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

Potri.016G143900.1

Common Name

POPTR_0016s15060g

Organism

Populus trichocarpa

Taxonomic ID

3694

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: 770aa MW: 84142.5 Da PI: 6.6949

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Potri.016G143900.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	412.3	4.5e-126	376	733	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilk 92 +lLl+cAeavs++++e+a+++L ++sel++p g++ qR+aayf eA++arl++s+ ++y++lp+ ++s ++++ ++a+++f+ + P++k Potri.016G143900.1 376 LTLLLQCAEAVSADNFEEANKMLLEISELSTPFGTSAQRVAAYFSEAMSARLVSSCLGIYATLPSMPQS--HTQKMASAFQVFNGIGPFVK 464 579**********************************************************999998..5899999********* PP GRAS 93 fshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlva 183 fsh+taNqaI ea+e+eervHiiD+d++qGlQWp L++ LasRp+gpp +R+Tg+g s e+le+tg+rL++fA++lg+pfef + va Potri.016G143900.1 465 FSHFTANQAIQEAFEREERVHIIDLDVMQGLQWPGLFHILASRPGGPPYVRLTGLGT----SLEALEATGKRLSDFAHKLGLPFEFIP-VA 550 *****************************************************....9***********************.7 PP GRAS 184 krledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleak 274 +++ +le+e+L+v+++Ea+aV++ h+l+d ++s ++ +L l+++l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl a+ Potri.016G143900.1 551 EKVGNLEPERLNVSKREAVAVHWLQ--HSLYDVTGSDTN----MLCLLQRLAPKVVTVVEQDLSH-AGSFLGRFVEAIHYYSALFDSLGAS 634 **********************9..999999999999....******************.899****************** PP GRAS 275 lpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdr 365 +++eseer++vE++ll+rei+nv+a g +r + + +++Wre+l+++GFk ++l +aa+qa lll +++sdgy++ e++g+l lgWkd Potri.016G143900.1 635 YGEESEERHVVEQQLLSREIRNVLAVGGPSRSGDVK-FHNWREKLQQSGFKGISLAGNAATQATLLLGMFPSDGYTLVEDNGTLKLGWKDL 724 **************************888877.************************************************** PP GRAS 366 pLvsvSaWr 374 L+++SaWr Potri.016G143900.1 725 CLLTASAWR 733 ******8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	62.276	349	713	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.6E-123	376	733	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 770 aa Download sequence Send to blast
MTRSTGASSF TSCSNNNNIN PNNPNSILYP VLNYSTTTSM LPSSTNLTAI TSGVSASLSV 60 SEFLSPTVLS TNLITSCNDT HTQSQLPAVC GFSGLPLFPP AEIKRNNIRS NAAADPPPGL 120 ITTSITAPTT STLASASMED ATSATAWIDG LIKDLLHTST NVSIPQLIQN VREIIYPCNP 180 NLASLLEYRL RSLTDPIIPP NILPVERSRN KEAAAAVPLP LQIQRRCNQG HASNSGLTLD 240 LDNIVSNSAP PVSSHVSHYS NWGPTPPLIC QPNIQQQHQQ PQIHLVHHDQ HLQQQKQKQQ 300 ESPSSTSNVT PTILAINQGQ PPQQQAQDQQ QEKSSSAETE QVSSSTSPPS SSAAASRDKK 360 EEMRQQKRDE EGLHLLTLLL QCAEAVSADN FEEANKMLLE ISELSTPFGT SAQRVAAYFS 420 EAMSARLVSS CLGIYATLPS MPQSHTQKMA SAFQVFNGIG PFVKFSHFTA NQAIQEAFER 480 EERVHIIDLD VMQGLQWPGL FHILASRPGG PPYVRLTGLG TSLEALEATG KRLSDFAHKL 540 GLPFEFIPVA EKVGNLEPER LNVSKREAVA VHWLQHSLYD VTGSDTNMLC LLQRLAPKVV 600 TVVEQDLSHA GSFLGRFVEA IHYYSALFDS LGASYGEESE ERHVVEQQLL SREIRNVLAV 660 GGPSRSGDVK FHNWREKLQQ SGFKGISLAG NAATQATLLL GMFPSDGYTL VEDNGTLKLG 720 WKDLCLLTAS AWRPFHVTIE TATTTPHHHH HHHHHQQQQQ HHHHRFVTA*

Sequence ? help Back to Top

Protein Sequence Length: 770 aa Download sequence Send to blast

MTRSTGASSF TSCSNNNNIN PNNPNSILYP VLNYSTTTSM LPSSTNLTAI TSGVSASLSV  60
SEFLSPTVLS TNLITSCNDT HTQSQLPAVC GFSGLPLFPP AEIKRNNIRS NAAADPPPGL  120
ITTSITAPTT STLASASMED ATSATAWIDG LIKDLLHTST NVSIPQLIQN VREIIYPCNP  180
NLASLLEYRL RSLTDPIIPP NILPVERSRN KEAAAAVPLP LQIQRRCNQG HASNSGLTLD  240
LDNIVSNSAP PVSSHVSHYS NWGPTPPLIC QPNIQQQHQQ PQIHLVHHDQ HLQQQKQKQQ  300
ESPSSTSNVT PTILAINQGQ PPQQQAQDQQ QEKSSSAETE QVSSSTSPPS SSAAASRDKK  360
EEMRQQKRDE EGLHLLTLLL QCAEAVSADN FEEANKMLLE ISELSTPFGT SAQRVAAYFS  420
EAMSARLVSS CLGIYATLPS MPQSHTQKMA SAFQVFNGIG PFVKFSHFTA NQAIQEAFER  480
EERVHIIDLD VMQGLQWPGL FHILASRPGG PPYVRLTGLG TSLEALEATG KRLSDFAHKL  540
GLPFEFIPVA EKVGNLEPER LNVSKREAVA VHWLQHSLYD VTGSDTNMLC LLQRLAPKVV  600
TVVEQDLSHA GSFLGRFVEA IHYYSALFDS LGASYGEESE ERHVVEQQLL SREIRNVLAV  660
GGPSRSGDVK FHNWREKLQQ SGFKGISLAG NAATQATLLL GMFPSDGYTL VEDNGTLKLG  720
WKDLCLLTAS AWRPFHVTIE TATTTPHHHH HHHHHQQQQQ HHHHRFVTA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	359	734	3	380	Protein SCARECROW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detected in the ground tissue of late heart-stage embryos. After germination, expressed also in the L1 layer throughout the shoot apical meristem including the peripheral zone. Detected in most tissues of young leaf primordia, except in the presumptive vasculature. In mature leaves, expressed in bundle sheath cells. Detected in inflorescence stems in a single internal cell layer corresponding to the starch sheath. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:8756724}.
Uniprot	TISSUE SPECIFICITY: Expressed in siliques, leaves and roots. Detected in the initial daughter cell before its asymmetric division and remains expressed only in the endodermal cell layer after the division. Expressed in the endodermis or starch sheath of the seedling hypocotyl, in the leaf bundle sheath cells and the root quiescent center. {ECO:0000269\|PubMed:10631180, ECO:0000269\|PubMed:10850497, ECO:0000269\|PubMed:11565032, ECO:0000269\|PubMed:8756724, ECO:0000269\|PubMed:9375406}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Potri.016G143900.1

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_024443296.1	0.0	LOW QUALITY PROTEIN: protein SCARECROW
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A2K1XFN6	0.0	A0A2K1XFN6_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
Representative plant	OGRP2183	14	37

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

Link Out ? help Back to Top
Phytozome	Potri.016G143900.1
Entrez Gene	7472508

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]