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

484073

Common Name

ARALYDRAFT_484073

Organism

Arabidopsis lyrata

Taxonomic ID

81972

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: 581aa MW: 63480.7 Da PI: 5.7866

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
484073	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	445.4	3.9e-136	214	574	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykal.ppsetseknsseelaalklfsevsPilkfshltaNqaI 102 lv++L++cAea+++++l+la+al++++ la +++ +m+++a+yf+eALa+r++r l pp+++ +++ s++l++ f+e++P+lkf+h+taNqaI 484073 214 LVHALMACAEAIQQNNLTLAEALVKQIGCLAVSQAGAMRKVATYFAEALARRIYR--------LsPPQNQIDHSLSDTLQM--HFYETCPYLKFAHFTANQAI 306 689**************************************************........414444444445555444..4*************** PP GRAS 103 leavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkp..gEala 203 lea+eg++rvH+iDf+++qGlQWpaL+qaLa R++gpp++R+Tg+g+p++++++ l+ +g rLa++Ae ++v+fe++ +va++l+dl+ ++L+++p Ea+a 484073 307 LEAFEGKKRVHVIDFSMNQGLQWPALMQALALREGGPPTFRLTGIGPPAPDNSDHLHDVGCRLAQLAEVIHVEFEYRGFVANSLADLDASMLELRPseTEAVA 409 *******************************************************************************************9999 PP GRAS 204 VnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerr 306 Vn+v++lh+ll +++ +e+ vL +vk+++P +++vveqe++hn++ Fl+rf+e+l+yys+lfdsle s++++++++++lg++i+n+vaceg +r+ 484073 410 VNSVFELHKLLGRPGGIEK----VLGVVKQIKPVIFTVVEQESNHNGPVFLDRFTESLHYYSTLFDSLEGV---PSSQDKVMSEVYLGKQICNLVACEGPDRV 505 ***********9999....*****************************************998...69999******************** PP GRAS 307 erhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374 erhetl++W +r++++GF p++l+++a kqa++ll+ ++ ++gyrvee++g+l+lgW++rpL+++SaW+ 484073 506 ERHETLSQWGNRFGSSGFAPANLGSNAFKQASMLLSVYNsGQGYRVEENNGCLMLGWHTRPLITTSAWK 574 ******************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF12041	2.5E-35	41	108	IPR021914	Transcriptional factor DELLA, N-terminal
SMART	SM01129	1.5E-40	41	114	No hit	No description
PROSITE profile	PS50985	66.113	188	553	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.3E-133	214	574	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: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:0010218	Biological Process	response to far red light
GO:0042176	Biological Process	regulation of protein catabolic process
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:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 581 aa Download sequence Send to blast
MKRDLHQFQG RLSNHGTSSS SSSKDKMMMV KKEEDGGNMD DELLAVLGYK VRSSEMAEVA 60 LKLEQLETMM GNVQEDGLSH LATDTVHYNP SELYSWLDNM LSDLNPPPPR SNGLDPILPS 120 PEIGGFPASD YDLKAIPGNA IYHQNQFPAI DSSSSSNNQS KRLKSCSSPD SMVTSTSTAT 180 QIGGVIGTTV TTTTAAESTR SVILVDSQEN GVRLVHALMA CAEAIQQNNL TLAEALVKQI 240 GCLAVSQAGA MRKVATYFAE ALARRIYRLS PPQNQIDHSL SDTLQMHFYE TCPYLKFAHF 300 TANQAILEAF EGKKRVHVID FSMNQGLQWP ALMQALALRE GGPPTFRLTG IGPPAPDNSD 360 HLHDVGCRLA QLAEVIHVEF EYRGFVANSL ADLDASMLEL RPSETEAVAV NSVFELHKLL 420 GRPGGIEKVL GVVKQIKPVI FTVVEQESNH NGPVFLDRFT ESLHYYSTLF DSLEGVPSSQ 480 DKVMSEVYLG KQICNLVACE GPDRVERHET LSQWGNRFGS SGFAPANLGS NAFKQASMLL 540 SVYNSGQGYR VEENNGCLML GWHTRPLITT SAWKLSTAAH *

Sequence ? help Back to Top

Protein Sequence Length: 581 aa Download sequence Send to blast

MKRDLHQFQG RLSNHGTSSS SSSKDKMMMV KKEEDGGNMD DELLAVLGYK VRSSEMAEVA  60
LKLEQLETMM GNVQEDGLSH LATDTVHYNP SELYSWLDNM LSDLNPPPPR SNGLDPILPS  120
PEIGGFPASD YDLKAIPGNA IYHQNQFPAI DSSSSSNNQS KRLKSCSSPD SMVTSTSTAT  180
QIGGVIGTTV TTTTAAESTR SVILVDSQEN GVRLVHALMA CAEAIQQNNL TLAEALVKQI  240
GCLAVSQAGA MRKVATYFAE ALARRIYRLS PPQNQIDHSL SDTLQMHFYE TCPYLKFAHF  300
TANQAILEAF EGKKRVHVID FSMNQGLQWP ALMQALALRE GGPPTFRLTG IGPPAPDNSD  360
HLHDVGCRLA QLAEVIHVEF EYRGFVANSL ADLDASMLEL RPSETEAVAV NSVFELHKLL  420
GRPGGIEKVL GVVKQIKPVI FTVVEQESNH NGPVFLDRFT ESLHYYSTLF DSLEGVPSSQ  480
DKVMSEVYLG KQICNLVACE GPDRVERHET LSQWGNRFGS SGFAPANLGS NAFKQASMLL  540
SVYNSGQGYR VEENNGCLML GWHTRPLITT SAWKLSTAAH *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	3e-63	209	573	14	378	Protein SCARECROW
5b3h_A	3e-63	209	573	13	377	Protein SCARECROW
5b3h_D	3e-63	209	573	13	377	Protein SCARECROW
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. Probably acts by participating in large multiprotein complexes that repress transcription of GA-inducible genes. Positively regulates XERICO expression in seeds. Upon GA application, it is degraded by the proteasome, allowing the GA signaling pathway. Compared to other DELLA proteins, it is the most sensitive to GA application. No effect of the BOI proteins on its stability. Its activity is probably regulated by other phytohormones such as auxin and ethylene, attenuation of auxin transport delaying its GA-induced degradation. {ECO:0000269\|PubMed:11606551, ECO:0000269\|PubMed:11606552, ECO:0000269\|PubMed:12610625, ECO:0000269\|PubMed:14615596, ECO:0000269\|PubMed:14973286, ECO:0000269\|PubMed:15128937, ECO:0000269\|PubMed:16034591, ECO:0000269\|PubMed:17933900, ECO:0000269\|PubMed:20093430, ECO:0000269\|PubMed:9490740}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00611	ChIP-seq	Transfer from AT2G01570	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	484073

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	GQ177725	0.0	GQ177725.1 Arabidopsis thaliana ecotype Ll-0 RGA gene, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_020880046.1	0.0	DELLA protein RGA isoform X1
Swissprot	Q9SLH3	0.0	RGA_ARATH; DELLA protein RGA
TrEMBL	D7LLT1	0.0	D7LLT1_ARALL; RGA1 protein
STRING	fgenesh2_kg.5__65__AT2G01570.1	0.0	(Arabidopsis lyrata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM837	28	121

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G01570.1	0.0	GRAS family protein

Link Out ? help Back to Top
Phytozome	484073
Entrez Gene	9312828

Publications ? help Back to Top
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] Stewart Lilley JL,Gan Y,Graham IA,Nemhauser JL The effects of DELLAs on growth change with developmental stage and brassinosteroid levels. Plant J., 2013. 76(1): p. 165-73 [PMID:23834248] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Oh E, et al. Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. Elife, 2015. [PMID:24867218] Gallego-Giraldo C, et al. Role of the gibberellin receptors GID1 during fruit-set in Arabidopsis. Plant J., 2014. 79(6): p. 1020-1032 [PMID:24961590] Fukazawa J, et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. Plant Cell, 2014. 26(7): p. 2920-38 [PMID:25035403] Tan L,Rong W,Luo H,Chen Y,He C The Xanthomonas campestris effector protein XopDXcc8004 triggers plant disease tolerance by targeting DELLA proteins. New Phytol., 2014. 204(3): p. 595-608 [PMID:25040905] Urano D,Dong T,Bennetzen JL,Jones AM Adaptive evolution of signaling partners. Mol. Biol. Evol., 2015. 32(4): p. 998-1007 [PMID:25568345] Montenegro-Johnson TD, et al. Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas. Plant Cell, 2015. 27(4): p. 1018-33 [PMID:25901089] Kim SI, et al. E3 SUMO ligase AtSIZ1 positively regulates SLY1-mediated GA signalling and plant development. Biochem. J., 2015. 469(2): p. 299-314 [PMID:26008766] Marín-de la Rosa N, et al. Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins. PLoS Genet., 2015. 11(7): p. e1005337 [PMID:26134422] Xu F, et al. DELLA proteins physically interact with CONSTANS to regulate flowering under long days in Arabidopsis. FEBS Lett., 2016. 590(4): p. 541-9 [PMID:26801684] Moubayidin L, et al. A SCARECROW-based regulatory circuit controls Arabidopsis thaliana meristem size from the root endodermis. Planta, 2016. 243(5): p. 1159-68 [PMID:26848984] Xie Y,Tan H,Ma Z,Huang J DELLA Proteins Promote Anthocyanin Biosynthesis via Sequestering MYBL2 and JAZ Suppressors of the MYB/bHLH/WD40 Complex in Arabidopsis thaliana. Mol Plant, 2016. 9(5): p. 711-721 [PMID:26854848] 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] Lee SA, et al. Interplay between ABA and GA Modulates the Timing of Asymmetric Cell Divisions in the Arabidopsis Root Ground Tissue. Mol Plant, 2016. 9(6): p. 870-84 [PMID:26970019] Liu B,De Storme N,Geelen D Gibberellin Induces Diploid Pollen Formation by Interfering with Meiotic Cytokinesis. Plant Physiol., 2017. 173(1): p. 338-353 [PMID:27621423] Jiang K, et al. Substituted Phthalimide AC94377 Is a Selective Agonist of the Gibberellin Receptor GID1. Plant Physiol., 2017. 173(1): p. 825-835 [PMID:27899534] Matsuoka K, et al. Differential Cellular Control by Cotyledon-Derived Phytohormones Involved in Graft Reunion of Arabidopsis Hypocotyls. Plant Cell Physiol., 2016. 57(12): p. 2620-2631 [PMID:27986917] Zhang Y, et al. GA-DELLA pathway is involved in regulation of nitrogen deficiency-induced anthocyanin accumulation. Plant Cell Rep., 2017. 36(4): p. 557-569 [PMID:28275852] Zheng H, et al. MLK1 and MLK2 Coordinate RGA and CCA1 Activity to Regulate Hypocotyl Elongation in Arabidopsis thaliana. Plant Cell, 2018. 30(1): p. 67-82 [PMID:29255112] Yamazaki K, et al. Suppression of DELLA signaling induces procambial cell formation in culture. Plant J., 2018. 94(1): p. 48-59 [PMID:29383774] Liu B,De Storme N,Geelen D Cold-Induced Male Meiotic Restitution in Arabidopsis thaliana Is Not Mediated by GA-DELLA Signaling. Front Plant Sci, 2018. 9: p. 91 [PMID:29459879] Kumar A,Singh A,Panigrahy M,Sahoo PK,Panigrahi KCS Carbon nanoparticles influence photomorphogenesis and flowering time in Arabidopsis thaliana. Plant Cell Rep., 2018. 37(6): p. 901-912 [PMID:29541883] Zhang Y, et al. DELLA proteins negatively regulate dark-induced senescence and chlorophyll degradation in Arabidopsis through interaction with the transcription factor WRKY6. Plant Cell Rep., 2018. 37(7): p. 981-992 [PMID:29574486]