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 CCG021944.1
Organism
Populus euphratica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family WRKY
Protein Properties Length: 1492aa    MW: 167469 Da    PI: 8.501
Description WRKY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
CCG021944.1genomeLZUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1WRKY795e-2512421299259
                   --SS-EEEEEEE--TT-SS-EEEEEE-STT---EEEEEE-SSSTTEEEEEEES--SS- CS
         WRKY    2 dDgynWrKYGqKevkgsefprsYYrCtsagCpvkkkversaedpkvveitYegeHnhe 59  
                    DgynWrKYG+K vkgs++ rsYYrC +++C++kkkv+++++ ++v++++Y g+H+h+
  CCG021944.1 1242 ADGYNWRKYGRKLVKGSKNLRSYYRCVYSSCCAKKKVQHCDQSGRVIDVVYIGDHHHD 1299
                   6********************************************************7 PP
2WRKY46.76.2e-15137114121859
                   -SS-EEEEEE-STT---EEEEEE-SSSTTEEEEEEES--SS- CS
         WRKY   18 sefprsYYrCtsagCpvkkkversaedpkvveitYegeHnhe 59  
                    + + sYYrC+s+ Cp++k+ver+++d + +++tYeg+H+h+
  CCG021944.1 1371 DDETESYYRCSSSACPAHKHVERATDDATSTTVTYEGKHDHD 1412
                   56678************************************7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF644841.89E-300341154No hitNo description
Gene3DG3DSA:3.90.1100.103.8E-6746220No hitNo description
PfamPF045632.3E-3151440IPR007644RNA polymerase, beta subunit, protrusion
CDDcd006530521146IPR015712DNA-directed RNA polymerase, subunit 2
Gene3DG3DSA:3.90.1110.101.9E-35221393IPR007642RNA polymerase Rpb2, domain 2
PfamPF045611.7E-16267402IPR007642RNA polymerase Rpb2, domain 2
Gene3DG3DSA:3.90.1100.103.8E-67394553No hitNo description
PfamPF045651.3E-16482540IPR007645RNA polymerase Rpb2, domain 3
PfamPF045667.8E-21577638IPR007646RNA polymerase Rpb2, domain 4
PfamPF045676.1E-8653700IPR007647RNA polymerase Rpb2, domain 5
Gene3DG3DSA:3.90.1100.103.8E-67703791No hitNo description
PfamPF005621.7E-997101080IPR007120DNA-directed RNA polymerase, subunit 2, domain 6
Gene3DG3DSA:2.40.270.107.6E-48792807IPR007120DNA-directed RNA polymerase, subunit 2, domain 6
Gene3DG3DSA:2.40.50.1501.3E-24808925IPR014724RNA polymerase Rpb2, OB-fold
Gene3DG3DSA:2.40.270.107.6E-489261058IPR007120DNA-directed RNA polymerase, subunit 2, domain 6
PROSITE patternPS011660933945IPR007121RNA polymerase, beta subunit, conserved site
PfamPF045604.3E-2010821153IPR007641RNA polymerase Rpb2, domain 7
Gene3DG3DSA:2.20.25.803.0E-2312361301IPR003657WRKY domain
SuperFamilySSF1182901.83E-2112391301IPR003657WRKY domain
SMARTSM007747.8E-2612411300IPR003657WRKY domain
PROSITE profilePS5081121.28712431301IPR003657WRKY domain
PfamPF031069.5E-2012431298IPR003657WRKY domain
SMARTSM007744.7E-713591413IPR003657WRKY domain
PROSITE profilePS5081117.54613691414IPR003657WRKY domain
PfamPF031061.3E-1013711411IPR003657WRKY domain
Gene3DG3DSA:2.20.25.801.2E-1313711414IPR003657WRKY domain
SuperFamilySSF1182902.75E-1113731414IPR003657WRKY domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006306Biological ProcessDNA methylation
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0030422Biological Processproduction of siRNA involved in RNA interference
GO:0050776Biological Processregulation of immune response
GO:0050832Biological Processdefense response to fungus
GO:0000418Cellular ComponentDNA-directed RNA polymerase IV complex
GO:0000419Cellular ComponentDNA-directed RNA polymerase V complex
GO:0005720Cellular Componentnuclear heterochromatin
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0003899Molecular FunctionDNA-directed RNA polymerase activity
GO:0032549Molecular Functionribonucleoside binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 1492 aa     Download sequence    Send to blast
MEDVGPSSKV AVDDMDMDGD LMDTANLNEL GKETLQSFCK KAASLFFEEY GLISHQINSY  60
NAFINSGLQR VFDSFGEVAV EPGYDSSKQK DGEWKRASVR LGKVTLDRPS FWGGTSSDAE  120
HNMFPRHARL QNMTYSARMK IHANVQVYTQ SVGRSDKFKT GIDKVVQKNV VHTENREIII  180
GRIPVMVKSD LCWLTAVEKG DCDFDHGGYF LIKGAEKVFI AQEQICMKRL WISNSQGWTV  240
SYKSEVKRNR LIVRLVELSK LEYIKGEKKG LCVYFLSTEI PLWILFFALG VRSDKEVIDL  300
IDYASNDASI VNIFFASIHD ADEKCEHFRR EDRALDYVDK LLKKTRFPPK ESIEDAISAY  360
LFPRLNSRGH KARFLGYMVK CLLEAYTGHR KCDNRDSFRN KRFELASELL ERELKVHVSH  420
ALRRMTKALQ RDLYGDRDVH PIEHYLDASI VTNGLTRAFS TGAWCHPFKW MERVSGVVGN  480
LGRANPLQTM IDLRKTRQQV LYTGKVGDAR YPHPSHWGRV CFLSTPDGEN CGLVKNLAVT  540
GVVSTNISES LVDKLFGSGM EKLVDDTYTK LDGKHKVFLN GEWVGVCEDS CLFVGELRSM  600
RRRRELPYQV EIKRDEQQRE VRIFSDAGRI LRPLLVVENL DKIKAFKGGN YIFTSLLDKG  660
IIEFIGTEEE EDCCTAWGIK FLLADIEGKQ PMKYTHCELD MSFLLGLSCG IIPFANHDHA  720
RRVLYQAQKH SQQAIGFSTT NPNIRVDTLS HQLHYPQRPL FRTMISDCLG KPGYPLGHNA  780
VLPKPELFNG QNAIVAVNVH LGYNQEDSLV MNRASLERGM FRSEHIRSYK AEVDNKELTD  840
KRRKSEDSIT FGKIQSKIGR VDSLDDDGFP FIGANMQSGD IVIGKCAESG ADHSVKLKHT  900
ERGMVQKVVL SSNDEGKNFA VVSLRQVRSP CLGDKFSSMH GQKGVLGFLE SQENFPFTIQ  960
GVVPDIVINP HAFPSRQTPG QLLEAALGKG IACGGSKRYA TPFSTLSVDD IIDQLHRAKF  1020
SRWGNERVYN GRTGEMVRSL IFMGPTFYQR LVHMAEDKVK FRNTGPVHPL TRQPVADRKR  1080
FGGIKFGEME RDCLIAHGAS ANLHERLFTL SDSSEMHICQ KCKNVANVIQ RAVPGGRKIR  1140
GPYCRVCESV DDLIKGGNEM FQQDACAVTK PEADRVQLEE HQAECANTSS EVLSLTPAVI  1200
SVPYPASVPQ KPRSMRALGL VINQQNSDCE TRHPHVVESP PADGYNWRKY GRKLVKGSKN  1260
LRSYYRCVYS SCCAKKKVQH CDQSGRVIDV VYIGDHHHDP PQKKRIRVVS SAKHAIGSQV  1320
VDPSVQKLVG LDISVCSADG RHSSLHVPES EQQSSSISNG NTGARIKDKS DDETESYYRC  1380
SSSACPAHKH VERATDDATS TTVTYEGKHD HDMPAPKKRQ CSESRLISPT ASTDDARCKK  1440
NRNLSSKKPS SRCSVDGGEV DLMGEKISKL GGEQALESAQ TLLSIGIDLR PR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5x4z_N0.0391139171202DNA-directed RNA polymerase subunit beta
5x50_B0.0391139171202DNA-directed RNA polymerase subunit beta
5x51_B0.0391139171202DNA-directed RNA polymerase subunit beta
5x51_N0.0391139171202DNA-directed RNA polymerase subunit beta
5xog_B0.0391139171202DNA-directed RNA polymerase subunit beta
5xon_B0.0391139171202DNA-directed RNA polymerase subunit beta
6a5l_B0.0391139171202DNA-directed RNA polymerase subunit beta
6a5o_B0.0391139171202DNA-directed RNA polymerase subunit beta
6a5p_B0.0391139171202DNA-directed RNA polymerase subunit beta
6a5r_B0.0391139171202DNA-directed RNA polymerase subunit beta
6a5t_B0.0391139171202DNA-directed RNA polymerase subunit beta
6a5u_B0.0391139171202DNA-directed RNA polymerase subunit beta
6inq_B0.0391139171202DNA-directed RNA polymerase subunit beta
6ir9_B0.0391139171202DNA-directed RNA polymerase subunit beta
6j4w_B0.0391139171202DNA-directed RNA polymerase subunit beta
6j4x_B0.0391139171202DNA-directed RNA polymerase subunit beta
6j4y_B0.0391139171202DNA-directed RNA polymerase subunit beta
6j4z_B0.0391139171202DNA-directed RNA polymerase subunit beta
6j50_B0.0391139171202DNA-directed RNA polymerase subunit beta
6j51_B0.0391139171202DNA-directed RNA polymerase subunit beta
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtDNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases IV and V which mediate short-interfering RNAs (siRNA) accumulation and subsequent RNA-directed DNA methylation-dependent (RdDM) transcriptional gene silencing (TGS) of endogenous repeated sequences, including transposable elements. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Also required for full erasure of methylation when the RNA trigger is withdrawn. Required for intercellular RNA interference (RNAi) leading to systemic post-transcriptional gene silencing. Involved in the maintenance of post-transcriptional RNA silencing. During interphase, mediates siRNA-independent heterochromatin association and methylation into chromocenters and condensation and cytosine methylation at pericentromeric major repeats. Required for complete maintenance of the 35S promoter homology-dependent TGS in transgenic plants and for the initial establishment of DNA methylation. {ECO:0000269|PubMed:15692015, ECO:0000269|PubMed:15766525, ECO:0000269|PubMed:15924141, ECO:0000269|PubMed:16140984, ECO:0000269|PubMed:16839878, ECO:0000269|PubMed:17360559, ECO:0000269|PubMed:17526749, ECO:0000269|PubMed:18425128, ECO:0000269|PubMed:19110459, ECO:0000269|PubMed:19825650, ECO:0000269|PubMed:21070421, ECO:0000269|PubMed:21150311}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEF1796070.0EF179607.1 (Populus tomentosa x P. bolleana) x P. tomentosa putative WRKY transcription factor 02 gene, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_011036682.10.0PREDICTED: DNA-directed RNA polymerases IV and V subunit 2-like
SwissprotQ9LK400.0NRPD2_ARATH; DNA-directed RNA polymerases IV and V subunit 2
TrEMBLA0A2K1WUE80.0A0A2K1WUE8_POPTR; DNA-directed RNA polymerase subunit beta
STRINGPOPTR_0018s02540.10.0(Populus trichocarpa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G30935.13e-39WRKY DNA-binding protein 32
Publications ? help Back to Top
  1. Elo A,Lyznik A,Gonzalez DO,Kachman SD,Mackenzie SA
    Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome.
    Plant Cell, 2003. 15(7): p. 1619-31
    [PMID:12837951]
  2. Herr AJ,Jensen MB,Dalmay T,Baulcombe DC
    RNA polymerase IV directs silencing of endogenous DNA.
    Science, 2005. 308(5718): p. 118-20
    [PMID:15692015]
  3. Onodera Y, et al.
    Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation.
    Cell, 2005. 120(5): p. 613-22
    [PMID:15766525]
  4. Kanno T, et al.
    Atypical RNA polymerase subunits required for RNA-directed DNA methylation.
    Nat. Genet., 2005. 37(7): p. 761-5
    [PMID:15924141]
  5. Pontier D, et al.
    Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis.
    Genes Dev., 2005. 19(17): p. 2030-40
    [PMID:16140984]
  6. Christensen AC, et al.
    Dual-domain, dual-targeting organellar protein presequences in Arabidopsis can use non-AUG start codons.
    Plant Cell, 2005. 17(10): p. 2805-16
    [PMID:16169894]
  7. Pontes O, et al.
    The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.
    Cell, 2006. 126(1): p. 79-92
    [PMID:16839878]
  8. Zhang X,Henderson IR,Lu C,Green PJ,Jacobsen SE
    Role of RNA polymerase IV in plant small RNA metabolism.
    Proc. Natl. Acad. Sci. U.S.A., 2007. 104(11): p. 4536-41
    [PMID:17360559]
  9. Huettel B, et al.
    RNA-directed DNA methylation mediated by DRD1 and Pol IVb: a versatile pathway for transcriptional gene silencing in plants.
    Biochim. Biophys. Acta, 2007 May-Jun. 1769(5-6): p. 358-74
    [PMID:17449119]
  10. Smith LM, et al.
    An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis.
    Plant Cell, 2007. 19(5): p. 1507-21
    [PMID:17526749]
  11. Li CF, et al.
    Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana.
    PLoS Genet., 2008. 4(2): p. e27
    [PMID:18266474]
  12. Kanno T, et al.
    A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation.
    Nat. Genet., 2008. 40(5): p. 670-5
    [PMID:18425128]
  13. Ream TS, et al.
    Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II.
    Mol. Cell, 2009. 33(2): p. 192-203
    [PMID:19110459]
  14. He XJ, et al.
    NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation.
    Genes Dev., 2009. 23(3): p. 318-30
    [PMID:19204117]
  15. Pontes O,Costa-Nunes P,Vithayathil P,Pikaard CS
    RNA polymerase V functions in Arabidopsis interphase heterochromatin organization independently of the 24-nt siRNA-directed DNA methylation pathway.
    Mol Plant, 2009. 2(4): p. 700-710
    [PMID:19825650]
  16. Sidorenko L, et al.
    A dominant mutation in mediator of paramutation2, one of three second-largest subunits of a plant-specific RNA polymerase, disrupts multiple siRNA silencing processes.
    PLoS Genet., 2009. 5(11): p. e1000725
    [PMID:19936058]
  17. Stonaker JL,Lim JP,Erhard KF,Hollick JB
    Diversity of Pol IV function is defined by mutations at the maize rmr7 locus.
    PLoS Genet., 2009. 5(11): p. e1000706
    [PMID:19936246]
  18. Mlotshwa S, et al.
    Transcriptional silencing induced by Arabidopsis T-DNA mutants is associated with 35S promoter siRNAs and requires genes involved in siRNA-mediated chromatin silencing.
    Plant J., 2010. 64(4): p. 699-704
    [PMID:21070421]
  19. Ito H, et al.
    An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress.
    Nature, 2011. 472(7341): p. 115-9
    [PMID:21399627]
  20. Dong L, et al.
    DRD1-Pol V-dependent self-silencing of an exogenous silencer restricts the non-cell autonomous silencing of an endogenous target gene.
    Plant J., 2011. 68(4): p. 633-45
    [PMID:21771120]
  21. Matsunaga W,Kobayashi A,Kato A,Ito H
    The effects of heat induction and the siRNA biogenesis pathway on the transgenerational transposition of ONSEN, a copia-like retrotransposon in Arabidopsis thaliana.
    Plant Cell Physiol., 2012. 53(5): p. 824-33
    [PMID:22173101]
  22. Lee EK, et al.
    A functional phylogenomic view of the seed plants.
    PLoS Genet., 2011. 7(12): p. e1002411
    [PMID:22194700]
  23. Rasmann S, et al.
    Herbivory in the previous generation primes plants for enhanced insect resistance.
    Plant Physiol., 2012. 158(2): p. 854-63
    [PMID:22209873]
  24. López A,Ramírez V,García-Andrade J,Flors V,Vera P
    The RNA silencing enzyme RNA polymerase v is required for plant immunity.
    PLoS Genet., 2011. 7(12): p. e1002434
    [PMID:22242006]
  25. Li X, et al.
    Antisilencing role of the RNA-directed DNA methylation pathway and a histone acetyltransferase in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(28): p. 11425-30
    [PMID:22733760]
  26. Finke A,Kuhlmann M,Mette MF
    IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation.
    Epigenetics, 2012. 7(8): p. 950-60
    [PMID:22810086]
  27. Popova OV,Dinh HQ,Aufsatz W,Jonak C
    The RdDM pathway is required for basal heat tolerance in Arabidopsis.
    Mol Plant, 2013. 6(2): p. 396-410
    [PMID:23376771]