PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G62090.1
Common NamePIF6, PIL2
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family bHLH
Protein Properties Length: 346aa    MW: 38449.4 Da    PI: 6.8647
Description phytochrome interacting factor 3-like 2
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G62090.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH24.26e-08177221655
                  HHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH   6 nerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  n  Er+ R++iN+++ +L+ llP++      K +  ++L +A++Y+ +Lq
  AT3G62090.1 177 NSPERNQRNDINKKMRTLQNLLPNS-----HKDDNESMLDEAINYMTNLQ 221
                  778*********************8.....699**************998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000838.11E-8167225No hitNo description
Gene3DG3DSA:4.10.280.101.3E-11168234IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474592.49E-13170240IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088812.779171220IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.2E-6177226IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000108.4E-6177221IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010017Biological Processred or far-red light signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000293anatomyguard cell
PO:0009005anatomyroot
PO:0009047anatomystem
PO:0020100anatomyhypocotyl
Sequence ? help Back to Top
Protein Sequence    Length: 346 aa     Download sequence    Send to blast
MELVFENGQI LAKGQRSNVS LHNQRTKSIM DLYEAEYNED FMKSIIHGGG GAITNLGDTQ  60
VVPQSHVAAA HETNMLESNK HVDDSETLKA SSSKRMMVDY HNRKKIKFIP PDEQSVVADR  120
SFKLGFDTSS VGFTEDSEGS MYLSSSLDDE SDDARPQVPA RTRKALVKRK RNAEAYNSPE  180
RNQRNDINKK MRTLQNLLPN SHKDDNESML DEAINYMTNL QLQVQMMTMG NRFVTPSMMM  240
PLGPNYSQMG LAMGVGMQMG EQQFLPAHVL GAGLPGINDS ADMLRFLNHP GLMPMQNSAP  300
FIPTENCSPQ SVPPSCAAFP NQIPNPNSLS NLDGATLHKK SRKTNR
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible251245_at0.0
Expression AtlasAT3G62090-
AtGenExpressAT3G62090-
ATTED-IIAT3G62090-
Functional Description ? help Back to Top
Source Description
TAIRencodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family.
Function -- GeneRIF ? help Back to Top
  1. PIF6 is expressed strongly during seed development, and two splice variants exist.
    [PMID: 19911288]
  2. PTB misexpression changes Alternative splicing (AS) of PHYTOCHROME INTERACTING FACTOR6, coinciding with altered rates of abscisic acid-dependent seed germination.
    [PMID: 23192226]
  3. The ability of Glc to induce IAA biosynthesis was upregulated in the pif1 pif3 pif4 pif5 quadruple mutant line compared with the wild type.
    [PMID: 23209113]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G62090.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G62090
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0331080.0BT033108.1 Arabidopsis thaliana unknown protein (At3g62090) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001078329.10.0transcription factor PIF6
RefseqNP_191768.20.0transcription factor PIF6
SwissprotQ8L5W70.0PIF6_ARATH; Transcription factor PIF6
TrEMBLC0SVF80.0C0SVF8_ARATH; Putative uncharacterized protein At3g62090 (Fragment)
STRINGAT3G62090.20.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
    [PMID:12679534]
  2. Yamashino T, et al.
    A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(6): p. 619-29
    [PMID:12826627]
  3. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
    [PMID:12897250]
  4. Bailey PC, et al.
    Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana.
    Plant Cell, 2003. 15(11): p. 2497-502
    [PMID:14600211]
  5. Rizhsky L, et al.
    When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress.
    Plant Physiol., 2004. 134(4): p. 1683-96
    [PMID:15047901]
  6. Khanna R, et al.
    A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors.
    Plant Cell, 2004. 16(11): p. 3033-44
    [PMID:15486100]
  7. Cao D,Cheng H,Wu W,Soo HM,Peng J
    Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis.
    Plant Physiol., 2006. 142(2): p. 509-25
    [PMID:16920880]
  8. Franklin KA,Whitelam GC
    Light-quality regulation of freezing tolerance in Arabidopsis thaliana.
    Nat. Genet., 2007. 39(11): p. 1410-3
    [PMID:17965713]
  9. Davi
    Transcriptional factor interaction: a central step in DELLA function.
    Curr. Opin. Genet. Dev., 2008. 18(4): p. 295-303
    [PMID:18590820]
  10. Penfield S,Josse EM,Halliday KJ
    A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy.
    Plant Mol. Biol., 2010. 73(1-2): p. 89-95
    [PMID:19911288]
  11. Gallego-Bartolomé J, et al.
    Transcriptional diversification and functional conservation between DELLA proteins in Arabidopsis.
    Mol. Biol. Evol., 2010. 27(6): p. 1247-56
    [PMID:20093430]
  12. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
    [PMID:20736450]
  13. Richter R,Behringer C,M
    The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS.
    Genes Dev., 2010. 24(18): p. 2093-104
    [PMID:20844019]
  14. Toettcher JE,Gong D,Lim WA,Weiner OD
    Light control of plasma membrane recruitment using the Phy-PIF system.
    Meth. Enzymol., 2011. 497: p. 409-23
    [PMID:21601096]
  15. Bu Q,Castillon A,Chen F,Zhu L,Huq E
    Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis.
    Plant Mol. Biol., 2011. 77(4-5): p. 501-11
    [PMID:21928113]
  16. R
    Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes.
    Plant Cell, 2012. 24(11): p. 4360-75
    [PMID:23192226]
  17. Sairanen I, et al.
    Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis.
    Plant Cell, 2012. 24(12): p. 4907-16
    [PMID:23209113]
  18. Dong J, et al.
    Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark.
    Plant Cell, 2014. 26(9): p. 3630-45
    [PMID:25248553]
  19. Qiu Y, et al.
    HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis.
    Plant Cell, 2015. 27(5): p. 1409-27
    [PMID:25944101]