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 XP_009112755.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family bHLH
Protein Properties Length: 606aa    MW: 67769.1 Da    PI: 4.9256
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009112755.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH469.4e-15415461455
                     HHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS
             HLH   4 ahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 
                     +h   Er+RR+++N++f +Lr+++P+ +      K +K++iL  +++Y+++Lq
  XP_009112755.1 415 NHALSERKRREKLNDRFMTLRSIIPSiS------KIDKVSILDDTIDYLQELQ 461
                     79999*********************66......******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF142153.6E-5113202IPR025610Transcription factor MYC/MYB N-terminal
PROSITE profilePS5088817.187411460IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000103.0E-12415461IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.94E-16415465No hitNo description
SuperFamilySSF474594.06E-19415483IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.104.1E-18415478IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.5E-17417466IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009957Biological Processepidermal cell fate specification
GO:0005634Cellular Componentnucleus
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 606 aa     Download sequence    Send to blast
MATGENRTVQ ENLKKHLAVS VRNIQWSYGI FWSISASQPG VLEWGDGYYN GDIKTRKTIQ  60
AVEVKADQLG LERSEQLREL YESLSVAESS ASGGSQVSRR ASATALSPED LTDTEWYYLV  120
CMSFVFNIGE GITGGALGNG EPIWLCNAHT ADSKVFTRSL LAKSASLLTV VCFPFLGGVL  180
EIGTTEHITE DFNVIQCVKT LFLEAHPYGT ISTRSDYQEI FDPLNSDKYI PTFGTEAFPT  240
TSTSVFEQEL EDHDSFINGG GASQVQSWQF VGEELNNCVH QPVNSSDCVS QTFVGGTTGR  300
VSCNPRKSRP QRLGQIQEQS NRLNMDDDVH YQGVISTIFK TAHQLVLGPQ FQNFDKRSSF  360
TRWRRLSLSA KTLGEKSQSM LKKIVFEVPR MHQKELLLPD TPEDNMFKIG DETGNHALSE  420
RKRREKLNDR FMTLRSIIPS ISKIDKVSIL DDTIDYLQEL QRRVQELESC REYTDTEMQM  480
PMKRKKPEDD DERASANCLN TKRKESDVNV GEDEPADDTG YAGLTDNLSI GSFGNEVVIE  540
LRCAWREGIL LEIMDVISHL NLDSHSVQSS TGDGLLCLTV NCKHKGTNIA TAGMIQEALQ  600
RVAWIC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4rqw_A3e-1582028192Transcription factor MYC3
4rqw_B3e-1582028192Transcription factor MYC3
4rs9_A3e-1582028192Transcription factor MYC3
4yz6_A3e-1582028192Transcription factor MYC3
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1419424ERKRRE
2420425RKRREK
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Localized in trichome developing region of leaves, prior to trichome initiation. Levels increase in initiating and young trichome cells, but dropped in the pavement cells between trichomes. Disappears in mature trichomes. {ECO:0000269|PubMed:12917293}.
UniprotTISSUE SPECIFICITY: Ubiquitous with higher levels in buds and flowers. Specifically localized in developing root hair cells. Expressed in epidermal root hair cells (trichoblasts) and moves to root hairless cells (atrichoblasts) by a cell-to-cell movement through plasmodesmata (at protein level). {ECO:0000269|PubMed:12956536, ECO:0000269|PubMed:14627722, ECO:0000269|PubMed:15590742}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator, when associated with MYB75/PAP1, MYB90/PAP2 or TT2. Involved in epidermal cell fate specification. Regulates negatively stomata formation but promotes trichome formation. Together with MYB66/WER, promotes the formation of non-hair cells in root epidermis cells in the N position. Whereas together with CPC, promotes the formation of hair cells in root epidermis cells in the H position by inhibiting non-hair cell formation. Seems also to play a role in the activation of anthocyanin biosynthesis, probably together with MYB75/PAP1. Involved in seed mucilage production. Activates the transcription of GL2. {ECO:0000269|PubMed:12917293, ECO:0000269|PubMed:12956536, ECO:0000269|PubMed:14627722, ECO:0000269|PubMed:15361138, ECO:0000269|PubMed:15590742}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009112755.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By UV treatment. Negatively regulated by MYB66/WER, GL3 and BHLH2 in the developing non-hair cells, and positively regulated by CPC and TRY in the developing hair cells. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:15590742}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKF1882070.0KF188207.1 Brassica villosa BVEGL3-1 (BVEGL3-1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009112755.10.0PREDICTED: transcription factor EGL1
RefseqXP_009112756.10.0PREDICTED: transcription factor EGL1
RefseqXP_013661574.10.0transcription factor EGL1-like
RefseqXP_013661576.10.0transcription factor EGL1-like
SwissprotQ9CAD00.0EGL1_ARATH; Transcription factor EGL1
TrEMBLA0A3P5YF860.0A0A3P5YF86_BRACM; Uncharacterized protein
TrEMBLM4EG820.0M4EG82_BRARP; Uncharacterized protein
STRINGBra027796.1-P0.0(Brassica rapa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G63650.30.0bHLH 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. Liu Z,Shi MZ,Xie DY
    Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins.
    Planta, 2014. 239(4): p. 765-81
    [PMID:24370633]
  3. Nayidu NK, et al.
    Comparison of five major trichome regulatory genes in Brassica villosa with orthologues within the Brassicaceae.
    PLoS ONE, 2014. 9(4): p. e95877
    [PMID:24755905]
  4. Cheng Y, et al.
    Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-bHLH-WD40 complex by GSK3-like kinases.
    Elife, 2018.
    [PMID:24771765]
  5. Ranocha P,Francoz E,Burlat V,Dunand C
    Expression of PRX36, PMEI6 and SBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion.
    Plant Signal Behav, 2014. 9(11): p. e977734
    [PMID:25531128]
  6. Nemie-Feyissa D,Heidari B,Blaise M,Lillo C
    Analysis of interactions between heterologously produced bHLH and MYB proteins that regulate anthocyanin biosynthesis: quantitative interaction kinetics by Microscale Thermophoresis.
    Phytochemistry, 2015. 111: p. 21-6
    [PMID:25659750]
  7. Kwak SH,Song SK,Lee MM,Schiefelbein J
    TORNADO1 regulates root epidermal patterning through the WEREWOLF pathway in Arabidopsis thaliana.
    Plant Signal Behav, 2015. 10(12): p. e1103407
    [PMID:26451798]
  8. Dai X, et al.
    A single amino acid substitution in the R3 domain of GLABRA1 leads to inhibition of trichome formation in Arabidopsis without affecting its interaction with GLABRA3.
    Plant Cell Environ., 2016. 39(4): p. 897-907
    [PMID:26667588]
  9. Friede A, et al.
    The Second Intron Is Essential for the Transcriptional Control of the Arabidopsis thaliana GLABRA3 Gene in Leaves.
    Front Plant Sci, 2017. 8: p. 1382
    [PMID:28848584]
  10. Feng K, et al.
    An R2R3-MYB transcription factor, OjMYB1, functions in anthocyanin biosynthesis in Oenanthe javanica.
    Planta, 2018. 247(2): p. 301-315
    [PMID:28965159]
  11. Wen J, et al.
    The C-terminal domains of Arabidopsis GL3/EGL3/TT8 interact with JAZ proteins and mediate dimeric interactions.
    Plant Signal Behav, 2018. 13(1): p. e1422460
    [PMID:29293407]