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Gene : PHYB A. thaliana

Gene ID  ? AT2G18790
Brief Description  phytochrome B  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? phytochrome B (PHYB); CONTAINS InterPro DOMAIN/s: Phytochrome, central region (InterPro:IPR013515), Signal transduction histidine kinase, core (InterPro:IPR005467), PAS fold (InterPro:IPR013767), PAS (InterPro:IPR000014), Phytochrome chromophore attachment domain (InterPro:IPR016132), ATPase-like, ATP-binding domain (InterPro:IPR003594), PAS fold-2 (InterPro:IPR013654), Phytochrome A/B/C/D/E (InterPro:IPR012129), Phytochrome (InterPro:IPR001294), Phytochrome chromophore binding site (InterPro:IPR013516), Signal transduction histidine kinase, subgroup 1, dimerisation/phosphoacceptor domain (InterPro:IPR003661), GAF (InterPro:IPR003018); BEST Arabidopsis thaliana protein match is: phytochrome D (TAIR:AT4G16250.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? 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. Promotes seedling etiolation in both the presence and absence of phytochrome A. Overexpression results in etiolation under far-red light. Accumulates in the nucleus after exposure to far red light. The phosphorylation state of the Ser-86 residue of the phytochrome B molecule alters dark reversion of the molecule.  Source: TAIR, Jun 30, 2015.
Name  ? phytochrome B
  • synonyms:
  • OUT OF PHASE 1,
  • HY3,
  • OOP1

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66 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
These results demonstrate roles for phytochromes in regulating both the elongation and gravitropic curvature of roots 15695459
The expression of 35S:NtPHYB:GFP and 35S:AtPHYB:GFP complemented the tobacco hgl2 and Arabidopsis phyB-9 mutations, whereas the 35S:AtPHYD:GFP only rescued the hgl2 mutant. 15753105
The nuclear-localization signal in the C-terminal PAS-related domain of phytochrome B is masked by interactions with the chromophore-attachment domains and unmasked by light-dependent conformational changes. 15823535
Mesophyll phytochrome B suppressed the expression of a key flowering regulator, FLOWERING LOCUS T, in the vascular bundles of cotyledons. 15965119
The extensive overlap in responses mediated by PHYA and PHYB is reported. 17419844
ARR4 directly modulates the activity state of phyB. 17545225
Photoconversion is not a prerequisite for phytochrome signaling. 17660358
Photobiological and genetic evidence indicated that the photoactivated phytochrome molecule acts to induce PIF5 phosphorylation, phyA and phyB redundantly dominate this process. 17827270
findings show that PIF4 and PIF5 act early in the phytochrome signaling pathways to promote the shade-avoidance response 18047474
Data show that the phyB degradation in the Arabidopsis thaliana overexpressing PIF5 depends on a functional phyB binding motif in PIF5 and involves the 26S proteasome pathway. 18065691
Data provide evidence that the mechanism by which PIFs operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels, in an additive or synergistic manner. 18252845
Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. 18287016
These data suggest that the second-phase decline in robustness of PIL1 derepression is an indirect consequence of the global developmental transition from the etiolated to the de-etiolated state. 18296722
Data show that phyB influence PIF1 degradation after prolonged illumination, and and PIF1 interacts with phyB through a conserved active phyB binding motif. 18539749
Data show that phytochrome-associated protein phosphatase type 2C interacts in the nucleus with phyA (phytochrome A) and phyB, both in vitro and in vivo. 18564962
The N-terminal of phyB is involved in signal transfer and the C-terminal is responsible for light perception. 18704165
phytochrome B Is the Dominant Photoreceptor Required for Light Quantity-Mediated Changes in Stomatal Development. 19185498
PhyB promotes stomata differentiation in open places, allowing plants to take advantage of the higher irradiances at the expense of a reduction of water-use efficiency, which is compensated by a reduced leaf area. 19363093
Phytochrome B and HDA6 control light-induced chromatin compaction. 19730687
Data indicate that in the phyB pathway leading to seed germination, DAG1 negatively regulates GA biosynthesis and suggest that DAG1 acts downstream of PIL5. 19874540
Results demonstrate that phyB and CRY might regulate stomatal opening, at least in part, by regulating MYB60 expression. 19965572
conclude that the branching integrators BRC1 and BRC2 are necessary for responses to phytochrome, but they contribute differentially to these responses, likely acting through divergent pathways 20154098
The integrative model suggested in this study captures the main features of phyB-mediated photomorphogenesis in Arabidopsis. 20502669
Both the 651- and 450-amino acid N-terminal fragments of PHYB mediate entrainment of the circadian clock. The 410-amino acid N-terminal fragment lacks any physiological functions of PHYB. 20530216
The inhibition by PhyB is not exclusive to either of the phot1 or phot2 signalling pathways. 20693413
Studies indicate that phytochromes inhibit hypocotyl negative gravitropism by inhibiting four phytochrome-interacting factors (PIF1, PIF3, PIF4, PIF5), as shown by hypocotyl agravitropism of dark-grown pif1 pif3 pif4 pif5 quadruple mutants. 21220341
Data show that phytochrome B regulates gynoecium formation in association with the transcription factor SPATULA. 21364315
phyB mutations reduce the shade avoidance syndrome responses to crowding in low, but not in high, levels of canopy cover. 21457375
This study shows that Arabidopsis (Arabidopsis thaliana) branching is modified by both varying photosynthetic photon flux density and phyB status and that significant interactions occur between these variables. 21726239
Functional interactions between the clock proteins LHY and CCA1 and the photoreceptor PhyB control organ elongation and flowering time. 21822060

Genomics

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12 Flanking Regions

Flank size: from most upstream transcription start site, or most downstream transcription stop site

Region Name Flank Size Direction Length Gene Included? Chromosome Location
AT2G18790 0.5kb upstream 0.5kb upstream 5206   true Chr2: 8139256-8144461
AT2G18790 0.5kb upstream 0.5kb upstream 500   false Chr2: 8139256-8139755
AT2G18790 0.5kb downstream 0.5kb downstream 5206   true Chr2: 8139756-8144961
AT2G18790 0.5kb downstream 0.5kb downstream 500   false Chr2: 8144462-8144961
AT2G18790 1.0kb upstream 1.0kb upstream 5706   true Chr2: 8138756-8144461
AT2G18790 1.0kb upstream 1.0kb upstream 1000   false Chr2: 8138756-8139755
AT2G18790 1.0kb downstream 1.0kb downstream 5706   true Chr2: 8139756-8145461
AT2G18790 1.0kb downstream 1.0kb downstream 1000   false Chr2: 8144462-8145461
AT2G18790 3.0kb upstream 3.0kb upstream 7706   true Chr2: 8136756-8144461
AT2G18790 3.0kb upstream 3.0kb upstream 3000   false Chr2: 8136756-8139755
AT2G18790 3.0kb downstream 3.0kb downstream 7706   true Chr2: 8139756-8147461
AT2G18790 3.0kb downstream 3.0kb downstream 3000   false Chr2: 8144462-8147461

Proteins

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1 Pathways

Data Source: KEGG

Identifier Name
04712 Circadian rhythm - plant

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12 Data Sets

Name Description Version
BAR Annotations Lookup Mapping(s) between AGI locus and Affy Probeset identifier 10/08/2013
Genome Annotation Araport11 protein-coding, non-coding and transposable element genes Araport11 (06/2016)
RNA-seq expression Measure of gene expression levels (Transcripts per Million, TPM) quantified by Salmon Araport11 (06/2016)
PubMed to gene mapping Curated associations between publications and NCBI Gene records 8/12/2016
GO Annotation from InterPro    
PO Annotation from TAIR Literature-based annotations of genes to Plant Ontology (PO) terms 06/30/2015
Swiss-Prot data set High-quality, manually annotated, non-redundant protein sequence database 2016_07
Panther data set PANTHER paralogs from Arabidopsis 11.0
KEGG pathways data set Wiring diagrams of molecular interactions, reactions, and relations 79.0
GeneRIF Concise phrase describing gene function and publication associated with NCBI Gene records 8/12/2016
IntAct interactions data set Curated binary and complex protein-protein interactions for Arabidopsis thaliana 8/02/2016
BioGRID interaction data set Curated set of genetic and physical interactions for Arabidopsis thaliana 3.4.139