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

Csa04g002660.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

GRAS

Protein Properties

Length: 616aa MW: 66955.7 Da PI: 5.3348

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa04g002660.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	441.1	7.8e-135	249	609	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykal.ppsetseknsseelaalklfsevsPilkfs 94 lv++L++cAeav++++l+ a+al++++ la +++ +m+++a+yf+eALa+r++r l pp+++ +++ s++l++ f+e++P+lkf+ Csa04g002660.1 249 LVHALMACAEAVQQNNLTIAEALVKQIGCLAVSQAGAMRKVATYFAEALARRIYR--------LsPPQNQIDHSLSDTLQM--HFYETCPYLKFA 333 689**************************************************........414444444445555444..4******* PP GRAS 95 hltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledl 189 h+taNqaIlea++g++rvH+iDf+++qGlQWpaL+qaLa R++gpp +R+Tg+g+p+++++++l+e+g +La++Ae+++v+fe++ +va++l+dl Csa04g002660.1 334 HFTANQAILEAFQGKKRVHVIDFSMNQGLQWPALMQALALREGGPPIFRLTGIGPPAPDNSDQLHEVGCKLAQLAEAIHVEFEYRGFVANSLADL 428 ******************************************************************************************* PP GRAS 190 eleeLrvkp..gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseer 282 + ++L+++p E++aVn+v++lh+ll +++ +e+ vL +vk+++P +++vveqe++hn++ Fl+rf+e+l+yys+lfdsle s+++ Csa04g002660.1 429 DASMLELRPseIESVAVNSVFELHKLLGRPGGIEK----VLGVVKQIKPVIFTVVEQESNHNGPVFLDRFTESLHYYSTLFDSLEGV---PSSQD 516 ****98889**************9999....*****************************************998...69999 PP GRAS 283 ikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374 +++++++lg++i+n+vaceg +r+erhetl++W r++++GF p++l+++a kqa++ll+ ++ ++gyrvee++g+l+lgW++rpL+++SaW+ Csa04g002660.1 517 KVMSEVYLGKQICNLVACEGPDRVERHETLSQWGYRFGSSGFAPAHLGSNAFKQASMLLSVFNsGQGYRVEENNGCLMLGWHTRPLITTSAWK 609 ******************************************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01129	3.0E-41	47	120	No hit	No description
Pfam	PF12041	3.9E-35	47	114	IPR021914	Transcriptional factor DELLA, N-terminal
PROSITE profile	PS50985	65.423	223	588	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.7E-132	249	609	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 616 aa Download sequence Send to blast
MKRDLHQYQG RLPNNHGTSS SSSSSSLPVS KDKMMMVKEE EDGANMDELL AVLGYKVRSS 60 EMAEVALKLE QLETMMGNVQ EDGLSQLATD TVHYNPSELY SWLDNMLTEL NPPPPGASSN 120 VCLDPILTSP EIVNNNSFLT AAGGDSSIII PASDYDFKVI PGNAIYQQRS QFAIDSSSPS 180 SNNNQNKRLK SCSSPDSMVT STSTATQIGG VIGTTVMTTT TTTTTAASAT AESTRSVILV 240 DSQDNGVRLV HALMACAEAV QQNNLTIAEA LVKQIGCLAV SQAGAMRKVA TYFAEALARR 300 IYRLSPPQNQ IDHSLSDTLQ MHFYETCPYL KFAHFTANQA ILEAFQGKKR VHVIDFSMNQ 360 GLQWPALMQA LALREGGPPI FRLTGIGPPA PDNSDQLHEV GCKLAQLAEA IHVEFEYRGF 420 VANSLADLDA SMLELRPSEI ESVAVNSVFE LHKLLGRPGG IEKVLGVVKQ IKPVIFTVVE 480 QESNHNGPVF LDRFTESLHY YSTLFDSLEG VPSSQDKVMS EVYLGKQICN LVACEGPDRV 540 ERHETLSQWG YRFGSSGFAP AHLGSNAFKQ ASMLLSVFNS GQGYRVEENN GCLMLGWHTR 600 PLITTSAWKL GGALS*

Sequence ? help Back to Top

Protein Sequence Length: 616 aa Download sequence Send to blast

MKRDLHQYQG RLPNNHGTSS SSSSSSLPVS KDKMMMVKEE EDGANMDELL AVLGYKVRSS  60
EMAEVALKLE QLETMMGNVQ EDGLSQLATD TVHYNPSELY SWLDNMLTEL NPPPPGASSN  120
VCLDPILTSP EIVNNNSFLT AAGGDSSIII PASDYDFKVI PGNAIYQQRS QFAIDSSSPS  180
SNNNQNKRLK SCSSPDSMVT STSTATQIGG VIGTTVMTTT TTTTTAASAT AESTRSVILV  240
DSQDNGVRLV HALMACAEAV QQNNLTIAEA LVKQIGCLAV SQAGAMRKVA TYFAEALARR  300
IYRLSPPQNQ IDHSLSDTLQ MHFYETCPYL KFAHFTANQA ILEAFQGKKR VHVIDFSMNQ  360
GLQWPALMQA LALREGGPPI FRLTGIGPPA PDNSDQLHEV GCKLAQLAEA IHVEFEYRGF  420
VANSLADLDA SMLELRPSEI ESVAVNSVFE LHKLLGRPGG IEKVLGVVKQ IKPVIFTVVE  480
QESNHNGPVF LDRFTESLHY YSTLFDSLEG VPSSQDKVMS EVYLGKQICN LVACEGPDRV  540
ERHETLSQWG YRFGSSGFAP AHLGSNAFKQ ASMLLSVFNS GQGYRVEENN GCLMLGWHTR  600
PLITTSAWKL GGALS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	2e-61	256	608	26	378	Protein SCARECROW
Search in ModeBase

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa04g002660.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC254604	0.0	AC254604.1 Capsella rubella clone CAP23-D18, complete sequence.
GenBank	AC254607	0.0	AC254607.1 Capsella rubella clone CAP08-M18, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010502135.1	0.0	PREDICTED: DELLA protein RGA-like
Swissprot	Q9SLH3	0.0	RGA_ARATH; DELLA protein RGA
TrEMBL	E4MVL7	0.0	E4MVL7_EUTHA; mRNA, clone: RTFL01-02-P11
TrEMBL	V4KPE3	0.0	V4KPE3_EUTSA; Uncharacterized protein
STRING	XP_010502135.1	0.0	(Camelina sativa)

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

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]