PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID KHN09413.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja
Family bHLH
Protein Properties Length: 281aa    MW: 31053.7 Da    PI: 8.1162
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KHN09413.1genomeTCUHKView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH49.76.6e-1676122455
                 HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
         HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  hn  ErrRRdriN+++  L+el+P +      K +Ka++L +A+ Y+ksLq
  KHN09413.1  76 VHNLSERRRRDRINEKMKALQELIPRC-----NKSDKASMLDEAISYLKSLQ 122
                 6*************************8.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5011013.061196IPR001789Signal transduction response regulator, receiver domain
Gene3DG3DSA:3.40.50.23006.7E-12251No hitNo description
SuperFamilySSF521723.98E-11352IPR011006CheY-like superfamily
PfamPF000721.1E-7450IPR001789Signal transduction response regulator, receiver domain
CDDcd001563.38E-9550No hitNo description
Gene3DG3DSA:4.10.280.109.0E-2169130IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474597.33E-2170138IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.07672121IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000835.97E-1775126No hitNo description
PfamPF000101.7E-1376122IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.1E-1878127IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000160Biological Processphosphorelay signal transduction system
GO:0005622Cellular Componentintracellular
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 281 aa     Download sequence    Send to blast
EMVHRKMLNS VGLKIQVAEN GKEAVEIHRS GQSFDLILMD RDMPVMNGIE DVDFESEAKK  60
QVCGSTSTKR SRAAEVHNLS ERRRRDRINE KMKALQELIP RCNKSDKASM LDEAISYLKS  120
LQLQVQMMSM GCGMVPMMFP GIQQYMPAMG MGVGMGMGME MGMNRPVMPF PNMLPGSALP  180
AATAAAAHLG PRFSMPPFHM PHVPAPDSSR MQAANQSDNN MVTSAGPPDP NQSRIPNFTD  240
PYQQYLGPHQ MQFQLIQNQA MNQPNVSKPS NNGGPANPEN H
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
18085ERRRRD
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator. Regulates negatively chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Binds to the G-box motif (5'-CACGTG-3') found in many light-regulated promoters. Promotes the expression of SOM, and thus modulates responses to abscisic acid (ABA) and gibberellic acid (GA). {ECO:0000269|PubMed:15448264, ECO:0000269|PubMed:16359394, ECO:0000269|PubMed:18487351, ECO:0000269|PubMed:18539749, ECO:0000269|PubMed:18591656}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapKHN09413.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by red (R) and far red (FR) light treatments in a phyB- and phyA-dependent manner. {ECO:0000269|PubMed:15448264}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKT0311020.0KT031102.1 Glycine max clone HN_CCL_196 bHLH transcription factor (Glyma03g32747.2) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_028225691.11e-168transcription factor PIF1-like isoform X1
RefseqXP_028225692.11e-168transcription factor PIF1-like isoform X1
SwissprotQ8GZM72e-53PIF1_ARATH; Transcription factor PIF1
TrEMBLA0A445LDD91e-167A0A445LDD9_GLYSO; Transcription factor PIF1 isoform B
STRINGGLYMA03G32747.31e-168(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF46073351
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G20180.14e-43phytochrome interacting factor 3-like 5
Publications ? help Back to Top
  1. 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]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. Luo Q, et al.
    COP1 and phyB Physically Interact with PIL1 to Regulate Its Stability and Photomorphogenic Development in Arabidopsis.
    Plant Cell, 2014. 26(6): p. 2441-2456
    [PMID:24951480]
  4. Qi X, et al.
    Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing.
    Nat Commun, 2014. 5: p. 4340
    [PMID:25004933]
  5. Krzymuski M, et al.
    Phytochrome A antagonizes PHYTOCHROME INTERACTING FACTOR 1 to prevent over-activation of photomorphogenesis.
    Mol Plant, 2014. 7(9): p. 1415-1428
    [PMID:25009301]
  6. Adams E,Diaz C,Hong JP,Shin R
    14-3-3 proteins participate in light signaling through association with PHYTOCHROME INTERACTING FACTORs.
    Int J Mol Sci, 2014. 15(12): p. 22801-14
    [PMID:25501334]
  7. Zhu L, et al.
    CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1.
    Nat Commun, 2015. 6: p. 7245
    [PMID:26037329]
  8. 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]
  9. Galvão VC,Collani S,Horrer D,Schmid M
    Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana.
    Plant J., 2015. 84(5): p. 949-62
    [PMID:26466761]
  10. Zhu L, et al.
    A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis.
    Plant Cell, 2016. 28(4): p. 855-74
    [PMID:27073231]
  11. Pacín M,Semmoloni M,Legris M,Finlayson SA,Casal JJ
    Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance.
    New Phytol., 2016. 211(3): p. 967-79
    [PMID:27105120]
  12. Kim J, et al.
    PIF1-Interacting Transcription Factors and Their Binding Sequence Elements Determine the in Vivo Targeting Sites of PIF1.
    Plant Cell, 2016. 28(6): p. 1388-405
    [PMID:27303023]
  13. Martin G,Soy J,Monte E
    Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes.
    Front Plant Sci, 2016. 7: p. 962
    [PMID:27458465]
  14. Zhu L,Xin R,Huq E
    A Protein-Based Genetic Screening Uncovers Mutants Involved in Phytochrome Signaling in Arabidopsis.
    Front Plant Sci, 2016. 7: p. 1086
    [PMID:27499759]
  15. Gangl R,Tenhaken R
    Raffinose Family Oligosaccharides Act As Galactose Stores in Seeds and Are Required for Rapid Germination of Arabidopsis in the Dark.
    Front Plant Sci, 2016. 7: p. 1115
    [PMID:27507985]
  16. Kim K, et al.
    PIF1 Regulates Plastid Development by Repressing Photosynthetic Genes in the Endodermis.
    Mol Plant, 2016. 9(10): p. 1415-1427
    [PMID:27591813]
  17. Kim J, et al.
    Epidermal Phytochrome B Inhibits Hypocotyl Negative Gravitropism Non-Cell-Autonomously.
    Plant Cell, 2016. 28(11): p. 2770-2785
    [PMID:27758895]
  18. Zhang D,Li Y,Zhang X,Zha P,Lin R
    The SWI2/SNF2 Chromatin-Remodeling ATPase BRAHMA Regulates Chlorophyll Biosynthesis in Arabidopsis.
    Mol Plant, 2017. 10(1): p. 155-167
    [PMID:27865928]
  19. Xu X, et al.
    Reciprocal proteasome-mediated degradation of PIFs and HFR1 underlies photomorphogenic development in Arabidopsis.
    Development, 2017. 144(10): p. 1831-1840
    [PMID:28420710]
  20. Shor E,Paik I,Kangisser S,Green R,Huq E
    PHYTOCHROME INTERACTING FACTORS mediate metabolic control of the circadian system in Arabidopsis.
    New Phytol., 2017. 215(1): p. 217-228
    [PMID:28440582]
  21. Gu D, et al.
    Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark.
    Nucleic Acids Res., 2017. 45(12): p. 7137-7150
    [PMID:28444370]
  22. Zhang X, et al.
    A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.
    Plant Physiol., 2017. 174(4): p. 2487-2500
    [PMID:28687557]
  23. 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]
  24. Li R, et al.
    Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1.
    Plant Physiol. Biochem., 2018. 123: p. 204-212
    [PMID:29248678]
  25. Wu M, et al.
    PIL5 represses floral transition in Arabidopsis under long day conditions.
    Biochem. Biophys. Res. Commun., 2018. 499(3): p. 513-518
    [PMID:29588173]
  26. Majee M, et al.
    KELCH F-BOX protein positively influences Arabidopsis seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1.
    Proc. Natl. Acad. Sci. U.S.A., 2018. 115(17): p. E4120-E4129
    [PMID:29632208]