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 RrC1605_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 HD-ZIP
Protein Properties Length: 704aa    MW: 77172.9 Da    PI: 6.8579
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1605_p5genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox58.31.2e-182580156
                TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
    Homeobox  1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56
                +++ +++t++ +++Le+ F+++++p+ ++r +L+++lgL  rq+k+WFqNrR++ k
  RrC1605_p5 25 KKRYHRHTAQKIQRLESSFKECPHPDDKQRNQLSRELGLAPRQIKFWFQNRRTQLK 80
                688899**********************************************9877 PP
2START145.16.4e-462164382206
                 HHHHHHHHHHHHHHHC-TT-EEEE.....EXCCTTEEEEEEESSS.......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEEEEE CS
       START   2 laeeaaqelvkkalaeepgWvkss.....esengdevlqkfeeskv......dsgealrasgvvdmvlallveellddkeqWdetla....kaetlevi 85 
                 +a++a++el+++   +ep+W++       + +n   +   f++s++       ++ea+r sg+v+m+++ lv  ++d   +W e ++    + +tl+v+
  RrC1605_p5 216 IALTATEELLRLFNTNEPLWTRADggggrDVLNLGSYENLFPRSGSrgknhnLRTEASRSSGIVFMNAMSLVDMFMDCV-KWGELFPcivaSSKTLAVV 313
                 67889999999999999999999989888777777777788777778888999**************************.**********9******** PP

                 CTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXX CS
       START  86 ssg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwvehvdlkgrlp 177
                 ssg      gal+lm+ el +lsplv+ R+f  +Ry++  ++g+w++v vS   +q+++ +s++ +   +pSg+li++++ng+skvtwvehv+ +++ p
  RrC1605_p5 314 SSGmggtyeGALHLMYEELEVLSPLVAtREFCELRYCQMIEQGSWIVVNVSYHLPQFVS-QSHSYK---FPSGCLIQDMPNGYSKVTWVEHVETEEKEP 408
                 ***********************************************************.777777...****************************** PP

                 .HHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
       START 178 .hwllrslvksglaegaktwvatlqrqcek 206
                  h+l+r ++++g+a+ga +wv tlqr ce+
  RrC1605_p5 409 tHELYREIIHQGVAFGAERWVTTLQRMCER 438
                 ****************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.601.0E-201176IPR009057Homeodomain-like
SuperFamilySSF466892.17E-181887IPR009057Homeodomain-like
PROSITE profilePS5007117.5242282IPR001356Homeobox domain
SMARTSM003894.6E-172386IPR001356Homeobox domain
PfamPF000463.7E-162580IPR001356Homeobox domain
CDDcd000866.70E-182583No hitNo description
PROSITE patternPS0002705780IPR017970Homeobox, conserved site
PROSITE profilePS5084847.293206441IPR002913START domain
SuperFamilySSF559617.28E-32207440No hitNo description
CDDcd088753.79E-102210437No hitNo description
SMARTSM002342.6E-38215438IPR002913START domain
PfamPF018525.0E-39216438IPR002913START domain
Gene3DG3DSA:3.30.530.202.9E-6274436IPR023393START-like domain
SuperFamilySSF559614.18E-18459691No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009828Biological Processplant-type cell wall loosening
GO:0010091Biological Processtrichome branching
GO:0005634Cellular Componentnucleus
GO:0000976Molecular Functiontranscription regulatory region sequence-specific DNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008289Molecular Functionlipid binding
Sequence ? help Back to Top
Protein Sequence    Length: 704 aa     Download sequence    Send to blast
VSGGDGGGGG GGRQHHDGTE TDRKKKRYHR HTAQKIQRLE SSFKECPHPD DKQRNQLSRE  60
LGLAPRQIKF WFQNRRTQLK AQHVRADNNA LKAENDKIRC ENIAIREALK HTICPNCGGP  120
PVSEDPYFDE HKLRIENAHL REELERMSTV ASKYMGRPIS SHLSTLHHPL HISPLDLSMT  180
GPSLDFDLLP GSSSMHSQPP NLATISDMDK PLMNDIALTA TEELLRLFNT NEPLWTRADG  240
GGGRDVLNLG SYENLFPRSG SRGKNHNLRT EASRSSGIVF MNAMSLVDMF MDCVKWGELF  300
PCIVASSKTL AVVSSGMGGT YEGALHLMYE ELEVLSPLVA TREFCELRYC QMIEQGSWIV  360
VNVSYHLPQF VSQSHSYKFP SGCLIQDMPN GYSKVTWVEH VETEEKEPTH ELYREIIHQG  420
VAFGAERWVT TLQRMCERFA SLLAPATSSR DLGGVIPSPE GKRSMMRLAH RMVSNYCISV  480
SRSNNTHSTI VAELNEVGVR VTAHKSPEPN GTILSAATTF WLPNSPQNVF NFLKDERTRP  540
QWDVLSNRNA VQEVAHIANG SHPGCCVSVL RASNASQSNN MLILQETSID SSGALVVYSP  600
VDLSALNIAM SGDDTSYIPL LSSGFAISPD GNHSSGEQGG GGASTSSGFG GGSLITVGFQ  660
IMVSNLPSAK LNMESVETVN NLIGTTVQQI KTGLNNCPSG STTA
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor which acts as positive regulator of drought stress tolerance. Can transactivate CIPK3, NCED3 and ERECTA (PubMed:18451323). Transactivates several cell-wall-loosening protein genes by directly binding to HD motifs in their promoters. These target genes play important roles in coordinating cell-wall extensibility with root development and growth (PubMed:24821957). Transactivates CYP74A/AOS, AOC3, OPR3 and 4CLL5/OPCL1 genes by directly binding to HD motifs in their promoters. These target genes are involved in jasmonate (JA) biosynthesis, and JA signaling affects root architecture by activating auxin signaling, which promotes lateral root formation (PubMed:25752924). Acts as negative regulator of trichome branching (PubMed:16778018, PubMed:24824485). Required for the establishment of giant cell identity on the abaxial side of sepals (PubMed:23095885). May regulate cell differentiation and proliferation during root and shoot meristem development (PubMed:25564655). {ECO:0000269|PubMed:16778018, ECO:0000269|PubMed:18451323, ECO:0000269|PubMed:23095885, ECO:0000269|PubMed:24821957, ECO:0000269|PubMed:24824485, ECO:0000269|PubMed:25564655, ECO:0000269|PubMed:25752924}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00232DAPTransfer from AT1G73360Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ1668210.0DQ166821.1 Brassica napus baby boom interacting protein 1A (BIP1A) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018457296.10.0PREDICTED: homeobox-leucine zipper protein HDG11-like
SwissprotQ9FX310.0HDG11_ARATH; Homeobox-leucine zipper protein HDG11
TrEMBLQ0H7430.0Q0H743_BRANA; Baby boom interacting protein 1B (Fragment)
STRINGBo6g116760.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM30042665
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G73360.10.0homeodomain GLABROUS 11
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Khosla A, et al.
    HD-Zip Proteins GL2 and HDG11 Have Redundant Functions in Arabidopsis Trichomes, and GL2 Activates a Positive Feedback Loop via MYB23.
    Plant Cell, 2014. 26(5): p. 2184-2200
    [PMID:24824485]
  3. Horstman A, et al.
    AIL and HDG proteins act antagonistically to control cell proliferation.
    Development, 2015. 142(3): p. 454-64
    [PMID:25564655]
  4. Cai XT,Xu P,Wang Y,Xiang CB
    Activated expression of AtEDT1/HDG11 promotes lateral root formation in Arabidopsis mutant edt1 by upregulating jasmonate biosynthesis.
    J Integr Plant Biol, 2015. 57(12): p. 1017-30
    [PMID:25752924]
  5. Yu LH, et al.
    Arabidopsis EDT1/HDG11 improves drought and salt tolerance in cotton and poplar and increases cotton yield in the field.
    Plant Biotechnol. J., 2016. 14(1): p. 72-84
    [PMID:25879154]
  6. Zhu Z, et al.
    Overexpression of AtEDT1/HDG11 in Chinese Kale (Brassica oleracea var. alboglabra) Enhances Drought and Osmotic Stress Tolerance.
    Front Plant Sci, 2016. 7: p. 1285
    [PMID:27625663]
  7. Liu Y, et al.
    Overexpression of AtEDT1 promotes root elongation and affects medicinal secondary metabolite biosynthesis in roots of transgenic Salvia miltiorrhiza.
    Protoplasma, 2017. 254(4): p. 1617-1625
    [PMID:27915455]
  8. Ueda M, et al.
    Transcriptional integration of paternal and maternal factors in the Arabidopsis zygote.
    Genes Dev., 2017. 31(6): p. 617-627
    [PMID:28404632]
  9. Lung SC, et al.
    Arabidopsis ACYL-COA-BINDING PROTEIN1 interacts with STEROL C4-METHYL OXIDASE1-2 to modulate gene expression of homeodomain-leucine zipper IV transcription factors.
    New Phytol., 2018. 218(1): p. 183-200
    [PMID:29288621]
  10. Zheng G, et al.
    Over-Expression of Arabidopsis EDT1 Gene Confers Drought Tolerance in Alfalfa (Medicago sativa L.).
    Front Plant Sci, 2017. 8: p. 2125
    [PMID:29326737]