Gene Details:

• Gene ID: AT4G16250
• Gene Symbol: PHYD
• Gene Name: phytochrome D
• Description: phytochrome D;(source:Araport11)
• TAIR Accession: locus:2005535
• Genome: Araport11_genome_release
• Species: Arabidopsis thaliana

Transcripts:

• AT4G16250.1

Plant Ontology Annotations:

• PO:0009005  — root — raíz (Spanish, exact), radices (exact, plural), radix (exact), 根 (Japanese, exact), aerial root (narrow), climbing root (narrow)

Gene Ontology:

• GO:0006355  — involved in — regulation of DNA-templated transcription
• GO:0042802  — enables — identical protein binding
• GO:0009883  — enables — red or far-red light photoreceptor activity
• GO:0009585  — involved in — red, far-red light phototransduction
• GO:0009584  — involved in — detection of visible light
• GO:0005515  — enables — protein binding
• GO:0010017  — acts upstream of or within — red or far-red light signaling pathway
• GO:0005886  — located in — plasma membrane
• GO:0005634  — is active in — nucleus
• GO:0005634  — located in — nucleus
• GO:0042803  — enables — protein homodimerization activity
• GO:0000155  — enables — phosphorelay sensor kinase activity

Function-related keywords:

• root

Literature:

• Phytochromes, cryptochromes, phototropin: photoreceptor interactions in plants.   DOI:  10.1562/0031-8655(2000)071<0001:pcppii>2.0.co;2 ;  PMID:  10649883
• Functional interaction of cryptochrome 1 and phytochrome D.   DOI:  10.1046/j.1365-313x.1999.t01-1-00599.x ;  PMID:  10571889
• Characterization of the gene encoding the apoprotein of phytochrome B2 in tomato, and identification of molecular lesions in two mutant alleles.   DOI:  10.1007/s004380051037 ;  PMID:  10485280
• Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation growth and flowering time.   DOI:  10.1104/pp.119.3.909 ;  PMID:  10069829
• Phytochrome E influences internode elongation and flowering time in Arabidopsis.   DOI:  10.1105/tpc.10.9.1479 ;  PMID:  9724694
• Coordination of phytochrome levels in phyB mutants of Arabidopsis as revealed by apoprotein-specific monoclonal antibodies.   DOI:  10.1093/genetics/149.2.523 ;  PMID:  9611171
• Differential patterns of expression of the Arabidopsis PHYB, PHYD, and PHYE phytochrome genes.   DOI:  10.1104/pp.115.3.959 ;  PMID:  9390432
• A deletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome D in red/far-red light sensing.   DOI:  10.1105/tpc.9.8.1317 ;  PMID:  9286109
• Computer analysis of phytochrome sequences and reevaluation of the phytochrome secondary structure by Fourier transform infrared spectroscopy.   DOI:  10.1016/s0167-4838(97)00050-2 ;  PMID:  9252112
• The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms.   DOI:  10.1093/oxfordjournals.molbev.a025677 ;  PMID:  8865668
• Impaired splicing of phytochrome B pre-mRNA in a novel phyB mutant of Arabidopsis.   DOI:  10.1007/BF00020886 ;  PMID:  7539307
• Tomato contains two differentially expressed genes encoding B-type phytochromes, neither of which can be considered an ortholog of Arabidopsis phytochrome B.   DOI:  10.1007/BF00239958 ;  PMID:  7580861
• The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE.   DOI:  10.1007/BF00043870 ;  PMID:  8049367
• Negative interference of endogenous phytochrome B with phytochrome A function in Arabidopsis.   DOI:  10.1104/pp.125.2.1036 ;  PMID:  11161059
• Molecular and phenotypic specificity of an antisense PHYB gene in Arabidopsis.   DOI:  10.1023/a:1010686805488 ;  PMID:  11437253
• shl, a New set of Arabidopsis mutants with exaggerated developmental responses to available red, far-red, and blue light.   DOI:  10.1104/pp.127.1.295 ;  PMID:  11553757
• Phytochromes A and B mediate red-light-induced positive phototropism in roots.   DOI:  10.1104/pp.013847 ;  PMID:  12644690
• Signaling activities among the Arabidopsis phyB/D/E-type phytochromes: a major role for the central region of the apoprotein.   DOI:  10.1046/j.1365-313x.2003.01722.x ;  PMID:  12713538
• Differential activities of the Arabidopsis phyB/D/E phytochromes in complementing phyB mutant phenotypes.   DOI:  10.1023/a:1023901718508 ;  PMID:  12825695
• Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways.   DOI:  10.1105/tpc.012971 ;  PMID:  12953104
• Constitutive photomorphogenesis 1 and multiple photoreceptors control degradation of phytochrome interacting factor 3, a transcription factor required for light signaling in Arabidopsis.   DOI:  10.1105/tpc.021568 ;  PMID:  15155879
• Heterodimerization of type II phytochromes in Arabidopsis.   DOI:  10.1073/pnas.0404286101 ;  PMID:  15273290
• The roles of phytochromes in elongation and gravitropism of roots.   DOI:  10.1093/pcp/pci038 ;  PMID:  15695459
• Analysis of the function of the photoreceptors phytochrome B and phytochrome D in Nicotiana plumbaginifolia and Arabidopsis thaliana.   DOI:  10.1093/pcp/pci073 ;  PMID:  15753105
• Changes in photoperiod or temperature alter the functional relationships between phytochromes and reveal roles for phyD and phyE.   DOI:  10.1104/pp.102.018135 ;  PMID:  12692350
• phyA dominates in transduction of red-light signals to rapidly responding genes at the initiation of Arabidopsis seedling de-etiolation.   DOI:  10.1111/j.1365-313X.2006.02914.x ;  PMID:  17076805
• Phytochrome A is an irradiance-dependent red light sensor.   DOI:  10.1111/j.1365-313X.2007.03036.x ;  PMID:  17346261
• Diversification of phytochrome contributions to germination as a function of seed-maturation environment.   DOI:  10.1111/j.1469-8137.2007.02281.x ;  PMID:  18028293
• Light-induced phosphorylation and degradation of the negative regulator PHYTOCHROME-INTERACTING FACTOR1 from Arabidopsis depend upon its direct physical interactions with photoactivated phytochromes.   DOI:  10.1105/tpc.108.060020 ;  PMID:  18539749
• Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor.   DOI:  10.1105/tpc.108.065227 ;  PMID:  19286967
• Blue light induces degradation of the negative regulator phytochrome interacting factor 1 to promote photomorphogenic development of Arabidopsis seedlings.   DOI:  10.1534/genetics.108.099887 ;  PMID:  19255368
• Phytochromes differentially regulate seed germination responses to light quality and temperature cues during seed maturation.   DOI:  10.1111/j.1365-3040.2009.01998.x ;  PMID:  19453482
• Phylogenetic relationships of B-related phytochromes in the Brassicaceae: Redundancy and the persistence of phytochrome D.   DOI:  10.1016/j.ympev.2008.07.026 ;  PMID:  18768161
• Arabidopsis PHYTOCHROME INTERACTING FACTOR proteins promote phytochrome B polyubiquitination by COP1 E3 ligase in the nucleus.   DOI:  10.1105/tpc.109.072520 ;  PMID:  20605855
• PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis.   DOI:  10.1111/j.1365-313X.2011.04815.x ;  PMID:  21985558
• The light-response BTB1 and BTB2 proteins assemble nuclear ubiquitin ligases that modify phytochrome B and D signaling in Arabidopsis.   DOI:  10.1104/pp.112.199109 ;  PMID:  22732244
• Comparative functional analysis of full-length and N-terminal fragments of phytochrome C, D and E in red light-induced signaling.   DOI:  10.1111/nph.12364 ;  PMID:  23772959
• Functional diversity of phytochrome family in the control of light and gibberellin-mediated germination in Arabidopsis.   DOI:  10.1111/pce.12286 ;  PMID:  24471455
• In response to partial plant shading, the lack of phytochrome A does not directly induce leaf senescence but alters the fine-tuning of chlorophyll biosynthesis.   DOI:  10.1093/jxb/eru060 ;  PMID:  24604733
• Mutants of phospholipase A (pPLA-I) have a red light and auxin phenotype.   DOI:  10.1111/pce.12278 ;  PMID:  24433169
• FHY3 and FAR1 Act Downstream of Light Stable Phytochromes.   DOI:  10.3389/fpls.2016.00175 ;  PMID:  26941752
• PHYD prevents secondary dormancy establishment of seeds exposed to high temperature and is associated with lower PIL5 accumulation.   DOI:  10.1093/jxb/ery140 ;  PMID:  29648603
• Differential phosphorylation of the N-terminal extension regulates phytochrome B signaling.   DOI:  10.1111/nph.16243 ;  PMID:  31596952
• Photoreceptors' gene expression of Arabidopsis thaliana grown with biophilic LED-sourced lighting systems.   DOI:  10.1371/journal.pone.0269868 ;  PMID:  35687579
• Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome.   DOI:  10.3390/ijms232214134 ;  PMID:  36430613
• Functional Mapping of Genes Modulating Plant Shade Avoidance Using Leaf Traits.   DOI:  10.3390/plants12030608 ;  PMID:  36771692
• Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.   DOI:  10.1093/molbev/msj051 ;  PMID:  16280546

Sequence: