PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Gh_A07G0263

Organism

Gossypium hirsutum

Taxonomic ID

3635

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

WRKY

Protein Properties

Length: 1442aa MW: 163369 Da PI: 8.7748

Description

WRKY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_A07G0263	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	WRKY	92.4	3.4e-29	153	212	1	59
---SS-EEEEEEE--TT-SS-EEEEEE-ST.T---EEEEEE-SSSTTEEEEEEES--SS- CS WRKY 1 ldDgynWrKYGqKevkgsefprsYYrCtsa.gCpvkkkversaedpkvveitYegeHnhe 59 ++Dg++WrKYGqK+ k ++fpr+Y+rC++a gCpvkkkv+r+ ed++++ +tYeg+Hnhe Gh_A07G0263 153 VKDGFQWRKYGQKVTKHNPFPRAYFRCSMApGCPVKKKVQRCMEDKNFLMVTYEGQHNHE 212 58*************************99**************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.20.25.80	1.8E-29	146	212	IPR003657	WRKY domain
PROSITE profile	PS50811	26.326	148	214	IPR003657	WRKY domain
SuperFamily	SSF118290	2.22E-25	149	213	IPR003657	WRKY domain
SMART	SM00774	5.3E-35	153	213	IPR003657	WRKY domain
Pfam	PF03106	3.5E-24	154	212	IPR003657	WRKY domain
SuperFamily	SSF64484	0	291	1439	No hit	No description
Gene3D	G3DSA:3.90.1100.10	1.7E-69	299	473	No hit	No description
Pfam	PF04563	3.8E-34	305	693	IPR007644	RNA polymerase, beta subunit, protrusion
CDD	cd00653	0	306	1438	IPR015712	DNA-directed RNA polymerase, subunit 2
Gene3D	G3DSA:3.90.1110.10	1.6E-33	474	646	IPR007642	RNA polymerase Rpb2, domain 2
Pfam	PF04561	1.7E-13	516	657	IPR007642	RNA polymerase Rpb2, domain 2
Gene3D	G3DSA:3.90.1100.10	1.7E-69	647	806	No hit	No description
Pfam	PF04565	1.1E-17	734	795	IPR007645	RNA polymerase Rpb2, domain 3
Pfam	PF04566	1.1E-19	834	895	IPR007646	RNA polymerase Rpb2, domain 4
Pfam	PF04567	2.5E-8	911	958	IPR007647	RNA polymerase Rpb2, domain 5
Gene3D	G3DSA:3.90.1100.10	1.7E-69	961	1049	No hit	No description
Pfam	PF00562	3.8E-96	968	1339	IPR007120	DNA-directed RNA polymerase, subunit 2, domain 6
Gene3D	G3DSA:2.40.270.10	1.2E-46	1050	1065	IPR007120	DNA-directed RNA polymerase, subunit 2, domain 6
Gene3D	G3DSA:2.40.50.150	6.2E-21	1066	1183	IPR014724	RNA polymerase Rpb2, OB-fold
Gene3D	G3DSA:2.40.270.10	1.2E-46	1184	1317	IPR007120	DNA-directed RNA polymerase, subunit 2, domain 6
PROSITE pattern	PS01166	0	1192	1204	IPR007121	RNA polymerase, beta subunit, conserved site
Pfam	PF04560	3.7E-31	1341	1439	IPR007641	RNA polymerase Rpb2, domain 7

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006306	Biological Process	DNA methylation
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0030422	Biological Process	production of siRNA involved in RNA interference
GO:0050776	Biological Process	regulation of immune response
GO:0050832	Biological Process	defense response to fungus
GO:0000418	Cellular Component	DNA-directed RNA polymerase IV complex
GO:0000419	Cellular Component	DNA-directed RNA polymerase V complex
GO:0005720	Cellular Component	nuclear heterochromatin
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0003899	Molecular Function	DNA-directed RNA polymerase activity
GO:0032549	Molecular Function	ribonucleoside binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 1442 aa Download sequence Send to blast
MVAVKTMNVE QKGLFLKTLA DLVLMMSSGL RNPEFKTKRK DQIPFRQPTF MDVPSSVKDK 60 AEGVEAELEQ LQKENAALRL MLQVMRNKYK MLSEAYFRES NSQVPTICRG LTRFDLCEDQ 120 HSHKNILIPQ LQLAANSSQV FVETDPRDES HIVKDGFQWR KYGQKVTKHN PFPRAYFRCS 180 MAPGCPVKKK VQRCMEDKNF LMVTYEGQHN HEVNPSIGQS LSFPSSSATT SISDFGAMGA 240 SPDGKGNVGM GSTSGEKFAN GTDLNMDIDE DDDVFDELVS VQELGEEFLR NFCRKAAVSF 300 FNQYGLISHQ INSYNDFIKY GLQNTFDSFG EFVIHSGYDP SKKGEGDWRH ARVKFGKVTV 360 ERPTFWAVTG GNELNMLPRH ARLQNMTYSS RMKVTVELQV YTAKSVKSDK FKTGREEIVE 420 EEIVHQDNRE IIIGRIPVMV KSELCWMNEV EKSDCDFDHG GYFLIKGAEK IFIAQEQISL 480 KRLWISNIQG WTVAYRSEVK RNRLIIRLVE NSKVEYIKGG EKILTVFFLS IEIPVWILFF 540 ALGVRSDKEV VSLIDYGSSD SSISNILFAS IRDADWKCRN FREESAALNH LDRLRKETRF 600 PPEESVEECL GKYLFPSLKG FKQKARFLGY MVKCLLQAFT GHRKCDNRDD FRNKRLELAG 660 ELLEREMKVH IAHARRRMAK TLQRDLYADR TVRPIEHYLD ASIVTNGLSR AFSTGAWSHP 720 YKKMERISGV VANLGRANPL QTMVDLRKTR QQVQYTGKVG DARYPHPSHW GKVCFLSTPD 780 GENCGLVKNL ATTALVSTNI VKSVVESIVD TLFDSGMEKV VNDTSSSLDG KDKVFLNGEW 840 VGVCEDSLFF AAELRRKRRR RELPYQVEIK RDEHKGEVRI FTDAGRILRP LLVVENLFKL 900 KAFKGKENYA FQPLLDKGIV ELIGAEEEED CRTAWGIRYL LTEVEGKQPV KYTHCELDMS 960 FLLGLSCGII PFANHDHARR VLYQAQKHSQ QAIGFSTTNP NIRVDTLSHQ MYYPQRPLFH 1020 TMTADCLGKS GFPLGQNRLD PKPELYNGQN AIVAVNVHLG YNQEDSLVMN RASIERGMFR 1080 TEHVRSYKAE VDNKEIQEKR RKAEDIVNFG KTESKIGRVD SLDDDGFPYI GASLQSGDIV 1140 IGRFAESGAD HGVKLKHTER GMVQKVVLSS NDDGKNFAVV SLRQVVRSPC LGDKFSSMHG 1200 QKGVLGFLES HENFPFTTQG IVPDIVINPH AFPSRQTPGQ LLEAALGKGI ACGGSKKHAT 1260 PFSTLSIDAI TEQLHRVGFS RWGNERVYNG RTGEMVRSLI FMGPTFYQRL VHMAEDKVKF 1320 RNTGPVHPLT RQPVADRKRY GGIKFGEMER DCLIAHGASA NLHERLFTLS DCSQMHVCQN 1380 CKNVANVIER TVAAGRKIRG PYCRVCQSGD EIVKVSVPYG AKLLCQELFS MGISLKFETQ 1440 LC

Sequence ? help Back to Top

Protein Sequence Length: 1442 aa Download sequence Send to blast

MVAVKTMNVE QKGLFLKTLA DLVLMMSSGL RNPEFKTKRK DQIPFRQPTF MDVPSSVKDK  60
AEGVEAELEQ LQKENAALRL MLQVMRNKYK MLSEAYFRES NSQVPTICRG LTRFDLCEDQ  120
HSHKNILIPQ LQLAANSSQV FVETDPRDES HIVKDGFQWR KYGQKVTKHN PFPRAYFRCS  180
MAPGCPVKKK VQRCMEDKNF LMVTYEGQHN HEVNPSIGQS LSFPSSSATT SISDFGAMGA  240
SPDGKGNVGM GSTSGEKFAN GTDLNMDIDE DDDVFDELVS VQELGEEFLR NFCRKAAVSF  300
FNQYGLISHQ INSYNDFIKY GLQNTFDSFG EFVIHSGYDP SKKGEGDWRH ARVKFGKVTV  360
ERPTFWAVTG GNELNMLPRH ARLQNMTYSS RMKVTVELQV YTAKSVKSDK FKTGREEIVE  420
EEIVHQDNRE IIIGRIPVMV KSELCWMNEV EKSDCDFDHG GYFLIKGAEK IFIAQEQISL  480
KRLWISNIQG WTVAYRSEVK RNRLIIRLVE NSKVEYIKGG EKILTVFFLS IEIPVWILFF  540
ALGVRSDKEV VSLIDYGSSD SSISNILFAS IRDADWKCRN FREESAALNH LDRLRKETRF  600
PPEESVEECL GKYLFPSLKG FKQKARFLGY MVKCLLQAFT GHRKCDNRDD FRNKRLELAG  660
ELLEREMKVH IAHARRRMAK TLQRDLYADR TVRPIEHYLD ASIVTNGLSR AFSTGAWSHP  720
YKKMERISGV VANLGRANPL QTMVDLRKTR QQVQYTGKVG DARYPHPSHW GKVCFLSTPD  780
GENCGLVKNL ATTALVSTNI VKSVVESIVD TLFDSGMEKV VNDTSSSLDG KDKVFLNGEW  840
VGVCEDSLFF AAELRRKRRR RELPYQVEIK RDEHKGEVRI FTDAGRILRP LLVVENLFKL  900
KAFKGKENYA FQPLLDKGIV ELIGAEEEED CRTAWGIRYL LTEVEGKQPV KYTHCELDMS  960
FLLGLSCGII PFANHDHARR VLYQAQKHSQ QAIGFSTTNP NIRVDTLSHQ MYYPQRPLFH  1020
TMTADCLGKS GFPLGQNRLD PKPELYNGQN AIVAVNVHLG YNQEDSLVMN RASIERGMFR  1080
TEHVRSYKAE VDNKEIQEKR RKAEDIVNFG KTESKIGRVD SLDDDGFPYI GASLQSGDIV  1140
IGRFAESGAD HGVKLKHTER GMVQKVVLSS NDDGKNFAVV SLRQVVRSPC LGDKFSSMHG  1200
QKGVLGFLES HENFPFTTQG IVPDIVINPH AFPSRQTPGQ LLEAALGKGI ACGGSKKHAT  1260
PFSTLSIDAI TEQLHRVGFS RWGNERVYNG RTGEMVRSLI FMGPTFYQRL VHMAEDKVKF  1320
RNTGPVHPLT RQPVADRKRY GGIKFGEMER DCLIAHGASA NLHERLFTLS DCSQMHVCQN  1380
CKNVANVIER TVAAGRKIRG PYCRVCQSGD EIVKVSVPYG AKLLCQELFS MGISLKFETQ  1440
LC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ip7_B	0.0	299	1439	35	1217	DNA-directed RNA polymerase II subunit RPB2
5ip9_B	0.0	299	1439	35	1217	DNA-directed RNA polymerase II subunit RPB2
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	854	860	RRKRRRR
2	854	861	RRKRRRRE
3	855	859	RKRRR

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Ghi.6556	0.0	boll

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	31406754	0.0

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Mostly expressed in seedlings, flowers and roots, present ubiquitously, except in sperm cells. {ECO:0000269\|PubMed:15766525, ECO:0000269\|PubMed:18667720}.

Functional Description ? help Back to Top
Source	Description
UniProt	DNA-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
GenBank	KM438465	0.0	KM438465.1 Gossypium aridum WRKY52 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017608025.1	0.0	PREDICTED: DNA-directed RNA polymerase D subunit 2b-like
Swissprot	Q9LK40	0.0	NRPD2_ARATH; DNA-directed RNA polymerases IV and V subunit 2
TrEMBL	A0A0B0MV80	0.0	A0A0B0MV80_GOSAR; DNA-directed RNA polymerase subunit beta
STRING	Gorai.001G037900.1	0.0	(Gossypium raimondii)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G31800.1	7e-31	WRKY DNA-binding protein 18

Publications ? help Back to Top
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] 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] 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] Kanno T, et al. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat. Genet., 2005. 37(7): p. 761-5 [PMID:15924141] 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] 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] 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] 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] 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] 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] Li CF, et al. Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana. PLoS Genet., 2008. 4(2): p. e27 [PMID:18266474] 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] 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] 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] 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] 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] 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] 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] Ito H, et al. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature, 2011. 472(7341): p. 115-9 [PMID:21399627] 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] 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] Lee EK, et al. A functional phylogenomic view of the seed plants. PLoS Genet., 2011. 7(12): p. e1002411 [PMID:22194700] 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] 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] 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] 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] 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]