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

CCG012286.1

Organism

Populus euphratica

Taxonomic ID

75702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus

Family

GRAS

Protein Properties

Length: 826aa MW: 90737.7 Da PI: 6.5063

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
CCG012286.1	genome	LZU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	411.8	6.3e-126	434	791	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaN 99 +lLl+cAeavs++++e+a+++L ++sel++p g++ qR+aayf eA++arl++s+ ++y++lp+ ++s ++++ ++a+++f+ + P++kfsh+taN CCG012286.1 434 LTLLLQCAEAVSADNFEEANKMLLEISELSTPFGTSAQRVAAYFSEAMSARLVSSCLGIYATLPSLPQS--HTQKMASAFQVFNGIGPFIKFSHFTAN 529 579**********************************************************999998..5899999**************** PP GRAS 100 qaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvk 197 qaI ea+e+eervHiiD+d++qGlQWp L++ LasRp+gpp +R+Tg+g s e+le+tg+rL++fA++lg+pfef + va+++ +le+e+L+v+ CCG012286.1 530 QAIQEAFEREERVHIIDLDVMQGLQWPGLFHILASRPGGPPYVRLTGLGT----SLEALEATGKRLSDFADKLGLPFEFIP-VAEKVGNLEPERLNVS 622 **********************************************....9**********************.7*********** PP GRAS 198 pgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreiv 295 ++Ea+aV++ h+l+d ++s ++ +L l+++l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl a++++eseer++vE++ll+rei+ CCG012286.1 623 KREAVAVHWLQ--HSLYDVTGSDTN----MLCLLQRLAPKVVTVVEQDLSH-AGSFLGRFVEAIHYYSALFDSLGASYGEESEERHVVEQQLLSREIR 713 ******9..999999999999....******************.899*************************************** PP GRAS 296 nvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 nv+a g +r + + +++Wre+l+++GFk ++l +aa+qa lll +++sdgy++ e++g+l lgWkd L+++SaWr CCG012286.1 714 NVLAVGGPSRSGDVK-FHNWREKLQQSGFKGISLAGNAATQATLLLGMFPSDGYTLVEDNGTLKLGWKDLCLLTASAWR 791 *****888877.************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	62.353	407	771	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.2E-123	434	791	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 826 aa Download sequence Send to blast
MMRKRMASEM MEVQSTITHQ NHQRLSRGNI ISGTNVYSLS ISDNNNNDDD NDVGMTRSTG 60 ASSFTSCSNN NNINPSNPNS ILYPVLNYHA TTSMLPSSTH LTAITSGGSA SLSVSGFLSP 120 TILSTNLITS CDDTHTHIHT QSQLPAVCGF SGLPLFPPAE IKRNNIRSNA AADPPPGLIT 180 TSITAPTTST VASVSMEDFT SATAWIDGLI KDLLHTSTNV SIPQLIQNVR EIIYPCNPNL 240 ASLLEYRLRS LTDPIIPSNI LPVERSRNKE AAAAVPLPLQ IQRRYNQGHV SNSGLTLDLD 300 NIVSNSAPPV SSHVSHYSNW GPTPPLICQP NIQQQHLQPQ IHLVHHDQHL QQQQQMQQES 360 PSSTSNVTPT ILALNQGQPP QQQEQDQQQE KSSSAEAEQV SSTTSPPSSS AAASRDKKEE 420 MRQQKRDEEG LHLLTLLLQC AEAVSADNFE EANKMLLEIS ELSTPFGTSA QRVAAYFSEA 480 MSARLVSSCL GIYATLPSLP QSHTQKMASA FQVFNGIGPF IKFSHFTANQ AIQEAFEREE 540 RVHIIDLDVM QGLQWPGLFH ILASRPGGPP YVRLTGLGTS LEALEATGKR LSDFADKLGL 600 PFEFIPVAEK VGNLEPERLN VSKREAVAVH WLQHSLYDVT GSDTNMLCLL QRLAPKVVTV 660 VEQDLSHAGS FLGRFVEAIH YYSALFDSLG ASYGEESEER HVVEQQLLSR EIRNVLAVGG 720 PSRSGDVKFH NWREKLQQSG FKGISLAGNA ATQATLLLGM FPSDGYTLVE DNGTLKLGWK 780 DLCLLTASAW RPFHDTIETA TTIPHHHHHH QQQHHHHHHH HRFVTA

Sequence ? help Back to Top

Protein Sequence Length: 826 aa Download sequence Send to blast

MMRKRMASEM MEVQSTITHQ NHQRLSRGNI ISGTNVYSLS ISDNNNNDDD NDVGMTRSTG  60
ASSFTSCSNN NNINPSNPNS ILYPVLNYHA TTSMLPSSTH LTAITSGGSA SLSVSGFLSP  120
TILSTNLITS CDDTHTHIHT QSQLPAVCGF SGLPLFPPAE IKRNNIRSNA AADPPPGLIT  180
TSITAPTTST VASVSMEDFT SATAWIDGLI KDLLHTSTNV SIPQLIQNVR EIIYPCNPNL  240
ASLLEYRLRS LTDPIIPSNI LPVERSRNKE AAAAVPLPLQ IQRRYNQGHV SNSGLTLDLD  300
NIVSNSAPPV SSHVSHYSNW GPTPPLICQP NIQQQHLQPQ IHLVHHDQHL QQQQQMQQES  360
PSSTSNVTPT ILALNQGQPP QQQEQDQQQE KSSSAEAEQV SSTTSPPSSS AAASRDKKEE  420
MRQQKRDEEG LHLLTLLLQC AEAVSADNFE EANKMLLEIS ELSTPFGTSA QRVAAYFSEA  480
MSARLVSSCL GIYATLPSLP QSHTQKMASA FQVFNGIGPF IKFSHFTANQ AIQEAFEREE  540
RVHIIDLDVM QGLQWPGLFH ILASRPGGPP YVRLTGLGTS LEALEATGKR LSDFADKLGL  600
PFEFIPVAEK VGNLEPERLN VSKREAVAVH WLQHSLYDVT GSDTNMLCLL QRLAPKVVTV  660
VEQDLSHAGS FLGRFVEAIH YYSALFDSLG ASYGEESEER HVVEQQLLSR EIRNVLAVGG  720
PSRSGDVKFH NWREKLQQSG FKGISLAGNA ATQATLLLGM FPSDGYTLVE DNGTLKLGWK  780
DLCLLTASAW RPFHDTIETA TTIPHHHHHH QQQHHHHHHH HRFVTA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	417	792	3	380	Protein SCARECROW
Search in ModeBase

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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_011015033.1	0.0	PREDICTED: protein SCARECROW-like
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A2K1R5F1	0.0	A0A2K1R5F1_POPTR; Uncharacterized protein
STRING	POPTR_0016s15060.1	0.0	(Populus trichocarpa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF2068	34	89

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]