Gene omics information

Query gene ID At1g09570
Gene name PHYA (PHYTOCHROME A)
Organism Arabidopsis thaliana


Co-expressed genes



As this page just shows up to 10 genes to the query, if you wish to have the complete list of co-expressed genes, click Gene/Probe ID.

VF%ileGene/Probe IDRepr.IDGene NameFunctional DescriptionS.X.H.G.Other DB
0.3235.7At1g09570837483PHYA (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.S.X.H.G.
0.2522.6At3g23880821971F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:nucleus;POS.X.H.G.
0.2217.5At3g62860825461esterase/lipase/thioesterase family proteinF:catalytic activity;P:unknown;C:plasma membrane;BOPMFVAS.X.H.G.
0.2014.4At1g12780837834UGE1 (UDP-D-glucose/UDP-D-galactose 4-epimerase 1)Encodes a UDP-glucose epimerase that catalyzes the interconversion of the sugar nucleotides UDP-glucose UDP-galactose via a UDP-4-keto-hexose intermediate. Responsive to stress.S.X.H.G.
0.2014.4At2g36080818181DNA-binding protein, putativeEncodes a plant-specific B3 DNA-binding domain transcription factor. Has transcription repressor activity.S.X.H.G.
0.135.8At4g25260828629invertase/pectin methylesterase inhibitor family proteinF:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:shade avoidance;C:endomembrane system;PS.X.H.G.
0.051.1At5g54080835494HGO (HOMOGENTISATE 1,2-DIOXYGENASE)homogentisate 1,2-dioxygenaseS.X.H.G.
0.020.4At3g60530825224zinc finger (GATA type) family proteinF:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;PFOMS.X.H.G.
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Specifically expressed experiments



As this page just shows up to 10 assays to the query, if you wish to have the complete list of assays that the query gene/probe was specifically expressed, click here.
Std2 GX%ileGSM IDAssay NameGSE IDExperiment Title
94.299.9GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seeds
49.999.8GSM282694arf2_mock_rep1GSE11216Brassinazole treatment of arf2 and wild-type dark-grown seedlings
46.799.8GSM282703arf2_brz_2GSE11216Brassinazole treatment of arf2 and wild-type dark-grown seedlings
45.699.8GSM133118RIKEN-YAMAUCHI1BGSE5687AtGenExpress: Different temperature treatment of seeds
44.599.8GSM282693arf2_brz_1GSE11216Brassinazole treatment of arf2 and wild-type dark-grown seedlings
41.599.8GSM282695arf2_mock_rep2GSE11216Brassinazole treatment of arf2 and wild-type dark-grown seedlings
39.499.8E-NASC-78-raw-cel-1463195187
38.999.8GSM282696arf2_mock_rep3GSE11216Brassinazole treatment of arf2 and wild-type dark-grown seedlings
38.199.8GSM282702Col_mock_rep3GSE11216Brassinazole treatment of arf2 and wild-type dark-grown seedlings
36.099.7E-NASC-78-raw-cel-1463195235
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Homologous genes



Paralogous genes



Click Gene ID to show a list of homologous genes.

HFEvBSGene IDRepr. IDGene NameFunctional descriptionC.G.S.X.Other DB
0.053e-552At4g18130827538PHYE (PHYTOCHROME DEFECTIVE E)member of Histidine KinaseC.G.S.X.
0.031e-450At4g16250827319PHYD (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.C.G.S.X.
0.024e-448At5g35840833570PHYC (phytochrome defective c)Encodes the apoprotein of phytochrome;one of a family of photoreceptors that modulate plant growth and development.C.G.S.X.
0.042e-346At2g18790816394PHYB (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.C.G.S.X.
0.013e-242At3g47910823946ubiquitin thiolesterase/ zinc ion bindingF:ubiquitin thiolesterase activity, zinc ion binding;P:ubiquitin-dependent protein catabolic process;C:intracellular;MOFPBAVC.G.S.X.
0.013e-242At3g47890823944ubiquitin thiolesterase/ zinc ion bindingF:ubiquitin thiolesterase activity, zinc ion binding;P:ubiquitin-dependent protein catabolic process;C:intracellular;MOPFBAVC.G.S.X.
0.014e-138At4g25730828678FtsJ-like methyltransferase family proteinF:methyltransferase activity;P:rRNA processing, rRNA methylation;C:nucleus;OMBFPVAC.G.S.X.
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Orthologous genes



Click Gene ID to show a list of orthologous genes.

HFEvBSSpeciesGene IDRepr. IDGene NameFunctional descriptionEvAGI codeArabidopsis gene nameC.G.S.X.Other DB
0.301e-51206Glycine maxGma.17524.1.S1_atL34844.1phytochrome A-9e-52At1g09570PHYA (PHYTOCHROME A)C.G.S.X.
0.023e-344Hordeum vulgareContig19621_atContig19621--1e-3At1g09570PHYA (PHYTOCHROME A)C.G.S.X.
0.147e-20101Oryza sativaOs03g0719800BM420310--5e-2At5g20180ribosomal protein L36 family proteinC.G.S.X.
0.532e-149531Populus trichocarpaPtp.145.1.S1_atAJ001318.1phytochrome-1e-149At1g09570PHYA (PHYTOCHROME A)C.G.S.X.
0.017e+034Triticum aestivumTaAffx.85556.1.S1_atCA621770--2e+0At5g51700PBS2 (PPHB SUSCEPTIBLE 2)C.G.S.X.
0.012e+034Vitis vinifera1610644_atCB345212--3e+0At1g26710unknown proteinC.G.S.X.
0.017e-136Zea maysZm.6156.1.S1_atCF005925protein SEY1-9e-3At1g72960root hair defective 3 GTP-binding (RHD3) family proteinC.G.S.X.
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Biological processes



Click GO ID to show a list of genes that are associated with the GO ID.

ECCGO IDProcess Name
XGO:0046685A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
XGO:0010161The series of molecular signals initiated upon sensing of red light by a photoreceptor molecule. Red light is electromagnetic radiation of wavelength of 580-700nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.
XGO:0009630The orientation of plant parts under the stimulation of gravity.
XGO:0009638The movement of an organism, or part of an organism, in response to a light stimulus, usually toward or away from it.
XGO:0010201A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the detection of a continuous far red light stimulus by the high-irradiance response system. Far red light is electromagnetic radiation of wavelength 700-800nm. The activity of the high-irradiance response system is characterized by stronger effects of continuous than pulsed light at equal total fluence.
XGO:0010203A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a very low fluence red light stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm. Very low fluence red light is defined in this case as short pulses of red light followed by darkness, providing light levels of less than 0.001 mmol/m2/sec.
CGO:0006355Any process that modulates the frequency, rate or extent of DNA-dependent transcription.
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Metabolic pathways



Click KaPPA-View ID to show a list of genes that are assigned to the KaPPA-View ID.

KaPPA-View IDLink to Kappa-ViewPathway Name



Click KEGG PATHWAY ID to show a list of genes that are assigned to the KEGG PATHWAY ID.

KEGG PATHWAY IDLink to KEGG PATHWAYPathway Name
04712Link to KEGG PATHWAYCircadian rhythm - plant
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