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

AT5G17490.1

Common Name

AtRGL3, K3M16.60, RGL3

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

GRAS

Protein Properties

Length: 523aa MW: 57326.7 Da PI: 4.4947

Description

RGA-like protein 3

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G17490.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	433	2.3e-132	157	516	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlta 98 lv++L++cAeav+ ++l+la+al++r+ la++++ +m ++a+yf+eALa+r++r ++ps+++ + s ee+ f++ +P+lkf+h+ta AT5G17490.1 157 LVQALVACAEAVQLENLSLADALVKRVGLLAASQAGAMGKVATYFAEALARRIYR--------IHPSAAAIDPSFEEILQ-MNFYDSCPYLKFAHFTA 245 689**************************************************........55555554445555444.46*********** PP GRAS 99 NqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrv 196 NqaIleav +++ vH+iD++++qG+QWpaL+qaLa Rp+gpps+R+Tgvg+p+ ++e ++e+g++La++A+++gv+f+fn l+++rl+dle++++++ AT5G17490.1 246 NQAILEAVTTSRVVHVIDLGLNQGMQWPALMQALALRPGGPPSFRLTGVGNPS--NREGIQELGWKLAQLAQAIGVEFKFNGLTTERLSDLEPDMFET 341 ***********************************************88..9**************************************** PP GRAS 197 kp.gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgre 293 ++ E+l+Vn+v++lh +l++++s+e+ +L +vk ++P +v+vveqea+hn+ Fl+rf eal+yys+lfdsle ++ s++r+ +++++lgr+ AT5G17490.1 342 RTeSETLVVNSVFELHPVLSQPGSIEK----LLATVKAVKPGLVTVVEQEANHNGDVFLDRFNEALHYYSSLFDSLEDGVVIPSQDRV-MSEVYLGRQ 434 99*********************....********************************************988888776.56677 PP GRAS 294 ivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374 i n+va+eg++r+erhetl++Wr+r+++aGF pv+l+++a kqa+lll+ + +dgyrvee++gsl+l W+++pL+++SaW+ AT5G17490.1 435 ILNLVATEGSDRIERHETLAQWRKRMGSAGFDPVNLGSDAFKQASLLLALSGgGDGYRVEENDGSLMLAWQTKPLIAASAWK 516 *******************************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF12041	1.1E-32	34	100	IPR021914	Transcriptional factor DELLA, N-terminal
SMART	SM01129	2.0E-41	34	106	No hit	No description
PROSITE profile	PS50985	64.222	131	495	IPR005202	Transcription factor GRAS
Pfam	PF03514	8.1E-130	157	516	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009723	Biological Process	response to ethylene
GO:0009737	Biological Process	response to abscisic acid
GO:0009739	Biological Process	response to gibberellin
GO:0009863	Biological Process	salicylic acid mediated signaling pathway
GO:0009867	Biological Process	jasmonic acid mediated signaling pathway
GO:0009938	Biological Process	negative regulation of gibberellic acid mediated signaling pathway
GO:0010187	Biological Process	negative regulation of seed germination
GO:0042538	Biological Process	hyperosmotic salinity response
GO:2000033	Biological Process	regulation of seed dormancy process
GO:2000377	Biological Process	regulation of reactive oxygen species metabolic process
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000293	anatomy	guard cell
PO:0009005	anatomy	root
PO:0009009	anatomy	plant embryo
PO:0009030	anatomy	carpel
PO:0009032	anatomy	petal
PO:0009049	anatomy	inflorescence
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 523 aa Download sequence Send to blast
MKRSHQETSV EEEAPSMVEK LENGCGGGGD DNMDEFLAVL GYKVRSSDMA DVAQKLEQLE 60 MVLSNDIASS SNAFNDTVHY NPSDLSGWAQ SMLSDLNYYP DLDPNRICDL RPITDDDECC 120 SSNSNSNKRI RLGPWCDSVT SESTRSVVLI EETGVRLVQA LVACAEAVQL ENLSLADALV 180 KRVGLLAASQ AGAMGKVATY FAEALARRIY RIHPSAAAID PSFEEILQMN FYDSCPYLKF 240 AHFTANQAIL EAVTTSRVVH VIDLGLNQGM QWPALMQALA LRPGGPPSFR LTGVGNPSNR 300 EGIQELGWKL AQLAQAIGVE FKFNGLTTER LSDLEPDMFE TRTESETLVV NSVFELHPVL 360 SQPGSIEKLL ATVKAVKPGL VTVVEQEANH NGDVFLDRFN EALHYYSSLF DSLEDGVVIP 420 SQDRVMSEVY LGRQILNLVA TEGSDRIERH ETLAQWRKRM GSAGFDPVNL GSDAFKQASL 480 LLALSGGGDG YRVEENDGSL MLAWQTKPLI AASAWKLAAE LRR

Sequence ? help Back to Top

Protein Sequence Length: 523 aa Download sequence Send to blast

MKRSHQETSV EEEAPSMVEK LENGCGGGGD DNMDEFLAVL GYKVRSSDMA DVAQKLEQLE  60
MVLSNDIASS SNAFNDTVHY NPSDLSGWAQ SMLSDLNYYP DLDPNRICDL RPITDDDECC  120
SSNSNSNKRI RLGPWCDSVT SESTRSVVLI EETGVRLVQA LVACAEAVQL ENLSLADALV  180
KRVGLLAASQ AGAMGKVATY FAEALARRIY RIHPSAAAID PSFEEILQMN FYDSCPYLKF  240
AHFTANQAIL EAVTTSRVVH VIDLGLNQGM QWPALMQALA LRPGGPPSFR LTGVGNPSNR  300
EGIQELGWKL AQLAQAIGVE FKFNGLTTER LSDLEPDMFE TRTESETLVV NSVFELHPVL  360
SQPGSIEKLL ATVKAVKPGL VTVVEQEANH NGDVFLDRFN EALHYYSSLF DSLEDGVVIP  420
SQDRVMSEVY LGRQILNLVA TEGSDRIERH ETLAQWRKRM GSAGFDPVNL GSDAFKQASL  480
LLALSGGGDG YRVEENDGSL MLAWQTKPLI AASAWKLAAE LRR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	6e-61	151	515	13	378	Protein SCARECROW
5b3h_A	5e-61	151	515	12	377	Protein SCARECROW
5b3h_D	5e-61	151	515	12	377	Protein SCARECROW
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	246432_at	0.0
Expression Atlas	AT5G17490	-
AtGenExpress	AT5G17490	-
ATTED-II	AT5G17490	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed at very low level. Mainly expressed in germinating seeds and flowers and siliques. Not expressed in other tissues. {ECO:0000269\|PubMed:11826301}.

Functional Description ? help Back to Top
Source	Description
TAIR	DELLA subfamily member involved in GA signal transduction
UniProt	Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. No effect of the BOI proteins on its stability. Probably acts by participating in large multiprotein complexes that repress transcription of GA-inducible genes. Its activity may be regulated by phytohormones such as auxin and ethylene (By similarity). {ECO:0000250, ECO:0000269\|PubMed:12610625, ECO:0000269\|PubMed:14615596}.

Function -- GeneRIF ? help Back to Top
Data documented that Lys-29 of ubiquitin is the major site for ubiquitin chain formation to mediate DELLA protein degradation that also required protein Ser/Thr dephosphorylation activity. The LZ domain is essential for both their stability and activity. [PMID: 19717618] MYC2 regulates RGL3 expression through a direct association with its promotor. RGL3 positively regulates jasmonate-mediated disease resistance. [PMID: 22892320] PIF3 lies downstream of PHYB and RGL3, and plays an important role in the inhibitory effect of NO on root growth of Arabidopsis seedlings in light. [PMID: 24157606]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G17490.1

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G12610 (A), AT4G25470 (A), AT4G25480 (A), AT4G25490 (A)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	gibberellin

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT5G54230, AT5G66730, AT1G09530, AT1G10585, AT1G32640, AT1G53170, AT1G75080

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Rga, gai, rgl1, rgl2 and rgl3 pentuple mutant displays constitutive GA responses even in the absence of GA treatment. {ECO:0000269\|PubMed:23482857}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G17490

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK117226	0.0	AK117226.1 Arabidopsis thaliana At5g17490 mRNA for RGA-like protein, complete cds, clone: RAFL16-78-A02.
GenBank	AL391150	0.0	AL391150.1 Arabidopsis thaliana DNA chromosome 5, BAC clone K3M16 (ESSA project).
GenBank	BT005905	0.0	BT005905.1 Arabidopsis thaliana At5g17490 gene, complete cds.
GenBank	CP002688	0.0	CP002688.1 Arabidopsis thaliana chromosome 5 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_197251.1	0.0	RGA-like protein 3
Swissprot	Q9LF53	0.0	RGL3_ARATH; DELLA protein RGL3
TrEMBL	A0A178UG12	0.0	A0A178UG12_ARATH; RGL3
STRING	AT5G17490.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM837	28	121
Representative plant	OGRP1251	15	50

Link Out ? help Back to Top
Phytozome	AT5G17490.1
Entrez Gene	831615
iHOP	AT5G17490
wikigenes	AT5G17490

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Dill A,Sun T Synergistic derepression of gibberellin signaling by removing RGA and GAI function in Arabidopsis thaliana. Genetics, 2001. 159(2): p. 777-85 [PMID:11606552] Wen CK,Chang C Arabidopsis RGL1 encodes a negative regulator of gibberellin responses. Plant Cell, 2002. 14(1): p. 87-100 [PMID:11826301] Lee S, et al. Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition. Genes Dev., 2002. 16(5): p. 646-58 [PMID:11877383] Seki M, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science, 2002. 296(5565): p. 141-5 [PMID:11910074] Fu X,Harberd NP Auxin promotes Arabidopsis root growth by modulating gibberellin response. Nature, 2003. 421(6924): p. 740-3 [PMID:12610625] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Achard P,Vriezen WH,Van Der Straeten D,Harberd NP Ethylene regulates arabidopsis development via the modulation of DELLA protein growth repressor function. Plant Cell, 2003. 15(12): p. 2816-25 [PMID:14615596] Tyler L, et al. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol., 2004. 135(2): p. 1008-19 [PMID:15173565] 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] Nakajima M, et al. Identification and characterization of Arabidopsis gibberellin receptors. Plant J., 2006. 46(5): p. 880-9 [PMID:16709201] Penfield S,Gilday AD,Halliday KJ,Graham IA DELLA-mediated cotyledon expansion breaks coat-imposed seed dormancy. Curr. Biol., 2006. 16(23): p. 2366-70 [PMID:17141619] Al-Samarrai TH,Kirk CA,Jones WT,Harvey D,Sun X Expression in Escherichia coli and in vitro refolding of the plant transcription factor Arabidopsis thaliana RGL3. Protein Expr. Purif., 2007. 53(2): p. 289-92 [PMID:17317218] Hussain A,Cao D,Peng J Identification of conserved tyrosine residues important for gibberellin sensitivity of Arabidopsis RGL2 protein. Planta, 2007. 226(2): p. 475-83 [PMID:17333251] Feng S, et al. Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature, 2008. 451(7177): p. 475-9 [PMID:18216856] Bassel GW, et al. Elucidating the germination transcriptional program using small molecules. Plant Physiol., 2008. 147(1): p. 143-55 [PMID:18359847] Magome H,Yamaguchi S,Hanada A,Kamiya Y,Oda K The DDF1 transcriptional activator upregulates expression of a gibberellin-deactivating gene, GA2ox7, under high-salinity stress in Arabidopsis. Plant J., 2008. 56(4): p. 613-26 [PMID:18643985] Achard P, et al. The cold-inducible CBF1 factor-dependent signaling pathway modulates the accumulation of the growth-repressing DELLA proteins via its effect on gibberellin metabolism. Plant Cell, 2008. 20(8): p. 2117-29 [PMID:18757556] Wang F, et al. Biochemical insights on degradation of Arabidopsis DELLA proteins gained from a cell-free assay system. Plant Cell, 2009. 21(8): p. 2378-90 [PMID:19717618] Josse EM, et al. A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling. Plant Cell, 2011. 23(4): p. 1337-51 [PMID:21478445] Siddiqua M,Nassuth A Vitis CBF1 and Vitis CBF4 differ in their effect on Arabidopsis abiotic stress tolerance, development and gene expression. Plant Cell Environ., 2011. 34(8): p. 1345-59 [PMID:21486303] Feurtado JA, et al. The Arabidopsis C2H2 zinc finger INDETERMINATE DOMAIN1/ENHYDROUS promotes the transition to germination by regulating light and hormonal signaling during seed maturation. Plant Cell, 2011. 23(5): p. 1772-94 [PMID:21571950] Li KL, et al. GsGASA1 mediated root growth inhibition in response to chronic cold stress is marked by the accumulation of DELLAs. J. Plant Physiol., 2011. 168(18): p. 2153-60 [PMID:21855169] Dutilleul C, et al. Phytosphingosine-phosphate is a signal for AtMPK6 activation and Arabidopsis response to chilling. New Phytol., 2012. 194(1): p. 181-91 [PMID:22236066] Hong GJ,Xue XY,Mao YB,Wang LJ,Chen XY Arabidopsis MYC2 interacts with DELLA proteins in regulating sesquiterpene synthase gene expression. Plant Cell, 2012. 24(6): p. 2635-48 [PMID:22669881] Wild M, et al. The Arabidopsis DELLA RGA-LIKE3 is a direct target of MYC2 and modulates jasmonate signaling responses. Plant Cell, 2012. 24(8): p. 3307-19 [PMID:22892320] Li QF, et al. An interaction between BZR1 and DELLAs mediates direct signaling crosstalk between brassinosteroids and gibberellins in Arabidopsis. Sci Signal, 2012. 5(244): p. ra72 [PMID:23033541] Wild M,Achard P The DELLA protein RGL3 positively contributes to jasmonate/ethylene defense responses. Plant Signal Behav, 2013. 8(4): p. e23891 [PMID:23425858] Park J,Nguyen KT,Park E,Jeon JS,Choi G DELLA proteins and their interacting RING Finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis. Plant Cell, 2013. 25(3): p. 927-43 [PMID:23482857] Vaistij FE, et al. Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA. Proc. Natl. Acad. Sci. U.S.A., 2013. 110(26): p. 10866-71 [PMID:23754415] Sarnowska EA, et al. DELLA-interacting SWI3C core subunit of switch/sucrose nonfermenting chromatin remodeling complex modulates gibberellin responses and hormonal cross talk in Arabidopsis. Plant Physiol., 2013. 163(1): p. 305-17 [PMID:23893173] Luo J, et al. A DELLA gene, RhGAI1, is a direct target of EIN3 and mediates ethylene-regulated rose petal cell expansion via repressing the expression of RhCesA2. J. Exp. Bot., 2013. 64(16): p. 5075-84 [PMID:24014864] Bai S, et al. PIF3 is involved in the primary root growth inhibition of Arabidopsis induced by nitric oxide in the light. Mol Plant, 2014. 7(4): p. 616-25 [PMID:24157606] Lumba S, et al. A mesoscale abscisic acid hormone interactome reveals a dynamic signaling landscape in Arabidopsis. Dev. Cell, 2014. 29(3): p. 360-72 [PMID:24823379] Davi Class I TCP-DELLA interactions in inflorescence shoot apex determine plant height. Curr. Biol., 2014. 24(16): p. 1923-8 [PMID:25127215] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Shi H,Wei Y,Wang Q,Reiter RJ,He C Melatonin mediates the stabilization of DELLA proteins to repress the floral transition in Arabidopsis. J. Pineal Res., 2016. 60(3): p. 373-9 [PMID:26887824] Shi H,Liu W,Wei Y,Ye T Integration of auxin/indole-3-acetic acid 17 and RGA-LIKE3 confers salt stress resistance through stabilization by nitric oxide in Arabidopsis. J. Exp. Bot., 2017. 68(5): p. 1239-1249 [PMID:28158805] Huang KC,Lin WC,Cheng WH Salt hypersensitive mutant 9, a nucleolar APUM23 protein, is essential for salt sensitivity in association with the ABA signaling pathway in Arabidopsis. BMC Plant Biol., 2018. 18(1): p. 40 [PMID:29490615]