PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Rsa1.0_02671.1_g00004.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family bHLH
Protein Properties Length: 503aa    MW: 55680.1 Da    PI: 6.7495
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02671.1_g00004.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH49.47.9e-16308354455
                              HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
                      HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                               hn  Er+RRdriN+++  L+el+P +      K +Ka++L +A+eY+ksLq
  Rsa1.0_02671.1_g00004.1 308 VHNLSERKRRDRINERMKALQELIPRC-----NKSDKASMLDEAIEYMKSLQ 354
                              6*************************8.....6******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088818.146304353IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000833.12E-16307358No hitNo description
SuperFamilySSF474599.16E-21307382IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.101.5E-20308365IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.6E-13308354IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003532.2E-17310359IPR011598Myc-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:0006783Biological Processheme biosynthetic process
GO:0009740Biological Processgibberellic acid mediated signaling pathway
GO:0009959Biological Processnegative gravitropism
GO:0010100Biological Processnegative regulation of photomorphogenesis
GO:0010161Biological Processred light signaling pathway
GO:0010187Biological Processnegative regulation of seed germination
GO:0015995Biological Processchlorophyll biosynthetic process
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0010313Molecular Functionphytochrome binding
GO:0042802Molecular Functionidentical protein binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 503 aa     Download sequence    Send to blast
MNHQHHFVPD FETDDDYVNA NTNPSSSNLA RKPIIGEQEE DGDLMELLWH NGQVVLHNQR  60
PNAKKQPPPP LPSSSSAPPP ALDHNLFIQE DEMSSWLHYP LRDDDDFCSD LFLPPERQTS  120
NQVVTAARPP VPSTVRPPEA SSMRPPAPLP SSVRPPVRNF MNFSRLRGDF TGRGGESGPS  180
VSKSTVREST QVSATPARES DLTRRTDGIG SRGTVDLASR SAVDGGGGAY TVGHNRKGKA  240
VVTTEPRNEN PAGASSSLAS KSEIEPFNET TIVDERKRKE REAIDETEEE AKQGRGSTST  300
KRSRAAEVHN LSERKRRDRI NERMKALQEL IPRCNKSDKA SMLDEAIEYM KSLQLQIQMM  360
SMGCGMMPMM YTGMQQYMPH MAMGMGMGME MGMNRPPPPP PPPPFMPFPN MLASQRPLPP  420
QPRMGGYPAV QASDPSRVYG SNQQFVPNSN QAPYSGYMDP YQQFRSLHPS QPPQFQNQAA  480
SYPSSSRVSS TKESEDQGNQ TTS
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1312317ERKRRD
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00074ChIP-chipTransfer from AT2G20180Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_02671.1_g00004.1
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018438188.10.0PREDICTED: transcription factor PIF1-like isoform X1
RefseqXP_018438191.10.0PREDICTED: transcription factor PIF1-like isoform X1
SwissprotQ8GZM70.0PIF1_ARATH; Transcription factor PIF1
TrEMBLA0A397YGV10.0A0A397YGV1_BRACM; Uncharacterized protein
STRINGBo7g003890.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM71082643
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G20180.31e-116phytochrome 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. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. Kim J, et al.
    Epidermal Phytochrome B Inhibits Hypocotyl Negative Gravitropism Non-Cell-Autonomously.
    Plant Cell, 2016. 28(11): p. 2770-2785
    [PMID:27758895]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. Zhang X, et al.
    A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis.
    Plant Physiol., 2017. 174(4): p. 2487-2500
    [PMID:28687557]
  22. 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]
  23. 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]
  24. 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]
  25. 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]