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 Neem_5117_f_1
Organism
Azadirachta indica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family bHLH
Protein Properties Length: 610aa    MW: 68416.3 Da    PI: 5.3478
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_5117_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH38.12.7e-12413459455
                    HHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS
            HLH   4 ahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 
                    +h   Er+RR+++N++f  L++++P+ +      K +K++iL  ++eY+++L+
  Neem_5117_f_1 413 SHVLSERKRREKLNQRFIMLKSIVPSiS------KFDKVSILDDTIEYLQELE 459
                    79999*********************66......****************995 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF142151.8E-4117168IPR025610Transcription factor MYC/MYB N-terminal
PROSITE profilePS5088815.955409458IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474592.09E-17412474IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.102.0E-18413476IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000106.0E-10413459IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.54E-12413463No hitNo description
SMARTSM003532.8E-15415464IPR011598Myc-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:0010091Biological Processtrichome branching
GO:0005634Cellular Componentnucleus
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 610 aa     Download sequence    Send to blast
MATGVQNQER LHCKSFRVLE WGDGYYNGDI KTRKTIQAVE LNYDQLGLQR SEQLRELYES  60
LSAGESNPQA RRPSAALSPE DLTDTEWYYL VCMSFVFNIG EGLPGRALAN SQPIWLCNAH  120
CADSKVFSRS LLAKTILCFP FLQGVVELGV TELVLEDHGL VQHIKSTFLE TPYPKISNKC  180
SSGAGHVRND KDLACTAALG SQILATTMGP VVGCEVLEMA SPSNSSNGIE HNQPAEGSFM  240
VEGINGAVSQ VQSWQFRDED FSNCVHHSMN SSDCISQTLG DPEKVVSALK EDEAIDHCLQ  300
EVQECNHIKL TSLDLQGNDL HYQSVLSSLL KTSHQLVLGP HFQKCNQESS FVCWKDDGLV  360
NYQRRRDGIS QRLLKKILFE VPRMNNDRLL ESPEDNGIKD DIWRPEADEI AASHVLSERK  420
RREKLNQRFI MLKSIVPSIS KFDKVSILDD TIEYLQELER KVEELESHRA ELETRTKGKA  480
KDTVERTSDN YGNNKTSNAK KSLVNKRKAC EIDELDPEFE SAVLKDDTAN IITVSMKDKD  540
VLVEIKCPWR EGILLEIMDA VSNLRLDSYS VQSSTTEGII SLTIKTKYNG STVASAGMIK  600
QSLQRVVWKC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4rqw_A1e-121816846192Transcription factor MYC3
4rqw_B1e-121816846192Transcription factor MYC3
4rs9_A1e-121816846192Transcription factor MYC3
4yz6_A1e-121816846192Transcription factor MYC3
5gnj_A6e-13413472867Transcription factor MYC2
5gnj_B6e-13413472867Transcription factor MYC2
5gnj_E6e-13413472867Transcription factor MYC2
5gnj_F6e-13413472867Transcription factor MYC2
5gnj_G6e-13413472867Transcription factor MYC2
5gnj_I6e-13413472867Transcription factor MYC2
5gnj_M6e-13413472867Transcription factor MYC2
5gnj_N6e-13413472867Transcription factor MYC2
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1417422ERKRRE
2418423RKRREK
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, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication. Regulates also trichome cell wall maturation. 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. Activates the transcription of GL2. {ECO:0000269|PubMed:11063707, ECO:0000269|PubMed:12917293, ECO:0000269|PubMed:12956536, ECO:0000269|PubMed:14561633, ECO:0000269|PubMed:14627722, ECO:0000269|PubMed:15361138, ECO:0000269|PubMed:15590742}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By nitrogen deficiency and UV light. 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, ECO:0000269|PubMed:17053893}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_007040249.20.0PREDICTED: transcription factor EGL1
SwissprotQ9FN690.0GL3_ARATH; Transcription factor GLABRA 3
TrEMBLA0A1L5YQU90.0A0A1L5YQU9_LITCN; BHLH3
STRINGEOY247500.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM25922867
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G41315.10.0bHLH 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. 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. Nemie-Feyissa D,Olafsdottir SM,Heidari B,Lillo C
    Nitrogen depletion and small R3-MYB transcription factors affecting anthocyanin accumulation in Arabidopsis leaves.
    Phytochemistry, 2014. 98: p. 34-40
    [PMID:24388610]
  4. 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]
  5. Wada T,Kunihiro A,Tominaga-Wada R
    Arabidopsis CAPRICE (MYB) and GLABRA3 (bHLH) control tomato (Solanum lycopersicum) anthocyanin biosynthesis.
    PLoS ONE, 2014. 9(9): p. e109093
    [PMID:25268379]
  6. 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]
  7. Sun L, et al.
    GLABROUS INFLORESCENCE STEMS3 (GIS3) regulates trichome initiation and development in Arabidopsis.
    New Phytol., 2015. 206(1): p. 220-30
    [PMID:25640859]
  8. 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]
  9. Yu D, et al.
    RPN1a, a subunit of the 26S proteasome, controls trichome development in Arabidopsis.
    Plant Physiol. Biochem., 2015. 88: p. 82-8
    [PMID:25676129]
  10. Huang M,Hu Y,Liu X,Li Y,Hou X
    Arabidopsis LEAFY COTYLEDON1 controls cell fate determination during post-embryonic development.
    Front Plant Sci, 2015. 6: p. 955
    [PMID:26579186]
  11. 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]
  12. Pan Y,Bo K,Cheng Z,Weng Y
    The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1.
    BMC Plant Biol., 2015. 15: p. 302
    [PMID:26714637]
  13. Alahakoon UI, et al.
    Hairy Canola (Brasssica napus) re-visited: Down-regulating TTG1 in an AtGL3-enhanced hairy leaf background improves growth, leaf trichome coverage, and metabolite gene expression diversity.
    BMC Plant Biol., 2016. 16: p. 12
    [PMID:26739276]
  14. Zheng K, et al.
    Ectopic expression of R3 MYB transcription factor gene OsTCL1 in Arabidopsis, but not rice, affects trichome and root hair formation.
    Sci Rep, 2016. 6: p. 19254
    [PMID:26758286]
  15. Shangguan XX,Yang CQ,Zhang XF,Wang LJ
    Functional characterization of a basic helix-loop-helix (bHLH) transcription factor GhDEL65 from cotton (Gossypium hirsutum).
    Physiol Plant, 2016. 158(2): p. 200-12
    [PMID:27080593]
  16. Petridis A,Döll S,Nichelmann L,Bilger W,Mock HP
    Arabidopsis thaliana G2-LIKE FLAVONOID REGULATOR and BRASSINOSTEROID ENHANCED EXPRESSION1 are low-temperature regulators of flavonoid accumulation.
    New Phytol., 2016. 211(3): p. 912-25
    [PMID:27125220]
  17. Gao C, et al.
    Genome-wide identification of GLABRA3 downstream genes for anthocyanin biosynthesis and trichome formation in Arabidopsis.
    Biochem. Biophys. Res. Commun., 2017. 485(2): p. 360-365
    [PMID:28216162]
  18. 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]
  19. Gao C, et al.
    Brassica napusGLABRA3-1 promotes anthocyanin biosynthesis and trichome formation in true leaves when expressed in Arabidopsis thaliana.
    Plant Biol (Stuttg), 2018. 20(1): p. 3-9
    [PMID:28940939]
  20. 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]
  21. Kim SY,Hyoung S,So WM,Shin JS
    The novel transcription factor TRP interacts with ZFP5, a trichome initiation-related transcription factor, and negatively regulates trichome initiation through gibberellic acid signaling.
    Plant Mol. Biol., 2018. 96(3): p. 315-326
    [PMID:29335898]