reference_id: PMID:12627958
          supporting_text: binds to double-stranded DNA weakly and to single-stranded
            DNA with higher affinity
  - term:
      id: GO:0042754
      label: negative regulation of circadian rhythm
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. CRY2 functions as a negative regulator
        in the circadian feedback loop.
      action: ACCEPT
      reason: CRY2 inhibits CLOCK:BMAL1 in the negative arm of the circadian clock.
      supported_by:
        - reference_id: PMID:17463251
          supporting_text: Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex
            that establish a negative-feedback loop
  - term:
      id: GO:0045892
      label: negative regulation of DNA-templated transcription
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. Consistent with the core transcriptional
        repressor function of CRY2.
      action: ACCEPT
      reason: Negative regulation of transcription is the primary molecular function
        of CRY2.
      supported_by:
        - reference_id: PMID:20840750
          supporting_text: negatively regulate the transcription of Per and Cry core
            clock genes
  - term:
      id: GO:0071949
      label: FAD binding
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2. FAD binding is experimentally confirmed
        for human CRY2.
      action: ACCEPT
      reason: FAD binding is directly demonstrated for purified human CRY2.
      supported_by:
        - reference_id: PMID:8909283
          supporting_text: were found to contain FAD and a pterin cofactor
  - term:
      id: GO:0007623
      label: circadian rhythm
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: CRY2 is a core component of the mammalian circadian clock, essential
        for generating approximately 24-hour rhythms.
      action: ACCEPT
      reason: CRY2 is a well-established core circadian clock component. Mice lacking
        both CRY1 and CRY2 are completely arrhythmic.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Transcriptional repressor which forms a core component
            of the circadian clock
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:9383998
    review:
      summary: PMID:9383998 demonstrates CRY2 specifically interacts with PP5. More
        informative terms (phosphatase binding, protein phosphatase inhibitor activity)
        are already annotated for this interaction.
      action: MARK_AS_OVER_ANNOTATED
      reason: Generic protein binding does not convey the specific functional interaction.
        Phosphatase binding (GO:0019902) and protein phosphatase inhibitor activity
        (GO:0004864) from the same reference are more informative.
      supported_by:
        - reference_id: PMID:9383998
          supporting_text: protein serine/threonine phosphatase 5 (PP5) that contains
            the TPR motif specifically interacted with hCRY2
  - term:
      id: GO:0019902
      label: phosphatase binding
    evidence_type: IPI
    original_reference_id: PMID:9383998
    review:
      summary: Zhao and Sancar 1997 demonstrated by yeast two-hybrid that PP5 specifically
        interacts with hCRY2 (PMID:9383998). This is a well-characterized direct interaction.
      action: ACCEPT
      reason: Direct experimental evidence for CRY2-PP5 interaction by yeast two-hybrid
        assay.
      supported_by:
        - reference_id: PMID:9383998
          supporting_text: protein serine/threonine phosphatase 5 (PP5) that contains
            the TPR motif specifically interacted with hCRY2
  - term:
      id: GO:0005576
      label: extracellular region
    evidence_type: IDA
    original_reference_id: PMID:9753616
    review:
      summary: PMID:9753616 (Ishibashi et al. 1998) describes the cloning of stanniocalcin-2
        (STC2), an unrelated protein. This appears to be a misannotation where the
        wrong gene was associated with this reference. CRY2 is not an extracellular
        protein.
      action: REMOVE
      reason: The cited reference is about STC2 (stanniocalcin-2), not CRY2. This
        is a clear misannotation. CRY2 is an intracellular protein localized to cytoplasm
        and nucleus.
      supported_by:
        - reference_id: PMID:9753616
          supporting_text: Molecular cloning of a second human stanniocalcin homologue
            (STC2)
  - term:
      id: GO:2000118
      label: regulation of sodium-dependent phosphate transport
    evidence_type: IDA
    original_reference_id: PMID:9753616
    review:
      summary: PMID:9753616 describes STC2-mediated inhibition of sodium-phosphate
        cotransporter. This is unrelated to CRY2. This is a clear misannotation.
      action: REMOVE
      reason: The cited reference concerns STC2 (stanniocalcin-2) biology, not CRY2.
        CRY2 has no demonstrated role in phosphate transport regulation.
      supported_by:
        - reference_id: PMID:9753616
          supporting_text: STC2-transfected CHO cells inhibited the promoter activity
            of Na-phosphate cotransporter
  - term:
      id: GO:0000122
      label: negative regulation of transcription by RNA polymerase II
    evidence_type: IDA
    original_reference_id: PMID:12397359
    review:
      summary: Honma et al. 2002 demonstrated that Cry proteins act together with
        Per proteins to inhibit CLOCK:BMAL1-driven transcription from E-box elements
        in the Per1 promoter (PMID:12397359). This is RNA Pol II-dependent transcription.
      action: ACCEPT
      reason: CRY2 inhibits CLOCK:BMAL1-driven transcription from E-box elements,
        which are RNA polymerase II promoter elements.
      supported_by:
        - reference_id: PMID:12397359
          supporting_text: Protein products of Per act together with Cry proteins
            to inhibit Per transcription, thus closing the autoregulatory feedback
            loop
  - term:
      id: GO:0000122
      label: negative regulation of transcription by RNA polymerase II
    evidence_type: IDA
    original_reference_id: PMID:14672706
    review:
      summary: Kawamoto et al. 2004 showed PERs and CRYs suppressed CLOCK/BMAL-induced
        expression of Dec1 through E-box elements (PMID:14672706).
      action: ACCEPT
      reason: Direct experimental evidence that CRY proteins suppress CLOCK/BMAL-induced
        transcription from E-box-containing promoters.
      supported_by:
        - reference_id: PMID:14672706
          supporting_text: PERs and CRYs suppressed the induced expression
  - term:
      id: GO:0000122
      label: negative regulation of transcription by RNA polymerase II
    evidence_type: IDA
    original_reference_id: PMID:15147242
    review:
      summary: Hamaguchi et al. 2004 showed Cry suppressed Clock/Bmal-induced transcription
        from the Dec2 promoter (PMID:15147242).
      action: ACCEPT
      reason: Direct experimental evidence that Cry proteins suppress CLOCK/BMAL-induced
        transcription of Dec2.
      supported_by:
        - reference_id: PMID:15147242
          supporting_text: Like Dec, Cry and Per also suppressed Clock/Bmal-induced
            transcription from the Dec2 promoter
  - term:
      id: GO:0005634
      label: nucleus
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation from mouse CRY2 for nuclear localization. Consistent
        with direct evidence from human cells.
      action: ACCEPT
      reason: Nuclear localization is well-established for CRY2 by multiple lines
        of evidence.
      supported_by:
        - reference_id: UniProtKB:Q49AN0
          supporting_text: Nucleus {ECO:0000269|PubMed:22798407, ECO:0000269|PubMed:9801304}
  - term:
      id: GO:0009785
      label: blue light signaling pathway
    evidence_type: NAS
    original_reference_id: PMID:8909283
    review:
      summary: Hsu et al. 1996 initially hypothesized human CRY proteins may function
        as blue-light photoreceptors (PMID:8909283). However, subsequent work by Griffin
        et al. 1999 (PMID:10531061) established that mammalian CRYs function as light-independent
        transcriptional repressors. There is no evidence for blue light signaling
        by human CRY2.
      action: REMOVE
      reason: The original NAS annotation was based on a hypothesis that has been
        superseded by definitive evidence that mammalian CRY2 functions as a light-independent
        repressor. Human CRY2 does not participate in blue light signaling.
      supported_by:
        - reference_id: PMID:8909283
          supporting_text: may function as blue-light photoreceptors in humans
  - term:
      id: GO:0009882
      label: blue light photoreceptor activity
    evidence_type: NAS
    original_reference_id: PMID:8909283
    review:
      summary: Hsu et al. 1996 speculated CRY proteins may be blue-light photoreceptors
        (PMID:8909283), but Griffin et al. 1999 (PMID:10531061) demonstrated a light-independent
        role for mammalian CRYs. Human CRY2 has no demonstrated photoreceptor activity.
      action: REMOVE
      reason: The original NAS annotation was speculative. Mammalian CRY2 does not
        function as a blue light photoreceptor. The annotation should be removed rather
        than merely marked as over-annotated because the function is not supported
        by any evidence.
      supported_by:
        - reference_id: PMID:8909283
          supporting_text: may function as blue-light photoreceptors in humans
  - term:
      id: GO:0000719
      label: photoreactive repair
    evidence_type: IDA
    original_reference_id: PMID:12627958
    negated: true
    review:
      summary: Ozgur and Sancar 2003 confirmed that hCRY2 lacks photorepair activity
        (PMID:12627958). This is a correctly negated annotation documenting the absence
        of photolyase function.
      action: ACCEPT
      reason: The negated annotation is correct and well-supported. CRY2 lacks photorepair
        activity despite its structural similarity to photolyases.
      supported_by:
        - reference_id: PMID:12627958
          supporting_text: appear to lack photorepair activity
  - term:
      id: GO:0003677
      label: DNA binding
    evidence_type: IDA
    original_reference_id: PMID:12627958
    review:
      summary: Ozgur and Sancar 2003 demonstrated that purified hCRY2 binds dsDNA
        weakly and ssDNA with higher affinity (PMID:12627958). This is a residual
        property from the photolyase ancestor rather than a core functional activity.
      action: KEEP_AS_NON_CORE
      reason: DNA binding is experimentally demonstrated but is not the primary mechanism
        of CRY2 function. CRY2 represses transcription through protein-protein interactions
        with CLOCK:BMAL1, not through direct DNA binding.
      supported_by:
        - reference_id: PMID:12627958
          supporting_text: binds to double-stranded DNA weakly and to single-stranded
            DNA with higher affinity
  - term:
      id: GO:0003684
      label: damaged DNA binding
    evidence_type: IDA
    original_reference_id: PMID:12627958
    review:
      summary: CRY2 DNA binding is stimulated by the presence of a (6-4) photoproduct
        (PMID:12627958). This reflects the ancestral photolyase substrate recognition
        capability retained in the protein structure but without associated repair
        activity.
      action: KEEP_AS_NON_CORE
      reason: Damaged DNA binding is experimentally demonstrated but is a vestigial
        property from the photolyase ancestor. CRY2 lacks photolyase activity and
        damaged DNA binding is not its primary function.
      supported_by:
        - reference_id: PMID:12627958
          supporting_text: this binding is further stimulated by the presence of a
            (6-4) photoproduct
  - term:
      id: GO:0003697
      label: single-stranded DNA binding
    evidence_type: IDA
    original_reference_id: PMID:12627958
    review:
      summary: Ozgur and Sancar 2003 showed hCRY2 binds ssDNA with higher affinity
        than dsDNA (PMID:12627958). This is a vestigial property from the photolyase
        ancestor.
      action: KEEP_AS_NON_CORE
      reason: Single-stranded DNA binding is experimentally demonstrated but is not
        the primary mechanism of CRY2 function. It represents a retained ancestral
        property.
      supported_by:
        - reference_id: PMID:12627958
          supporting_text: single-stranded DNA with higher affinity
  - term:
      id: GO:0003904
      label: deoxyribodipyrimidine photo-lyase activity
    evidence_type: IDA
    original_reference_id: PMID:8909283
    negated: true
    review:
      summary: Hsu et al. 1996 demonstrated that purified hCRY2 lacks photolyase activity
        on cyclobutane pyrimidine dimers (PMID:8909283). Correctly negated annotation.
      action: ACCEPT
      reason: The negated annotation is correct. CRY2 lacks CPD photolyase activity
        despite its structural similarity to DNA photolyases.
      supported_by:
        - reference_id: PMID:8909283
          supporting_text: lacked photolyase activity on the cyclobutane pyrimidine
            dimer and the (6-4) photoproduct
  - term:
      id: GO:0003914
      label: DNA (6-4) photolyase activity
    evidence_type: IDA
    original_reference_id: PMID:8909283
    negated: true
    review:
      summary: Hsu et al. 1996 demonstrated that purified hCRY2 lacks (6-4) photolyase
        activity (PMID:8909283). Correctly negated annotation.
      action: ACCEPT
      reason: The negated annotation is correct. CRY2 lacks (6-4) photolyase activity
        despite its homology to the Drosophila (6-4) photolyase.
      supported_by:
        - reference_id: PMID:8909283
          supporting_text: lacked photolyase activity on the cyclobutane pyrimidine
            dimer and the (6-4) photoproduct
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:17463251
    review:
      summary: Busino et al. 2007 identified CRY2 interaction with FBXL3 as part of
        the SCF(FBXL3) ubiquitin ligase complex that targets CRY proteins for degradation
        (PMID:17463251). The specific ubiquitin ligase interaction is functionally
        important but annotated as generic protein binding.
      action: MARK_AS_OVER_ANNOTATED
      reason: The CRY2-FBXL3 interaction is a specific ubiquitin ligase substrate
        recognition event. Generic protein binding does not convey the functional
        significance of this interaction.
      supported_by:
        - reference_id: PMID:17463251
          supporting_text: both Cry1 and Cry2 proteins are ubiquitinated and degraded
            via the SCF(Fbxl3) ubiquitin ligase complex
core_functions:
  - molecular_function:
      id: GO:0004864
      label: protein phosphatase inhibitor activity
    directly_involved_in:
      - id: GO:0032922
        label: circadian regulation of gene expression
      - id: GO:0000122
        label: negative regulation of transcription by RNA polymerase II
      - id: GO:0042754
        label: negative regulation of circadian rhythm
    locations:
      - id: GO:0005634
        label: nucleus
    description: CRY2 functions as a transcriptional corepressor in the mammalian
      circadian clock. It partners with PER proteins (PER1/2/3) to form nuclear repressor
      complexes that inhibit CLOCK:BMAL1-driven transcription of E-box containing
      genes including Per, Cry, Dec1, Dec2, and other clock-controlled genes. CRY2
      also inhibits PP5 phosphatase activity, modulating CKIepsilon-dependent phosphorylation
      of clock proteins. CRY2 repression and stability are regulated through the FAD
      pocket, which mediates FBXL3-dependent ubiquitination and degradation.
    supported_by:
      - reference_id: PMID:12397359
        supporting_text: Protein products of Per act together with Cry proteins to
          inhibit Per transcription, thus closing the autoregulatory feedback loop
      - reference_id: PMID:17463251
        supporting_text: Cry1 and Cry2, encode inhibitors of the Clock-Bmal1 complex
          that establish a negative-feedback loop
      - reference_id: PMID:9383998
        supporting_text: hCRY2, but not the highly homologous (6-4) photolyase, inhibits
          the phosphatase activity of PP5
  - molecular_function:
      id: GO:0071949
      label: FAD binding
    description: CRY2 binds FAD as a cofactor in its photolyase homology region. Although
      FAD occupancy is low in mammalian CRYs, the FAD-binding pocket is functionally
      critical as a regulatory hub for ubiquitin ligase (FBXL3) recognition, PER2
      competitive binding, and small-molecule stabilizer binding.
    supported_by:
      - reference_id: PMID:8909283
        supporting_text: were found to contain FAD and a pterin cofactor
  - molecular_function:
      id: GO:0016922
      label: nuclear receptor binding
    directly_involved_in:
      - id: GO:2000323
        label: negative regulation of nuclear receptor-mediated glucocorticoid signaling
          pathway
    locations:
      - id: GO:0005634
        label: nucleus
    description: CRY2 interacts with nuclear receptors including the glucocorticoid
      receptor (NR3C1/GR), androgen receptor (AR), HNF4A, PPARA, PPARD, PPARG, NR1I2,
      NR1I3, and VDR in a ligand-dependent manner. Through these interactions, CRY2
      mediates circadian modulation of nuclear receptor target gene expression, including
      rhythmic repression of glucocorticoid-responsive genes.
    supported_by:
      - reference_id: PMID:22170608
        supporting_text: cryptochromes 1 and 2, interact with the glucocorticoid receptor
          in a ligand-dependent fashion and globally alter the transcriptional response
          to glucocorticoids
      - reference_id: PMID:30530698
        supporting_text: HNF4A strongly transrepresses the transcriptional activity
          of the CLOCK:BMAL1 heterodimer
references:
  - 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:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
    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:0000052
    title: Gene Ontology annotation based on curation of immunofluorescence data
    findings: []
  - id: GO_REF:0000107
    title: Automatic transfer of experimentally verified manual GO annotation data
      to orthologs using Ensembl Compara
    findings: []
  - id: GO_REF:0000117
    title: Electronic Gene Ontology annotations created by ARBA machine learning models
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: PMID:8909283
    title: Putative human blue-light photoreceptors hCRY1 and hCRY2 are flavoproteins.
    findings:
      - statement: hCRY1 and hCRY2 contain FAD and pterin cofactors but lack photolyase
          activity on cyclobutane pyrimidine dimers and (6-4) photoproducts.
        supporting_text: were found to contain FAD and a pterin cofactor. Like the
          plant blue-light photoreceptors, both hCRY1 and hCRY2 lacked photolyase
          activity on the cyclobutane pyrimidine dimer and the (6-4) photoproduct
  - id: PMID:9383998
    title: Human blue-light photoreceptor hCRY2 specifically interacts with protein
      serine/threonine phosphatase 5 and modulates its activity.
    findings:
      - statement: hCRY2 specifically interacts with PP5 and inhibits its phosphatase
          activity.
        supporting_text: protein serine/threonine phosphatase 5 (PP5) that contains
          the TPR motif specifically interacted with hCRY2
  - id: PMID:9753616
    title: Molecular cloning of a second human stanniocalcin homologue (STC2).
    findings:
      - statement: This paper is about STC2, not CRY2. Annotations citing this reference
          for CRY2 are misannotations.
  - id: PMID:10531061
    title: Light-independent role of CRY1 and CRY2 in the mammalian circadian clock.
    findings:
      - statement: CRY1 and CRY2 function as light-independent components of the mammalian
          circadian clock, inhibiting CLOCK:BMAL1-mediated transcription.
  - id: PMID:12397359
    title: Dec1 and Dec2 are regulators of the mammalian molecular clock.
    findings:
      - statement: Cry proteins act together with Per proteins to inhibit Per transcription
          and close the autoregulatory feedback loop.
        supporting_text: Protein products of Per act together with Cry proteins to
          inhibit Per transcription, thus closing the autoregulatory feedback loop
  - id: PMID:12627958
    title: Purification and properties of human blue-light photoreceptor cryptochrome
      2.
    findings:
      - statement: Purified hCRY2 binds dsDNA weakly and ssDNA with higher affinity,
          stimulated by (6-4) photoproducts. CRY2 lacks photorepair activity.
        supporting_text: binds to double-stranded DNA weakly and to single-stranded
          DNA with higher affinity, and this binding is further stimulated by the
          presence of a (6-4) photoproduct
  - id: PMID:14672706
    title: A novel autofeedback loop of Dec1 transcription involved in circadian rhythm
      regulation.
    findings:
      - statement: PERs and CRYs suppress CLOCK/BMAL-induced Dec1 expression through
          E-box elements.
        supporting_text: PERs and CRYs suppressed the induced expression
  - id: PMID:15147242
    title: Expression of the gene for Dec2, a basic helix-loop-helix transcription
      factor, is regulated by a molecular clock system.
    findings:
      - statement: Cry and Per proteins suppress Clock/Bmal-induced transcription
          from the Dec2 promoter.
  - id: PMID:15751956
    title: Role of structural plasticity in signal transduction by the cryptochrome
      blue-light photoreceptor.
    findings:
      - statement: Light-dependent conformational change demonstrated for Arabidopsis
          Cry1, not human CRY2. The paper characterizes CRY structure but does not
          demonstrate light response function for human CRY2.
        supporting_text: we demonstrate a light-dependent conformational change in
          the C-terminal domain of Arabidopsis Cry1
  - id: PMID:16790549
    title: Posttranslational regulation of the mammalian circadian clock by cryptochrome
      and protein phosphatase 5.
    findings:
      - statement: Cryptochrome regulates clock protein phosphorylation by modulating
          the effect of PP5 on CKIepsilon.
        supporting_text: cryptochrome regulates clock protein phosphorylation by modulating
          the effect of PP5 on CKIepsilon
  - id: PMID:17463251
    title: SCFFbxl3 controls the oscillation of the circadian clock by directing the
      degradation of cryptochrome proteins.
    findings:
      - statement: CRY1 and CRY2 are ubiquitinated and degraded by SCF(FBXL3), which
          is essential for clock oscillation.
        supporting_text: both Cry1 and Cry2 proteins are ubiquitinated and degraded
          via the SCF(Fbxl3) ubiquitin ligase complex
  - id: PMID:20840750
    title: Identification of two amino acids in the C-terminal domain of mouse CRY2
      essential for PER2 interaction.
    findings:
      - statement: CRY2 residues R501 and K503 are essential for PER2 interaction
          and circadian transcriptional repression.
        supporting_text: negatively regulate the transcription of Per and Cry core
          clock genes
  - id: PMID:22170608
    title: Cryptochromes mediate rhythmic repression of the glucocorticoid receptor.
    findings:
      - statement: CRY1 and CRY2 interact with the glucocorticoid receptor in a ligand-dependent
          manner, globally altering glucocorticoid transcriptional response. Cryptochrome
          deficiency causes glucose intolerance and constitutively high corticosterone.
        supporting_text: cryptochromes 1 and 2, interact with the glucocorticoid receptor
          in a ligand-dependent fashion and globally alter the transcriptional response
          to glucocorticoids
  - id: PMID:25416956
    title: A proteome-scale map of the human interactome network.
    findings: []
  - id: PMID:30530698
    title: Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific
      circadian networks.
    findings:
      - statement: HNF4A interacts with CRY2 and modulates tissue-specific circadian
          networks.
        supporting_text: HNF4A strongly transrepresses the transcriptional activity
          of the CLOCK:BMAL1 heterodimer
  - id: PMID:32296183
    title: A reference map of the human binary protein interactome.
    findings: []
  - id: PMID:32814053
    title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins
      and Uncovers Widespread Protein Aggregation in Affected Brains.
    findings: []

CRY2

Gene Description

Existing Annotations Review

Core Functions

CRY2 binds FAD as a cofactor in its photolyase homology region. Although FAD occupancy is low in mammalian CRYs, the FAD-binding pocket is functionally critical as a regulatory hub for ubiquitin ligase (FBXL3) recognition, PER2 competitive binding, and small-molecule stabilizer binding.

References

📚 Additional Documentation

Deep Research Falcon

Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Output

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Research Report: Human CRY2 (Cryptochrome-2; UniProt Q49AN0, gene CRY2/KIAA0658)

Executive summary

1) Key concepts and definitions (current understanding)

1.1 Cryptochrome-2 (CRY2) and the mammalian TTFL

1.2 Domain architecture and family context

1.3 FAD binding in mammalian cryptochromes: weak but functionally central

2) Molecular function, pathways, and cellular localization

2.1 Primary molecular function: transcriptional repression of CLOCK:BMAL1

2.2 Key protein interactions that implement CRY2 function

2.3 Post-translational regulation and proteostasis

2.4 Subcellular localization

3) Recent developments and latest research (emphasis 2023–2024)

3.1 2023: Clarifying the regulatory role of the FAD pocket

3.2 2023: CRY2–PER2 interface determinants and functional output (adipogenesis)

3.3 2023: Human variant p.Ser420Phe reveals a “new” degradation pathway

3.4 2024: Translational advance—CRY2-targeting compounds in glioblastoma and Phase I safety

4) Current applications and real-world implementations

4.1 Chemical biology tool compounds targeting CRY2 stability

4.2 Glioblastoma: from mechanism to early clinical testing

5) Expert opinions and analysis (authoritative sources)

5.1 FAD pocket as a druggable control node

5.2 Proteostasis complexity: multiple turnover routes

6) Relevant statistics and quantitative data (recent studies)

6.1 CRY2 stability (human cells) and PER2 protection

6.2 SHP1705 Phase I trial design and adverse events (2024)

Functional annotation snapshot (table)

Limitations of this report

Key references (with dates and URLs)

Citations

📄 View Raw YAML