Metabolic pathway to genes

Genes assigned in the pathway

Query pathway ID 04712
Pathway name Circadian rhythm - plant
Organism Arabidopsis_thaliana

Click Gene ID to show a list of co-expressed genes.

Gene ID Repr. ID Gene name Functional description O.I. H.G. Other DB
At1g01060839341LHY (LATE ELONGATED HYPOCOTYL)LHY encodes a myb-related putative transcription factor involved in circadian rhythm along with another myb transcription factor CCA1O.I.H.G.
At1g04400839529CRY2 (CRYPTOCHROME 2)Blue light receptor mediating blue-light regulated cotyledon expansion and flowering time. Positive regulator of the flowering-time gene CONSTANS. This gene possesses a light-induced CNT2 N-terminal homodimerisation domain.Involved in blue-light induced stomatal opening. Involved in triggering chromatin decondensation. An 80-residue motif (NC80) is sufficient to confer CRY2's physiological function. It is proposed that the PHR domain and the C-terminal tail of the unphosphorylated CRY2 form a "closed" conformation to suppress the NC80 motif in the absence of light. In response to blue light, the C-terminal tail of CRY2 is phosphorylated and electrostatically repelled from the surface of the PHR domain to form an "open" conformation, resulting in derepression of the NC80 motif and signal transduction to trigger photomorphogenic responses. Cry2 phosphorylation and degradation both occur in the nucleus.O.I.H.G.
At1g09530837479PIF3 (PHYTOCHROME INTERACTING FACTOR 3)Transcription factor interacting with photoreceptors phyA and phyB. Forms a ternary complex in vitro with G-box element of the promoters of LHY, CCA1. Acts as a negative regulator of phyB signalling. It degrades rapidly after irradiation of dark grown seedlings in a process controlled by phytochromes. Does not play a significant role in controlling light input and function of the circadian clockwork. Binds to G- and E-boxes, but not to other ACEs. Binds to anthocyanin biosynthetic genes in a light- and HY5-independent fashion. PIF3 function as a transcriptional activator can be functionally and mechanistically separated from its role in repression of PhyB mediated processes.O.I.H.G.
At1g09570837483PHYA (PHYTOCHROME A)Light-labile cytoplasmic red/far-red light photoreceptor involved in the regulation of photomorphogenesis. It exists in two inter-convertible forms: Pr and Pfr (active) and functions as a dimer.The N terminus carries a single tetrapyrrole chromophore, and the C terminus is involved in dimerization. It is the sole photoreceptor mediating the FR high irradiance response (HIR). Major regulator in red-light induction of phototropic enhancement. Involved in the regulation of de-etiolation. Involved in gravitropism and phototropism. Requires FHY1 for nuclear accumulation.O.I.H.G.
At1g22770838883GI (GIGANTEA)Together with CONSTANTS (CO) and FLOWERING LOCUS T (FT), GIGANTEA promotes flowering under long days in a circadian clock-controlled flowering pathway. GI acts earlier than CO and FT in the pathway by increasing CO and FT mRNA abundance. Located in the nucleus. Regulates several developmental processes, including photoperiod-mediated flowering, phytochrome B signaling, circadian clock, carbohydrate metabolism, and cold stress response. The gene's transcription is controlled by the circadian clock and it is post-transcriptionally regulated by light and dark. Forms a complex with FKF1 on the CO promoter to regulate CO expression.O.I.H.G.
At1g68050843133FKF1 (FLAVIN-BINDING, KELCH REPEAT, F BOX 1)Encodes FKF1, a flavin-binding kelch repeat F box protein, is clock-controlled, regulates transition to flowering. Forms a complex with GI on the CO promoter to regulate CO expression.O.I.H.G.
At2g18790816394PHYB (PHYTOCHROME B)Red/far-red photoreceptor involved in the regulation of de-etiolation. Exists in two inter-convertible forms: Pr and Pfr (active). Involved in the light-promotion of seed germination and in the shade avoidance response.O.I.H.G.
At2g18915816408LKP2 (LOV KELCH PROTEIN 2)encodes a member of F-box proteins that includes two other proteins in Arabidopsis (ZTL and FKF1). These proteins contain a unique structure containing a PAS domain at their N-terminus, an F-box motif, and 6 kelch repeats at their C-terminus. Overexpression results in arrhythmic phenotypes for a number of circadian clock outputs in both constant light and constant darkness, long hypocotyls under multiple fluences of both red and blue light, and a loss of photoperiodic control of flowering time. Although this the expression of this gene itself is not regulated by circadian clock, it physically interacts with Dof transcription factors that are transcriptionally regulated by circadian rhythm. LKP2 interacts with Di19, CO/COL family proteins.O.I.H.G.
At2g23070816837casein kinase II alpha chain, putativeF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast;MOPFBVAO.I.H.G.
At2g23080816838casein kinase II alpha chain, putativeF:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOPFBVAO.I.H.G.
At2g25930817134ELF3 (EARLY FLOWERING 3)Encodes a novel nuclear protein that is expressed rhythmically and interacts with phytochrome B to control plant development and flowering through a signal transduction pathway Elf3 controls rhythmic circadian outputs under constant light conditions.O.I.H.G.
At2g44680819076CKB4 (CASEIN KINASE II BETA SUBUNIT 4)Encodes casein kinase II beta chain, a CK2 regulatory subunit. Nuclear-localized CKB4 protein exists in vivo as different isoforms, resulting from phosphorylation on serine residues. The phosphorylated isoforms are the preferred substrate for ubiquitination and degradation by the proteasome pathway. Involved in regulation of circadian clock.O.I.H.G.
At2g46790819292APRR9 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9)Pseudo-response regulator PRR9. Involved in clock function. PRR7 and PRR9 are partially redundant essential components of a temperature-sensitive circadian system. CCA1 and LHY had a positive effect on PRR9. Interact with TOC1 in a yeast two-hybrid assay.O.I.H.G.
At2g46830819296CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)Encodes a transcriptional repressor that performs overlapping functions with LHY in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis. Binds to the evening element in the promoter of TOC1 and represses TOC1 transcription. CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.O.I.H.G.
At3g04910819651WNK1 (WITH NO LYSINE (K) 1)Serine/threonine protein kinase, whose transcription is regulated by circadian rhythm.O.I.H.G.
At3g50000824162CKA2 (CASEIN KINASE II, ALPHA CHAIN 2)casein kinase II catalytic subunit alphaO.I.H.G.
At3g60250825196CKB3Regulatory (beta) subunit of the protein kinase CK2. Involved in regulation of the circadian clock in ArabidopsisO.I.H.G.
At4g08920826470CRY1 (CRYPTOCHROME 1)Encodes CRY1, a flavin-type blue-light photoreceptor with ATP binding and autophosphorylation activity. The photoreceptor may be involved in electron transport. Mutant phenotype displays a blue light-dependent inhibition of hypocotyl elongation. Photoreceptor activity requires light-induced homodimerisation of the N-terminal CNT1 domains of CRY1. Involved in blue-light induced stomatal opening. The C-terminal domain of the protein undergoes a light dependent conformational change. Also involved in response to circadian rhythm. Mutants exhibit long hypocotyl under blue light and are out of phase in their response to circadian rhythm. CRY1 is present in the nucleus and cytoplasm. Different subcellular pools of CRY1 have different functions during photomorphogenesis of Arabidopsis seedlings.O.I.H.G.
At4g16250827319PHYD (PHYTOCHROME DEFECTIVE D)Encodes a phytochrome photoreceptor with a function similar to that of phyB that absorbs the red/far-red part of the light spectrum and is involved in light responses. It cannot compensate for phyB loss in Arabidopsis but can substitute for tobacco phyB in vivo.O.I.H.G.
At4g17640827484CKB2Encodes casein kinase II beta (regulatory) subunit.O.I.H.G.
At4g18130827538PHYE (PHYTOCHROME DEFECTIVE E)member of Histidine KinaseO.I.H.G.
At5g02810831793PRR7 (PSEUDO-RESPONSE REGULATOR 7)PRR7 and PRR9 are partially redundant essential components of a temperature-sensitive circadian system. CCA1 and LHY had a positive effect on PRR7 expression levels.O.I.H.G.
At5g13930831241TT4 (TRANSPARENT TESTA 4)Encodes chalcone synthase (CHS), a key enzyme involved in the biosynthesis of flavonoids. Required for the accumulation of purple anthocyanins in leaves and stems. Also involved in the regulation of auxin transport and the modulation of root gravitropism.O.I.H.G.
At5g15840831441CO (CONSTANS)Encodes a protein showing similarities to zinc finger transcription factors, involved in regulation of flowering under long days. Acts upstream of FT and SOC1.O.I.H.G.
At5g24470832518APRR5 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5)Encodes a pseudo-response regulator whose mutation affects various circadian-associated biological events such as flowering time in the long-day photoperiod conditions, red light sensitivity of seedlings during early photomorphogenesis, and the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light.O.I.H.G.
At5g57360835842ZTL (ZEITLUPE)Encodes clock-associated PAS protein ZTL; Also known as FKF1-like protein 2 or ADAGIO1(ADO1). A protein containing a PAS domain ZTL contributes to the plant fitness (carbon fixation, biomass) by influencing the circadian clock period. ZTL is the F-box component of an SCF complex implicated in the degradation of TOC1.O.I.H.G.
At5g60100836132APRR3 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 3)Encodes pseudo-response regulator 3 (APRR3/PRR3). PRR3 transcript levels vary in a circadian pattern with peak expression at dusk under long and short day conditions. PRR3 affects the period of the circadian clock and seedlings with reduced levels of PRR3 have shorter periods, based on transcriptional assays of clock-regulated genes. PRR3 is expressed in the vasculature of cotyledons and leaves where it may help stabilize the TOC1 protein by preventing interactions between TOC1 and the F-box protein ZTL.O.I.H.G.
At5g61380836259TOC1 (TIMING OF CAB EXPRESSION 1)Pseudo response regulator involved in the generation of circadian rhythms. TOC1 appears to shorten the period of circumnutation speed. TOC1 contributes to the plant fitness (carbon fixation, biomass) by influencing the circadian clock period. PRR3 may increase the stability of TOC1 by preventing interactions between TOC1 and the F-box protein ZTL. Expression of TOC1 is correlated with rhythmic changes in chromatin organization.O.I.H.G.
At3g16500820898PAP1 (PHYTOCHROME-ASSOCIATED PROTEIN 1)phytochrome-associated protein 1 (PAP1)O.I.H.G.

Comparison with co-expressed genes

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