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 RrC5416_p5
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: 457aa    MW: 51216.6 Da    PI: 6.308
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC5416_p5genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH37.83.3e-12303349455
                 HHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS
         HLH   4 ahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 
                 +h e+Er+RR+++N++f  Lr ++P+ +      K++Ka+ L  A+ YI ++q
  RrC5416_p5 303 NHVEAERQRREKLNQRFYVLRAVVPNiS------KMDKASLLADAITYITDMQ 349
                 799***********************66......***************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF142154.2E-4150229IPR025610Transcription factor MYC/MYB N-terminal
PROSITE profilePS5088816.031299348IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.57E-17299365IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.25E-13302353No hitNo description
PfamPF000109.8E-10303349IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.101.3E-16303365IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003534.5E-14305354IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 457 aa     Download sequence    Send to blast
MSGGQKFWEN EEDRAMVEST IGTEACDFFI SSNTSKLLPP PPHPPTDPNL QQGLRHLVEA  60
SSDWDYAVFW IASISNTSSD DCVLIWGDGH YRPHKKNSEE TKEEDETKRS VLRKLHSSFF  120
LGEEDRRLLA KSGGGLTDLD VFYLASLYFY FRCDSTKYGP AGTYISGKAL WASDLPSCLS  180
YYRVRSFLAR SAGFKTVLSV PVNSGVVELG SLKLIPEDKS VIEMVKSVFG GGKEAPKIFG  240
RQLSLSINFS PKMEDDTTGG FSLDAYEVGG SNHQVYGKDE ATDEQKPRKR GRKPANGREE  300
ALNHVEAERQ RREKLNQRFY VLRAVVPNIS KMDKASLLAD AITYITDMQK KIRVYETEKQ  360
VMKRRESSQI TPGDVDYQER QEDEAVVKVS CALETHPVSK AIRMFRENEV TPHDTNVAVT  420
EEGVVHTFTI RPQGGCTAEE LKDKLLASLS HSSVVNM
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5gnj_A2e-25297363268Transcription factor MYC2
5gnj_B2e-25297363268Transcription factor MYC2
5gnj_E2e-25297363268Transcription factor MYC2
5gnj_F2e-25297363268Transcription factor MYC2
5gnj_G2e-25297363268Transcription factor MYC2
5gnj_I2e-25297363268Transcription factor MYC2
5gnj_M2e-25297363268Transcription factor MYC2
5gnj_N2e-25297363268Transcription factor MYC2
Search in ModeBase
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00099PBMTransfer from AT4G16430Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By UV treatment. {ECO:0000269|PubMed:12679534}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1896321e-173AC189632.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrS003O10, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018484627.10.0PREDICTED: transcription factor bHLH3-like
SwissprotO234870.0BH003_ARATH; Transcription factor bHLH3
TrEMBLA0A398AAI30.0A0A398AAI3_BRACM; Uncharacterized protein
STRINGBo7g104400.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM66112741
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16430.10.0bHLH family protein
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. Sasaki-Sekimoto Y,Saito H,Masuda S,Shirasu K,Ohta H
    Comprehensive analysis of protein interactions between JAZ proteins and bHLH transcription factors that negatively regulate jasmonate signaling.
    Plant Signal Behav, 2014. 9(1): p. e27639
    [PMID:24394987]
  3. Fonseca S, et al.
    bHLH003, bHLH013 and bHLH017 are new targets of JAZ repressors negatively regulating JA responses.
    PLoS ONE, 2014. 9(1): p. e86182
    [PMID:24465948]
  4. Ezer D, et al.
    The G-Box Transcriptional Regulatory Code in Arabidopsis.
    Plant Physiol., 2017. 175(2): p. 628-640
    [PMID:28864470]