PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G61270.1
Common NameBHLH72, EN109, MFB13.4, PIF7
Organism
Arabidopsis thaliana
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: 366aa    MW: 40826.3 Da    PI: 8.1097
Description phytochrome-interacting factor7
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G61270.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH49.76.6e-16171216555
                  HHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH   5 hnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  hne ErrRRdriN+++ +L++llP+a      K +K++iL  ++e++k+Lq
  AT5G61270.1 171 HNESERRRRDRINQRMRTLQKLLPTA-----SKADKVSILDDVIEHLKQLQ 216
                  *************************9.....7******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088817.06166215IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.105.8E-17169225IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474593.66E-18169236IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000834.51E-9171220No hitNo description
PfamPF000103.8E-13171216IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.9E-16172221IPR011598Myc-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:0009585Biological Processred, far-red light phototransduction
GO:0009704Biological Processde-etiolation
GO:0016607Cellular Componentnuclear speck
GO:0003690Molecular Functiondouble-stranded DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000293anatomyguard cell
Sequence ? help Back to Top
Protein Sequence    Length: 366 aa     Download sequence    Send to blast
MSNYGVKELT WENGQLTVHG LGDEVEPTTS NNPIWTQSLN GCETLESVVH QAALQQPSKF  60
QLQSPNGPNH NYESKDGSCS RKRGYPQEMD RWFAVQEESH RVGHSVTASA SGTNMSWASF  120
ESGRSLKTAR TGDRDYFRSG SETQDTEGDE QETRGEAGRS NGRRGRAAAI HNESERRRRD  180
RINQRMRTLQ KLLPTASKAD KVSILDDVIE HLKQLQAQVQ FMSLRANLPQ QMMIPQLPPP  240
QSVLSIQHQQ QQQQQQQQQQ QQQQQFQMSL LATMARMGMG GGGNGYGGLV PPPPPPPMMV  300
PPMGNRDCTN GSSATLSDPY SAFFAQTMNM DLYNKMAAAI YRQQSDQTTK VNIGMPSSSS  360
NHEKRD
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1174179ERRRRD
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.291140.0leaf
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1865326320.0
Expression AtlasAT5G61270-
AtGenExpressAT5G61270-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Barely detectable in dark-grown seedlings. Induced after 2 hours of light exposure.
UniprotTISSUE SPECIFICITY: Expressed in flowers. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
TAIRBasic helix-loop-helix (bHLH) phytochrome interacting factor. Interacts specifically with the far-red lightabsorbing Pfr form of phyB through a conserved domain called the active phyB binding motif. Upon light exposure, PIF7 rapidly migrates to intranuclear speckles, where it colocalizes with phyB. Role as negative regulator of phyB-mediated seedling deetiolation.
UniProtTranscription factor acting negatively in the phytochrome B signaling pathway under prolonged red light. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. May regulate the expression of a subset of genes by binding to the G-box motif. {ECO:0000269|PubMed:15486100, ECO:0000269|PubMed:18252845}.
Function -- GeneRIF ? help Back to Top
  1. Data provide evidence that the mechanism by which PIF7 operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels, in an additive or synergistic manner.
    [PMID: 18252845]
  2. PIF7 functions as a transcriptional repressor for DREB1C expression and its activity is regulated by PIF7-interacting factors TIMING OF CAB EXPRESSION1 and Phytochrome B.
    [PMID: 19837816]
  3. New auxin synthesized through a PIF7-regulated pathway is required for shade-induced growth, linking directly the perception of a light quality signal to a rapid growth response.
    [PMID: 22508725]
  4. PIF7 regulates the expression of shade-responsive genes.PIF7 recruits MRG1 and MRG2 that binds H3K4me3/H3K36me3 and brings histone-acetylases to induce histone acetylations to promote expression of shade responsive genes.
    [PMID: 29187567]
  5. Shade-induced nuclear localization of PIF7 is regulated by phosphorylation and 14-3-3 proteins in Arabidopsis.
    [PMID: 29926790]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00571DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G61270.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By red light. Stable upon light exposure.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT4G25470(R), AT4G25490(R)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G09530
IntActSearch Q570R7
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Plants are hypersensitive to red light, exhibiting shorter hypocotyls and larger cotyledons. {ECO:0000269|PubMed:18252845}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G61270
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2206400.0AK220640.1 Arabidopsis thaliana mRNA for bHLH transcription factor like protein, complete cds, clone: RAFL21-57-L18.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_200935.20.0phytochrome-interacting factor7
SwissprotQ570R70.0PIF7_ARATH; Transcription factor PIF7
TrEMBLC0SVV20.0C0SVV2_ARATH; Uncharacterized protein At5g61270 (Fragment)
STRINGAT5G61270.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM141231822
Representative plantOGRP25816128
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. 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]
  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. Castelli V, et al.
    Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation.
    Genome Res., 2004. 14(3): p. 406-13
    [PMID:14993207]
  6. Gong W, et al.
    Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes.
    Plant Physiol., 2004. 135(2): p. 773-82
    [PMID:15208423]
  7. 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]
  8. Osuna D, et al.
    Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings.
    Plant J., 2007. 49(3): p. 463-91
    [PMID:17217462]
  9. Leivar P, et al.
    The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels.
    Plant Cell, 2008. 20(2): p. 337-52
    [PMID:18252845]
  10. Jaspers P, et al.
    Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors.
    Plant J., 2009. 60(2): p. 268-79
    [PMID:19548978]
  11. Kidokoro S, et al.
    The phytochrome-interacting factor PIF7 negatively regulates DREB1 expression under circadian control in Arabidopsis.
    Plant Physiol., 2009. 151(4): p. 2046-57
    [PMID:19837816]
  12. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  13. Josse EM, et al.
    A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling.
    Plant Cell, 2011. 23(4): p. 1337-51
    [PMID:21478445]
  14. 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]
  15. Li L, et al.
    Linking photoreceptor excitation to changes in plant architecture.
    Genes Dev., 2012. 26(8): p. 785-90
    [PMID:22508725]
  16. Lee CM,Thomashow MF
    Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(37): p. 15054-9
    [PMID:22927419]
  17. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  18. Liu Y,Liu Q,Yan Q,Shi L,Fang Y
    Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model.
    Mol. Biol. Cell, 2014. 25(8): p. 1366-73
    [PMID:24554768]
  19. 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]
  20. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  21. 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]
  22. de Wit M,Ljung K,Fankhauser C
    Contrasting growth responses in lamina and petiole during neighbor detection depend on differential auxin responsiveness rather than different auxin levels.
    New Phytol., 2015. 208(1): p. 198-209
    [PMID:25963518]
  23. Bou-Torrent J, et al.
    Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors.
    Plant Physiol., 2015. 169(3): p. 1584-94
    [PMID:26082398]
  24. Mizuno T,Oka H,Yoshimura F,Ishida K,Yamashino T
    Insight into the mechanism of end-of-day far-red light (EODFR)-induced shade avoidance responses in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2015. 79(12): p. 1987-94
    [PMID:26193333]
  25. Huang H, et al.
    Identification of Evening Complex Associated Proteins in Arabidopsis by Affinity Purification and Mass Spectrometry.
    Mol. Cell Proteomics, 2016. 15(1): p. 201-17
    [PMID:26545401]
  26. Paik I,Kathare PK,Kim JI,Huq E
    Expanding Roles of PIFs in Signal Integration from Multiple Processes.
    Mol Plant, 2017. 10(8): p. 1035-1046
    [PMID:28711729]
  27. Peng M, et al.
    Linking PHYTOCHROME-INTERACTING FACTOR to Histone Modification in Plant Shade Avoidance.
    Plant Physiol., 2018. 176(2): p. 1341-1351
    [PMID:29187567]
  28. Huang X, et al.
    Shade-induced nuclear localization of PIF7 is regulated by phosphorylation and 14-3-3 proteins in Arabidopsis.
    Elife, 2019.
    [PMID:29926790]