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

AT4G39410.1

Common Name

ATWRKY13, F23K16.40, WRKY13

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

WRKY

Protein Properties

Length: 304aa MW: 34203.6 Da PI: 7.5969

Description

WRKY DNA-binding protein 13

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G39410.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	WRKY	101.9	3.6e-32	222	280	1	59
---SS-EEEEEEE--TT-SS-EEEEEE-STT---EEEEEE-SSSTTEEEEEEES--SS- CS WRKY 1 ldDgynWrKYGqKevkgsefprsYYrCtsagCpvkkkversaedpkvveitYegeHnhe 59 ldDgy+WrKYGqK+vk++++prsYYrCt+ +C+vkk+ver a+dp++v++tYeg+H h+ AT4G39410.1 222 LDDGYRWRKYGQKVVKNTQHPRSYYRCTQDKCRVKKRVERLADDPRMVITTYEGRHLHS 280 59*******************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.20.25.80	1.6E-33	207	280	IPR003657	WRKY domain
SuperFamily	SSF118290	2.88E-28	215	281	IPR003657	WRKY domain
PROSITE profile	PS50811	29.344	217	282	IPR003657	WRKY domain
SMART	SM00774	9.9E-37	222	281	IPR003657	WRKY domain
Pfam	PF03106	4.1E-25	223	279	IPR003657	WRKY domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:1901141	Biological Process	regulation of lignin biosynthetic process
GO:1904369	Biological Process	positive regulation of sclerenchyma cell differentiation
GO:0005634	Cellular Component	nucleus
GO:0001046	Molecular Function	core promoter sequence-specific DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 304 aa Download sequence Send to blast
MGAINQGISL FDESQTVINP INTNHLGFFF SFPSHSTLSS SSSSSSSSPS SLVSPFLGHN 60 SLNSFLHNNP SSFISHPQDS INLMTNLPET LISSLSSSKQ RDDHDGFLNL DHHRLTGSIS 120 SQRPLSNPWA WSCQAGYGSS QKNNHGSEID VDDNDDEVGD GGGINDDDNG RHHHHDTPSR 180 HDKHNTASLG VVSSLKMKKL KTRRKVREPR FCFKTLSEVD VLDDGYRWRK YGQKVVKNTQ 240 HPRSYYRCTQ DKCRVKKRVE RLADDPRMVI TTYEGRHLHS PSNHLDDDSL STSHLHPPLS 300 NFFW

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1wj2_A	3e-25	214	279	9	74	Probable WRKY transcription factor 4
2lex_A	3e-25	214	279	9	74	Probable WRKY transcription factor 4
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	30692349	0.0
Genevisible	252891_at	0.0
Expression Atlas	AT4G39410	-
AtGenExpress	AT4G39410	-
ATTED-II	AT4G39410	-

Functional Description ? help Back to Top
Source	Description
TAIR	member of WRKY Transcription Factor; Group II-c
UniProt	Transcription factor. Interacts specifically with the W box (5'-(T)TGAC[CT]-3'), a frequently occurring elicitor-responsive cis-acting element (By similarity). {ECO:0000250}.

Function -- GeneRIF ? help Back to Top
WRKY13 acts in stem development. Mutants take on a weaker stem phenotype. The number of sclerenchyma cells, stem diameter and the number of vascular bundles were reduced in wrky13 mutants. Lignin-synthesis-related genes were repressed in wrky13 mutants. [PMID: 26025534] WRKY12 and WRKY13 oppositely modulate flowering time under SD conditions [PMID: 27592586]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G39410.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G39410

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF421153	0.0	AF421153.1 Arabidopsis thaliana WRKY transcription factor 13 (WRKY13) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_195651.1	0.0	WRKY DNA-binding protein 13
Swissprot	Q9SVB7	0.0	WRK13_ARATH; Probable WRKY transcription factor 13
TrEMBL	A0A384L728	0.0	A0A384L728_ARATH; WRKY13
TrEMBL	C0SVM6	0.0	C0SVM6_ARATH; Uncharacterized protein At4g39410 (Fragment)
STRING	AT4G39410.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6106	27	46
Representative plant	OGRP14	17	875

Link Out ? help Back to Top
Phytozome	AT4G39410.1
Entrez Gene	830096
iHOP	AT4G39410
wikigenes	AT4G39410

Publications ? help Back to Top
Eulgem T,Rushton PJ,Robatzek S,Somssich IE The WRKY superfamily of plant transcription factors. Trends Plant Sci., 2000. 5(5): p. 199-206 [PMID:10785665] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Folta KM,Pontin MA,Karlin-Neumann G,Bottini R,Spalding EP Genomic and physiological studies of early cryptochrome 1 action demonstrate roles for auxin and gibberellin in the control of hypocotyl growth by blue light. Plant J., 2003. 36(2): p. 203-14 [PMID:14535885] Dal Bosco C, et al. Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. J. Biol. Chem., 2004. 279(2): p. 1060-9 [PMID:14576160] Hass C, et al. The response regulator 2 mediates ethylene signalling and hormone signal integration in Arabidopsis. EMBO J., 2004. 23(16): p. 3290-302 [PMID:15282545] Miao Y,Laun T,Zimmermann P,Zentgraf U Targets of the WRKY53 transcription factor and its role during leaf senescence in Arabidopsis. Plant Mol. Biol., 2004. 55(6): p. 853-67 [PMID:15604721] Zhao Z,Zhu Y,Erhardt M,Ruan Y,Shen WH A non-canonical transferred DNA insertion at the BRI1 locus in Arabidopsis thaliana. J Integr Plant Biol, 2009. 51(4): p. 367-73 [PMID:19341406] Li W,Tian Z,Yu D WRKY13 acts in stem development in Arabidopsis thaliana. Plant Sci., 2015. 236: p. 205-13 [PMID:26025534] Li W,Wang H,Yu D Arabidopsis WRKY Transcription Factors WRKY12 and WRKY13 Oppositely Regulate Flowering under Short-Day Conditions. Mol Plant, 2016. 9(11): p. 1492-1503 [PMID:27592586]