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PIF3 phytochrome interacting factor 3 [ Arabidopsis thaliana (thale cress) ]

Gene ID: 837479, updated on 18-Sep-2024

Summary

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Official Symbol
PIF3
Official Full Name
phytochrome interacting factor 3
Primary source
TAIR:AT1G09530
Locus tag
AT1G09530
See related
Araport:AT1G09530
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Arabidopsis thaliana (ecotype: Columbia)
Lineage
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as
F14J9.19; F14J9_19; PAP3; PHOTOCURRENT 1; phytochrome interacting factor 3; PHYTOCHROME INTERACTING FACTOR 3; PHYTOCHROME-ASSOCIATED PROTEIN 3; POC1; purple acid phosphatase 3
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.
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Genomic context

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See PIF3 in Genome Data Viewer
Location:
chromosome: 1
Exon count:
8
Sequence:
Chromosome: 1; NC_003070.9 (3075768..3079654)

Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene NAD(P)-binding Rossmann-fold superfamily protein Neighboring gene uncharacterized protein Neighboring gene ncRNA Neighboring gene myb domain protein 61

Genomic regions, transcripts, and products

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Genomic Sequence:
NC_003070.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. PIF3 is a repressor of chloroplast development. Stephenson PG, et al. Proc Natl Acad Sci U S A, 2009 May 5. PMID 19380736, Free PMC Article
  2. Integration of Ethylene and Light Signaling Affects Hypocotyl Growth in Arabidopsis. Yu Y, et al. Front Plant Sci, 2017. PMID 28174592, Free PMC Article
  3. Functional characterization of phytochrome interacting factor 3 for the Arabidopsis thaliana circadian clockwork. Viczián A, et al. Plant Cell Physiol, 2005 Oct. PMID 16055924
  4. DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis. Li K, et al. Nat Commun, 2016 Jun 10. PMID 27282989, Free PMC Article
  5. PIF3 is a negative regulator of the CBF pathway and freezing tolerance in Arabidopsis. Jiang B, et al. Proc Natl Acad Sci U S A, 2017 Aug 8. PMID 28739888, Free PMC Article

See all (97) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Discovery of a second-site nia2 mutation in the background of multiple Arabidopsis PIF-related mutants containing the pif3-3 allele.
    Title: Discovery of a second-site nia2 mutation in the background of multiple Arabidopsis PIF-related mutants containing the pif3-3 allele.
  2. The PIF1/PIF3-MED25-HDA19 transcriptional repression complex regulates phytochrome signaling in Arabidopsis.
    Title: The PIF1/PIF3-MED25-HDA19 transcriptional repression complex regulates phytochrome signaling in Arabidopsis.
  3. PIF3 is phosphorylated by MAPK to modulate plant immunity.
    Title: PIF3 is phosphorylated by MAPK to modulate plant immunity.
  4. The Arabidopsis endosperm is a temperature-sensing tissue that implements seed thermoinhibition through phyB.
    Title: The Arabidopsis endosperm is a temperature-sensing tissue that implements seed thermoinhibition through phyB.
  5. Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B.
    Title: Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B.
  6. SUMOylation of PHYTOCHROME INTERACTING FACTOR 3 promotes photomorphogenesis in Arabidopsis thaliana.
    Title: SUMOylation of PHYTOCHROME INTERACTING FACTOR 3 promotes photomorphogenesis in Arabidopsis thaliana.
  7. Cold-Induced CBF-PIF3 Interaction Enhances Freezing Tolerance by Stabilizing the phyB Thermosensor in Arabidopsis.
    Title: Cold-Induced CBF-PIF3 Interaction Enhances Freezing Tolerance by Stabilizing the phyB Thermosensor in Arabidopsis.
  8. Phytochrome B Induces Intron Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR3.
    Title: Phytochrome B Induces Intron Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR3.
  9. phyB and AGB1 antagonistically regulate PIF3 stability by dynamically interacting with each other and PIF3
    Title: Phytochrome B and AGB1 Coordinately Regulate Photomorphogenesis by Antagonistically Modulating PIF3 Stability in Arabidopsis.
  10. MPK6 was activated by red light, and the cotyledon opening angle in red light was reduced in mpk6 seedlings. MKK10, a MAPKK whose function is currently unclear, appears to act as a kinase upstream of MPK6 in regulating cotyledon opening. Activation of MPK6 by MKK10 led to the phosphorylation of PIF3 and accelerated its turnover in transgenic seedlings.
    Title: Arabidopsis MKK10-MPK6 mediates red-light-regulated opening of seedling cotyledons through phosphorylation of PIF3.
Submit: New GeneRIF Correction See all GeneRIFs (44)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

NM_001331836.1
NM_001331837.1
NM_001331839.1
NM_100824.3
NM_179295.3

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
NOT involved_in circadian rhythm IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within de-etiolation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within gibberellic acid mediated signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of anthocyanin metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within red or far-red light signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of photosynthesis, light reaction IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of plant organ morphogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to abscisic acid IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in response to auxin IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in response to cold IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in response to ethylene IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in response to heat IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within response to red or far red light IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to salt IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in response to water-immersion restraint stress IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within signal transduction TAS
Traceable Author Statement
more info
 PubMed 
involved_in unidimensional cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISM
Inferred from Sequence Model
more info
  

General protein information

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Preferred Names
phytochrome interacting factor 3
NP_001318964.1
  • 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); Has 4326 Blast hits to 4310 proteins in 315 species: Archae - 0; Bacteria - 2; Metazoa - 732; Fungi - 183; Plants - 3377; Viruses - 7; Other Eukaryotes - 25 (source: NCBI BLink).
NP_001318965.1
  • 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); Has 4326 Blast hits to 4310 proteins in 315 species: Archae - 0; Bacteria - 2; Metazoa - 732; Fungi - 183; Plants - 3377; Viruses - 7; Other Eukaryotes - 25 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

  1. NC_003070.9 Reference assembly

    Range
    3075768..3079654
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001331838.1 → NP_001322700.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
    UniProtKB/TrEMBL
    A0A178W5U6, A0A5S9TG51, A0A654EA77
    Conserved Domains (1) summary
    cd11445
    Location:343 → 405
    bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

  2. NM_001331837.1 → NP_001318965.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
    UniProtKB/TrEMBL
    A0A178W5U6, A0A5S9TG51, A0A654EA77
    Conserved Domains (1) summary
    cd11445
    Location:343 → 405
    bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

  3. NM_001331836.1 → NP_001318964.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
    UniProtKB/TrEMBL
    A0A178W5U6, A0A5S9TG51, A0A654EA77
    Conserved Domains (1) summary
    cd11445
    Location:343 → 405
    bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

  4. NM_001331839.1 → NP_001322701.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
    UniProtKB/TrEMBL
    A0A178W5U6, A0A5S9TG51, A0A654EA77
    Conserved Domains (1) summary
    cd11445
    Location:343 → 405
    bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

  5. NM_179295.3 → NP_849626.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_849626.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
    UniProtKB/TrEMBL
    A0A178W5U6, A0A5S9TG51, A0A654EA77
    Conserved Domains (1) summary
    cd11445
    Location:343 → 405
    bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins

  6. NM_100824.3 → NP_172424.1  phytochrome interacting factor 3 [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_172424.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    A5Y7A2, A5Y7A3, A5Y7A4, A5Y7A5, A5Y7A6, A5Y7A7, A5Y7A8, A5Y7A9, A5Y7B0, A5Y7B1, A5Y7B2, A5Y7B3, A5Y7B4, A5Y7B5, A5Y7B6, O80536, Q9SBC5
    UniProtKB/TrEMBL
    A0A178W5U6, A0A5S9TG51, A0A654EA77
    Conserved Domains (1) summary
    cd11445
    Location:343 → 405
    bHLH_AtPIF_like; basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O80536.1

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