Gene omics information

Query gene ID At2g43010
Gene name PIF4 (phytochrome interacting factor 4)
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
1.00100.0At2g43010818903PIF4 (phytochrome interacting factor 4)Isolated as a semidominant mutation defective in red -light responses. Encodes a nuclear localized bHLH protein that interacts with active PhyB protein. Negatively regulates phyB mediated red light responses. Involved in shade avoidance response. Protein abundance is negatively regulated by PhyB.S.X.H.G.
0.5267.4At3g50750824239brassinosteroid signalling positive regulator-relatedF:transcription regulator activity;P:biological_process unknown;C:vacuole;OPFMBS.X.H.G.
0.4862.5At3g59060825075PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6)Encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B.S.X.H.G.
0.4761.2At1g03130838400PSAD-2 (photosystem I subunit D-2)Encodes a protein predicted by sequence similarity with spinach PsaD to be photosystem I reaction center subunit II (PsaD2)S.X.H.G.
0.4558.3At1g51400841564photosystem II 5 kD proteinF:molecular_function unknown;P:response to UV-B, response to wounding, response to ozone;C:chloroplast thylakoid membrane, chloroplast photosystem II, chloroplast thylakoid lumen;PS.X.H.G.
0.4558.3At3g08940820043LHCB4.2 (light harvesting complex PSII)Lhcb4.2 protein (Lhcb4.2, protein involved in the light harvesting complex of photosystem IIS.X.H.G.
0.4457.2At5g19940832116plastid-lipid associated protein PAP-related / fibrillin-relatedF:structural molecule activity;P:biological_process unknown;C:chloroplast, chloroplast envelope;PBOS.X.H.G.
0.4253.9At2g25080817046ATGPX1 (GLUTATHIONE PEROXIDASE 1)Encodes glutathione peroxidase.S.X.H.G.
0.4152.4At2g35260818093unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PS.X.H.G.
0.3948.4At2g29650817515PHT4Encodes an inorganic phosphate transporter (PHT4;1) that is localized to the thylakoid membrane.S.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
26.599.7GSM157378Truman_1-6_Pst-DC3000(avrRpm1)-4hpi_Rep2_ATH1GSE6831Systemic response to avirulent bacterial infection
19.899.6GSM38670DSNPGSE2268Arabidopsis polysome microarray
18.199.5GSM157376Truman_1-4_Pst-DC3000-4hpi_Rep2_ATH1GSE6831Systemic response to avirulent bacterial infection
17.999.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis root
16.599.5GSM157377Truman_1-5_Pst-DC3000(hrpA)-4hpi_Rep2_ATH1GSE6831Systemic response to avirulent bacterial infection
16.299.5GSM38668NSNPGSE2268Arabidopsis polysome microarray
15.799.5GSM157300JPritchard_A-2_CTR_Rep2_ATH1GSE6823The molecular basis of plant insect interactions
15.699.5E-MEXP-838-raw-cel-1160703964
15.699.5GSM157373Truman_1-1_Pst-DC3000-4hpi_Rep1_ATH1GSE6831Systemic response to avirulent bacterial infection
15.399.4GSM128667Underwood_1-20_Mock-Inoculum-10h_Rep2_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
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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
0.333e-58226At3g59060825075PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6)Encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B.C.G.S.X.
0.102e-25117At2g20180816538PIL5 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 5)Encodes a novel Myc-related bHLH transcription factor that has transcriptional activation activity in the dark. It is a key negative regulator of phytochrome-mediated seed germination and acts by inhibiting chlorophyll biosynthesis, light-mediated suppression of hypocotyl elongation and far-red light-mediated suppression of seed germination, and promoting negative gravitropism in hypocotyls. Light reduces this activity in a phy-dependent manner. The protein preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB), is physically associated with APRR1/TOC1 and is degraded in red (R) and far-red (FR) light through the ubiquitin (ub)-26S proteasome pathway to optimize photomorphogenic development in Arabidopsis. It also negatively regulates GA3 oxidase expression.C.G.S.X.
0.054e-859At4g288115008170transcription regulatorF:transcription regulator activity;P:regulation of transcription;C:nucleus;PMFOBVC.G.S.X.
0.063e-654At4g288155008171transcription regulatorF:transcription regulator activity;P:regulation of transcription;C:endomembrane system, nucleus;PMFOC.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
0.054e-344Glycine maxGmaAffx.6008.1.S1_atBU550119--9e-31At2g20180PIL5 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 5)C.G.S.X.
0.065e-342Hordeum vulgareHV_CEb0009B15r2_atHV_CEb0009B15r2--8e-11At1g09530PIF3 (PHYTOCHROME INTERACTING FACTOR 3)C.G.S.X.
0.086e-1273Oryza sativaOs12g0610200AK066763.1-Phytochrome-interacting factor 3(Phytochrome-associated protein 3) (Basichelix-loop-helix protein 8) (bHLH8) (AtbHLH008)5e-12At2g43010PIF4 (phytochrome interacting factor 4)C.G.S.X.
0.134e-1893Populus trichocarpaPtpAffx.1627.1.S1_a_atAJ767188hypothetical protein-3e-18At2g43010PIF4 (phytochrome interacting factor 4)C.G.S.X.
0.024e-240Triticum aestivumTaAffx.54650.1.S1_atCA678847--4e-3At5g66815unknown proteinC.G.S.X.
0.022e-136Vitis vinifera1611668_s_atCF212347hypothetical protein LOC100259663-7e-5At5g61310cytochrome c oxidase subunit Vc, putative / COX5C, putativeC.G.S.X.
0.022e-240Zea maysZmAffx.855.1.S1_atAI770678--1e+1At5g23035-C.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: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:0009704The greening response of plants grown in the dark (etiolated) as a result of chloroplast biogenesis and the accumulation of chlorophyll.
XGO:0010017The series of molecular signals initiated upon sensing by photoreceptor molecules of red light or far red light. Red light is electromagnetic radiation of wavelength of 580-700nm. Far red light is electromagnetic radiation of wavelength 700-800nm. 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.
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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
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