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

Dca30033.1

Organism

Dianthus caryophyllus

Taxonomic ID

3570

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Caryophyllaceae; Caryophylleae; Dianthus

Family

GRAS

Protein Properties

Length: 654aa MW: 71066.3 Da PI: 6.763

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Dca30033.1	genome	DCA	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	394.4	1.2e-120	284	639	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaNq 100 +lLl+cAea+s++++ +a+++L ++ e a+p g++ qR+aayf eA++arl++ +l ++lp+ + ++ ++a+++f+ +sP++kfsh+taNq Dca30033.1 284 LTLLLQCAEAISANHHDAASKMLVEIAEWATPFGTSAQRVAAYFSEAMSARLVSARLGLHASLPTIPH----YQKLVSAFQVFNGISPFVKFSHFTANQ 378 579*************************************************88888888888887....589999***************** PP GRAS 101 aIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpg 199 aI ea+ +eervHiiD+di+qGlQWp L++ LasRp+gpp +R+Tg+gs s e+le+tg+rL++fAe+lg++fef va+++ +l++e+L+v+++ Dca30033.1 379 AIQEAFVREERVHIIDLDIMQGLQWPGLFHILASRPGGPPYVRLTGLGS----SPEALEATGKRLSDFAEKLGLNFEFVG-VAEKVGNLDVEKLHVSKR 472 *********************************************....9**********************.7************* PP GRAS 200 EalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvv 298 Ea+aV++ h+l+d ++s + +L+l+++l Pkvv++veq++++ ++ Fl rf+ea++yysalfdsl a+++++seer++vE++ll+rei+nv+ Dca30033.1 473 EAVAVHWLQ--HSLYDVTGSDIN----TLWLLQRLAPKVVTIVEQDLSR-TGAFLGRFVEAVHYYSALFDSLGASYSEDSEERHVVEQQLLSREIRNVL 564 ****9..999999999999....*****************9.789****************************************** PP GRAS 299 acegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 a g +r+ ++++Wre+l+++GF+ ++l +aa+qa lll +++sdgy++ e++g+l lgWkd L+++SaWr Dca30033.1 565 AVGGPSRTGAA-KFASWREKLQQSGFRGISLAGNAAAQATLLLGMFPSDGYTLVEDNGTLKLGWKDLCLLTASAWR 639 *977765.5************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	60.552	257	619	IPR005202	Transcription factor GRAS
Pfam	PF03514	4.3E-118	284	639	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008356	Biological Process	asymmetric cell division
GO:0009630	Biological Process	gravitropism
GO:0009956	Biological Process	radial pattern formation
GO:0048366	Biological Process	leaf development
GO:0051457	Biological Process	maintenance of protein location in nucleus
GO:0090610	Biological Process	bundle sheath cell fate specification
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 654 aa Download sequence Send to blast
MAASPSLFLL DPPPPPPPYY NYSSSSLPPY YVNLYNNLNL EENFITMSSP NNNNPPPSVS 60 GPSRKRPASE MDPTTHEDLP LVCGFSGLPL FPPDRGNSGL GVGVGVGVNE PVTGPAEHPG 120 WVDGIIKDLI QTSNSVSIPH LIQNVRDIIY PCNPSLGSVI EFRLRSLAEP APYSIQPPPQ 180 QQQQQQIQLQ QTASSSSLPK KTNNNTNTNN NNNNSNNWAV TAAKNLGAAT AAEEKTVSVS 240 PPTPSPPPPR PPSPPPAVPL ASAKAAEREE MRRRKRDEEG LHLLTLLLQC AEAISANHHD 300 AASKMLVEIA EWATPFGTSA QRVAAYFSEA MSARLVSARL GLHASLPTIP HYQKLVSAFQ 360 VFNGISPFVK FSHFTANQAI QEAFVREERV HIIDLDIMQG LQWPGLFHIL ASRPGGPPYV 420 RLTGLGSSPE ALEATGKRLS DFAEKLGLNF EFVGVAEKVG NLDVEKLHVS KREAVAVHWL 480 QHSLYDVTGS DINTLWLLQR LAPKVVTIVE QDLSRTGAFL GRFVEAVHYY SALFDSLGAS 540 YSEDSEERHV VEQQLLSREI RNVLAVGGPS RTGAAKFASW REKLQQSGFR GISLAGNAAA 600 QATLLLGMFP SDGYTLVEDN GTLKLGWKDL CLLTASAWRP SNAHTMSTVC TRSQ

Sequence ? help Back to Top

Protein Sequence Length: 654 aa Download sequence Send to blast

MAASPSLFLL DPPPPPPPYY NYSSSSLPPY YVNLYNNLNL EENFITMSSP NNNNPPPSVS  60
GPSRKRPASE MDPTTHEDLP LVCGFSGLPL FPPDRGNSGL GVGVGVGVNE PVTGPAEHPG  120
WVDGIIKDLI QTSNSVSIPH LIQNVRDIIY PCNPSLGSVI EFRLRSLAEP APYSIQPPPQ  180
QQQQQQIQLQ QTASSSSLPK KTNNNTNTNN NNNNSNNWAV TAAKNLGAAT AAEEKTVSVS  240
PPTPSPPPPR PPSPPPAVPL ASAKAAEREE MRRRKRDEEG LHLLTLLLQC AEAISANHHD  300
AASKMLVEIA EWATPFGTSA QRVAAYFSEA MSARLVSARL GLHASLPTIP HYQKLVSAFQ  360
VFNGISPFVK FSHFTANQAI QEAFVREERV HIIDLDIMQG LQWPGLFHIL ASRPGGPPYV  420
RLTGLGSSPE ALEATGKRLS DFAEKLGLNF EFVGVAEKVG NLDVEKLHVS KREAVAVHWL  480
QHSLYDVTGS DINTLWLLQR LAPKVVTIVE QDLSRTGAFL GRFVEAVHYY SALFDSLGAS  540
YSEDSEERHV VEQQLLSREI RNVLAVGGPS RTGAAKFASW REKLQQSGFR GISLAGNAAA  600
QATLLLGMFP SDGYTLVEDN GTLKLGWKDL CLLTASAWRP SNAHTMSTVC TRSQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_A	0.0	268	640	3	379	Protein SCARECROW
5b3h_D	0.0	268	640	3	379	Protein SCARECROW
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor required for quiescent center cells specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Essential for cell division but not differentiation of the ground tissue. Also required for normal shoot gravitropism. Regulates the radial organization of the shoot axial organs. Binds to the promoter of MGP, NUC, RLK and SCL3. Restricts SHR movment and sequesters it into the nucleus of the endodermis. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:12569126, ECO:0000269\|PubMed:15142972, ECO:0000269\|PubMed:15314023, ECO:0000269\|PubMed:16640459, ECO:0000269\|PubMed:17446396, ECO:0000269\|PubMed:22921914, ECO:0000269\|PubMed:24302889, ECO:0000269\|PubMed:8819871, ECO:0000269\|PubMed:9375406, ECO:0000269\|PubMed:9670559}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by SHR and by itself. {ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:11565032, ECO:0000269\|PubMed:15314023}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021685832.1	0.0	protein SCARECROW-like
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A2C9VBS4	0.0	A0A2C9VBS4_MANES; Uncharacterized protein
TrEMBL	A0A2G9G7V0	0.0	A0A2G9G7V0_9LAMI; Uncharacterized protein
STRING	cassava4.1_001737m	0.0	(Manihot esculenta)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G54220.1	0.0	GRAS family protein

Publications ? help Back to Top
Liu YG, et al. Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc. Natl. Acad. Sci. U.S.A., 1999. 96(11): p. 6535-40 [PMID:10339623] Ticconi CA, et al. ER-resident proteins PDR2 and LPR1 mediate the developmental response of root meristems to phosphate availability. Proc. Natl. Acad. Sci. U.S.A., 2009. 106(33): p. 14174-9 [PMID:19666499] Moubayidin L, et al. Spatial coordination between stem cell activity and cell differentiation in the root meristem. Dev. Cell, 2013. 26(4): p. 405-15 [PMID:23987513] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Tian H,Jia Y,Niu T,Yu Q,Ding Z The key players of the primary root growth and development also function in lateral roots in Arabidopsis. Plant Cell Rep., 2014. 33(5): p. 745-53 [PMID:24504658] Reyes-Hernández BJ, et al. The root indeterminacy-to-determinacy developmental switch is operated through a folate-dependent pathway in Arabidopsis thaliana. New Phytol., 2014. 202(4): p. 1223-36 [PMID:24635769] Gao X,Wang C,Cui H Identification of bundle sheath cell fate factors provides new tools for C3-to-C4 engineering. Plant Signal Behav, 2018. [PMID:24819776] Ron M, et al. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol., 2014. 166(2): p. 455-69 [PMID:24868032] Jia Y, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. J. Exp. Bot., 2015. 66(15): p. 4631-42 [PMID:25998905] Zhang M, et al. A tetratricopeptide repeat domain-containing protein SSR1 located in mitochondria is involved in root development and auxin polar transport in Arabidopsis. Plant J., 2015. 83(4): p. 582-99 [PMID:26072661] Moreno-Risueno MA, et al. Transcriptional control of tissue formation throughout root development. Science, 2015. 350(6259): p. 426-30 [PMID:26494755] Gong X, et al. SEUSS Integrates Gibberellin Signaling with Transcriptional Inputs from the SHR-SCR-SCL3 Module to Regulate Middle Cortex Formation in the Arabidopsis Root. Plant Physiol., 2016. 170(3): p. 1675-83 [PMID:26818732] 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] Madmon O, et al. Expression of MAX2 under SCARECROW promoter enhances the strigolactone/MAX2 dependent response of Arabidopsis roots to low-phosphate conditions. Planta, 2016. 243(6): p. 1419-27 [PMID:26919985] 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] Benfey PN Defining the Path from Stem Cells to Differentiated Tissue. Curr. Top. Dev. Biol., 2016. 116: p. 35-43 [PMID:26970612] Li Q,Zhao Y,Yue M,Xue Y,Bao S The Protein Arginine Methylase 5 (PRMT5/SKB1) Gene Is Required for the Maintenance of Root Stem Cells in Response to DNA Damage. J Genet Genomics, 2016. 43(4): p. 187-97 [PMID:27090604] Clark NM, et al. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. Elife, 2017. [PMID:27288545] Choi JW,Lim J Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation. Mol. Cells, 2016. 39(7): p. 524-9 [PMID:27306644] Yoon EK, et al. Conservation and Diversification of the SHR-SCR-SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots. Mol Plant, 2016. 9(8): p. 1197-1209 [PMID:27353361] Waszczak C, et al. SHORT-ROOT Deficiency Alleviates the Cell Death Phenotype of the Arabidopsis catalase2 Mutant under Photorespiration-Promoting Conditions. Plant Cell, 2016. 28(8): p. 1844-59 [PMID:27432873] Goh T, et al. Quiescent center initiation in the Arabidopsis lateral root primordia is dependent on the SCARECROW transcription factor. Development, 2016. 143(18): p. 3363-71 [PMID:27510971] Yu Q, et al. A P-Loop NTPase Regulates Quiescent Center Cell Division and Distal Stem Cell Identity through the Regulation of ROS Homeostasis in Arabidopsis Root. PLoS Genet., 2016. 12(9): p. e1006175 [PMID:27583367] Sparks EE, et al. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Dev. Cell, 2016. 39(5): p. 585-596 [PMID:27923776] Hirano Y, et al. Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD. Nat Plants, 2017. 3: p. 17010 [PMID:28211915] Kobayashi A,Miura S,Kozaki A INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves. Plant Mol. Biol., 2017. 94(1-2): p. 1-13 [PMID:28324206] Díaz-Triviño S,Long Y,Scheres B,Blilou I Analysis of a Plant Transcriptional Regulatory Network Using Transient Expression Systems. Methods Mol. Biol., 2017. 1629: p. 83-103 [PMID:28623581] Long Y, et al. In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots. Nature, 2017. 548(7665): p. 97-102 [PMID:28746306] Bruno L, et al. In Arabidopsis thaliana Cadmium Impact on the Growth of Primary Root by Altering SCR Expression and Auxin-Cytokinin Cross-Talk. Front Plant Sci, 2017. 8: p. 1323 [PMID:28798767] Mira MM, et al. Expression of Arabidopsis class 1 phytoglobin (AtPgb1) delays death and degradation of the root apical meristem during severe PEG-induced water deficit. J. Exp. Bot., 2017. 68(20): p. 5653-5668 [PMID:29059380] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938] Ercoli MF, et al. GIF Transcriptional Coregulators Control Root Meristem Homeostasis. Plant Cell, 2018. 30(2): p. 347-359 [PMID:29352064] Shimotohno A,Heidstra R,Blilou I,Scheres B Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules. Genes Dev., 2018. 32(15-16): p. 1085-1100 [PMID:30018102]