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Gene : PIF3 A. thaliana

Gene ID  ? AT1G09530
Brief Description  phytochrome interacting factor 3  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? phytochrome interacting factor 3 (PIF3); CONTAINS InterPro DOMAIN/s: Helix-loop-helix DNA-binding domain (InterPro:IPR001092), Helix-loop-helix DNA-binding (InterPro:IPR011598); BEST Arabidopsis thaliana protein match is: phytochrome interacting factor 3-like 1 (TAIR:AT2G46970.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? 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.  Source: TAIR, Jun 30, 2015.
Name  ? phytochrome interacting factor 3
  • synonyms:
  • PAP3,
  • POC1,

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24 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
PIF3 acts transiently, and its major function is to mediate phytochrome-induced signaling during the developmental switch from skotomorphogenesis to photomorphogenesis and/or dark to light transitions 15155879
PIF3 may function in early phytochrome signaling at the dark-to-light transition, not only during initial seedling deetiolation, but daily at dawn under diurnal light-dark cycles. 15505214
Data suggest that PIF3 may represent the primary intermolecular signaling transaction of the activated photoreceptor, tagging the target protein for proteosomal degradation. 16885032
Gibberellins signaling regulates protein stability of HY5, and the activity of PIF3. 18053005
Data provide evidence that the mechanism by which PIFs3operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels, in an additive or synergistic manner. 18252845
Data show that dephosphorylation of PIF3 is mediated by phytochrome-associated protein phosphatase type 2C. 18564962
Results suggest that many type I and type II phytochromes, such as E and C, appear to function through PIF3-mediated pathways. 19286967
PIF3 was circadian regulated in dark-grown seedlings. 19380736
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
PIF3 regulates genes misexpressed in the dark, named MIDA genes 22108407
The PIF3 protein abundance oscillates under diurnal conditions as a result of a progressive decline in PIF3 protein degradation mediated by photoactivated phyB, and consequent accumulation of the bHLH factor during the dark period. 22409654
The nuclear import of phyB can be facilitated by phytochrome-interacting factor 3 (PIF3). 22451940
These results showed an altered response to light in seedlings with an impaired PIF3/MIDA regulatory network. 22499182
directly activated by ETHYLENE-INSENSITIVE 3 and indispensible for ethylene-induced hypocotyl elongation in light 22818915
The ability of Glc to induce IAA biosynthesis was upregulated in the pif1 pif3 pif4 pif5 quadruple mutant line compared with the wild type. 23209113
Data indicate that HDA15 and PIF3 cotarget to the genes involved in chlorophyll biosynthesis and photosynthesis in the dark and repress gene expression. 23548744
Data indicate that the PIF1/PIF3-HY5/HYH transcriptional modules mediate crosstalk between light and ROS signaling and a mechanism by which plants adapt to the light environments. 23645630
Data show that photoreceptor phyB-induced transcription factor PIF3 phosphorylation is required for the known negative feedback modulation of phyB levels in prolonged light, potentially through codegradation of phyB and PIF3. 23903316
PIF3 lies downstream of PHYB and RGL3, and plays an important role in the inhibitory effect of NO on root growth of Arabidopsis seedlings in light. 24157606
PIF1, PIF3, PIF4, and PIF5 act together to promote and optimize growth under photoperiodic conditions. 24420574
PIF3 phosphorylation induces, and is necessary for, recruitment of LRB [Light-Response Bric-a-Brack/Tramtrack/Broad (BTB)] E3 ubiquitin ligases to the PIF3-phyB complex. 24904166
The expression level of PIF3, 4, and 5 was significantly up-regulated during both age-triggered and dark-induced leaf senescence. 25296857
Under negative day-night temperature difference, lower auxin biosynthesis activity limits the signaling in this pathway, resulting in low activity of PIF3 and short hypocotyls. 25516603
In vivo results support a regulatory mechanism for PIFs in which HMR is a transcriptional coactivator binding directly to PIFs and the 9aaTAD of HMR couples the degradation of PIF1 and PIF3 with the transactivation of PIF target genes. 25944101


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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
AT1G09530 0.5kb upstream 0.5kb upstream 4387   true Chr1: 3075268-3079654
AT1G09530 0.5kb upstream 0.5kb upstream 500   false Chr1: 3075268-3075767
AT1G09530 0.5kb downstream 0.5kb downstream 4387   true Chr1: 3075768-3080154
AT1G09530 0.5kb downstream 0.5kb downstream 500   false Chr1: 3079655-3080154
AT1G09530 1.0kb upstream 1.0kb upstream 4887   true Chr1: 3074768-3079654
AT1G09530 1.0kb upstream 1.0kb upstream 1000   false Chr1: 3074768-3075767
AT1G09530 1.0kb downstream 1.0kb downstream 4887   true Chr1: 3075768-3080654
AT1G09530 1.0kb downstream 1.0kb downstream 1000   false Chr1: 3079655-3080654
AT1G09530 3.0kb upstream 3.0kb upstream 6887   true Chr1: 3072768-3079654
AT1G09530 3.0kb upstream 3.0kb upstream 3000   false Chr1: 3072768-3075767
AT1G09530 3.0kb downstream 3.0kb downstream 6887   true Chr1: 3075768-3082654
AT1G09530 3.0kb downstream 3.0kb downstream 3000   false Chr1: 3079655-3082654


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2 Pathways

Data Source: KEGG

Identifier Name
04712 Circadian rhythm - plant
04075 Plant hormone signal transduction

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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 TIGR GO annotations assigned by TIGR Arabidopsis annotation effort 8/01/2016
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