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Gene : PIL5 A. thaliana

Gene ID  ? AT2G20180
Brief Description  phytochrome interacting factor 3-like 5  Source: Araport11 (06/2016).
Is Obsolete?  false
Computational Description  ? phytochrome interacting factor 3-like 5 (PIL5); 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: basic helix-loop-helix (bHLH) DNA-binding superfamily protein (TAIR:AT4G28800.1).  Source: TAIR, Jun 30, 2015.
Curator Summary  ? 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.  Source: TAIR, Jun 30, 2015.
Name  ? phytochrome interacting factor 3-like 5
  • synonyms:
  • PIF1,

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23 GeneRIFs (Gene References Into Functions)

Data Source: NCBI

Annotation PubMed Id
negatively regulates chlorophyll biosynthesis 15448264
PIF1 is degraded in red (R) and far-red (FR) light through the ubiquitin (ub)-26S proteasome pathway to optimize photomorphogenic development in Arabidopsis.[PIF1] 16359394
PIL5 binds directly to GAI and RGA promoters but not to Giberellic and Abscisic metabolic gene promoters in arabidopsis. 17449805
Data shows that PIL5 activates the expression of SOM by binding directly to its promoter, suggesting that PIL5 regulates ABA and GA metabolic genes partly through SOM. 18487351
Data suggest that removal of PIF1 by light-induced proteolytic degradation might be sufficient to promote photomorphogenesis. 18539749
These data strongly suggest that PIF1 directly and indirectly regulates key genes involved in chlorophyll biosynthesis to optimize the greening process in Arabidopsis. 18591656
PIL5 inhibits seed germination not just through GA and ABA, but also by coordinating hormone signals and modulating cell wall properties in imbibed seeds. 19244139
Data show that AtGA3ox1 is directly regulated by DAG1, and suggest that DAG1 is not a direct regulatory target of PIL5. 19874540
PIF1 and other PIFs have roles in transducing light signals to regulate PSY gene expression and carotenoid accumulation during daily cycles of light and dark in mature plants 20534526
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 suggest that CK2-mediated phosphorylation enhances the light-induced degradation of PIF1 to promote photomorphogenesis. 21330376
ABI3 and PIL5 collaboratively activate the expression of SOM mRNA by directly binding to and interacting with each other at the SOM promoter. 21467583
Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis. 22634759
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 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
HFR1 prevents PIF1 from binding to its target genes and antagonistically regulates PIF1-mediated gene expression. HFR1 and PIF1 are the major transcription regulators responsible for light-directed Transcriptome changes in seed germination. 24179122
PIF1, PIF3, PIF4, and PIF5 act together to promote and optimize growth under photoperiodic conditions. 24420574
VQ29 is a negative transcriptional regulator of light-mediated inhibition of hypocotyl elongation that likely promotes the transcriptional activity of PIF1 during early seedling development. 24569844
EFS is necessary for high-level expression of PIF1 mRNA in imbibed seeds. 24635727
DET1 maximizes PIF1's action by both removing PIF1's transcriptional repressor HFR1 and protecting PIF1 from proteasome-mediated degradation. 25775589
The results suggest that AtHB1 acts downstream of PIF1 to promote hypocotyl elongation, especially in response to short-day photoperiods. 25865500
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
Results indicate that LEUNIG_HOMOLOG (LUH) functions with PHYTOCHROME-INTERACTING FACTOR1 (PIF1) as a transcriptional coregulator to inhibit seed germination. 26276832


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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
AT2G20180 0.5kb upstream 0.5kb upstream 3486   true Chr2: 8704024-8707509
AT2G20180 0.5kb upstream 0.5kb upstream 500   false Chr2: 8707010-8707509
AT2G20180 0.5kb downstream 0.5kb downstream 3486   true Chr2: 8703524-8707009
AT2G20180 0.5kb downstream 0.5kb downstream 500   false Chr2: 8703524-8704023
AT2G20180 1.0kb upstream 1.0kb upstream 3986   true Chr2: 8704024-8708009
AT2G20180 1.0kb upstream 1.0kb upstream 1000   false Chr2: 8707010-8708009
AT2G20180 1.0kb downstream 1.0kb downstream 3986   true Chr2: 8703024-8707009
AT2G20180 1.0kb downstream 1.0kb downstream 1000   false Chr2: 8703024-8704023
AT2G20180 3.0kb upstream 3.0kb upstream 5986   true Chr2: 8704024-8710009
AT2G20180 3.0kb upstream 3.0kb upstream 3000   false Chr2: 8707010-8710009
AT2G20180 3.0kb downstream 3.0kb downstream 5986   true Chr2: 8701024-8707009
AT2G20180 3.0kb downstream 3.0kb downstream 3000   false Chr2: 8701024-8704023


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11 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 TAIR GO annotations assigned by TAIR 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
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