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 RrC3517_p4
Organism
Raphanus raphanistrum
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: 303aa    MW: 33643.9 Da    PI: 7.641
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC3517_p4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH50.15e-16197242555
                 HHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
         HLH   5 hnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                 hne ErrRRdriN+++ +L++llP+a      K +K++iL  ++e++k+Lq
  RrC3517_p4 197 HNESERRRRDRINQRMRTLQKLLPTA-----SKADKVSILDDVIEHLKQLQ 242
                 *************************9.....7******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088817.06192241IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474592.09E-17195251IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.106.5E-17195249IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000839.34E-10197246No hitNo description
PfamPF000102.8E-13197242IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.9E-17198247IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
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
Sequence ? help Back to Top
Protein Sequence    Length: 303 aa     Download sequence    Send to blast
MTKMSSFIGF LGAERGFWSL RGQGTSNPLP HMSNYGVKEL TWENGQLTVH GLGQGVEPTT  60
SANLLWTQAL NGCETLESVV HQAALQQQSK NGRDHNNSES KDGSCSRKRG YPQEMDCWFS  120
PQEESHRVGH SVTASASGTN MSWASFESGR SLKTARTGDR DYLFSGSETQ ETEGDEQETR  180
GEGGRSNGRR GRAAAIHNES ERRRRDRINQ RMRTLQKLLP TASKADKVSI LDDVIEHLKQ  240
LQAQVQDCTN ASSSDPYSAF LAQTMNMDLY NKMAAAIYRQ QSDQTTKVNT GMPSSSTNHE  300
KRD
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1200205ERRRRD
Functional Description ? help Back to Top
Source Description
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00571DAPTransfer from AT5G61270Download
Motif logo
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
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3527341e-173AK352734.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-03-L18.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013594159.11e-143PREDICTED: transcription factor PIF7
SwissprotQ570R71e-131PIF7_ARATH; Transcription factor PIF7
TrEMBLA0A0D3DDJ61e-142A0A0D3DDJ6_BRAOL; Uncharacterized protein
TrEMBLA0A3P6EI361e-141A0A3P6EI36_BRAOL; Uncharacterized protein
STRINGBo7g098470.11e-143(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM141231822
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G61270.11e-103phytochrome-interacting factor7
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. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]