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

MDP0000397638

Organism

Malus domestica

Taxonomic ID

3750

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Malus

Family

GRAS

Protein Properties

Length: 825aa MW: 88421.8 Da PI: 6.4309

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000397638	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	417.7	1e-127	452	811	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlt 97 +lLl+cAeavs++++ +a+++L ++sel++p g++ qR+aayf eA++arl++s+ ++y++lp s+ +++++++ ++a+++f+ +sP++kfsh+t MDP0000397638 452 LTLLLKCAEAVSADNFDEATKILLEISELSTPFGTSAQRVAAYFSEAMSARLVSSCLGIYASLPRSSVPTTHTQKMVSAFQVFNGISPFVKFSHFT 547 579***************************************************************999********************* PP GRAS 98 aNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledlelee 193 aNqaI ea+e+e+rvHi+D+di+qGlQWp L++ LasRp+gpp +R+Tg+g s e+le+tg+rL++fA++lg+pfef + va+++++l++e+ MDP0000397638 548 ANQAIQEAFEREDRVHIVDLDIMQGLQWPGLFHILASRPGGPPYVRLTGLGT----SMEALEATGKRLSDFADKLGLPFEFFP-VAEKVANLDPER 638 ************************************************....***********************.7******* PP GRAS 194 LrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErel 289 L+++++Ea+aV++ h+l+d ++s +s +L+l+++l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl a++++eseer++vE++l MDP0000397638 639 LNISKREAVAVHWLQ--HSLYDVTGSDSS----TLWLLQRLAPKVVTVVEQDLSH-AGSFLGRFVEAIHYYSALFDSLGASYGEESEERHVVEQQL 727 **********9..999999999888....******************.899********************************* PP GRAS 290 lgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 l+rei+nv+a g +r + + +++Wre++++ GF+ ++l +aa+qa lll +++sdgy++ e++g+l lgWkd L+++SaWr MDP0000397638 728 LSREIRNVLAVGGPSRSGEVK-FHNWREKFQQTGFRGISLAGNAANQAALLLGMFPSDGYTLVEDNGTLKLGWKDLCLLTASAWR 811 ***********888776.************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	62.22	425	791	IPR005202	Transcription factor GRAS
Pfam	PF03514	3.6E-125	452	811	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: 825 aa Download sequence Send to blast
MATCALLGDN GGDRISGNGS SNNNNSDSLG GGGGNPSYPM NNSTTNSNSS SVGQQPPKMV 60 RKRMASEIEV QTTLTSRTAG SDYFRLSRRG IINNSPPVQP VNQNPNASKV NSSMFYPNHS 120 TMQLPVPSST NFAALTSPGG ALLSXTSPSP SPSSAAXAGT WGPIDPLSFH RPLPVQPTTT 180 SQTTTTPAVC GFSGLPLFPP EKTTPLNTSI TATTPSSVSM EDGSSAATAW IDGIIKDLVH 240 SSTNVSIPQL IHNVREIIFP CNPSLAALLE YRLRSISEPL PPPPLPLPVP SFNPTPIPDI 300 RRRQQGGPGP GAFKLNXDSG ALQDVAIFNP STVENNDLYL QSWSGGAGGG GVXLSLPQPN 360 PTPAPITCNQ TNPHHQSPSF NQAIHQTQDK QLENSSPSSP AAEATTPTXA PAPTTTXATA 420 PPEPTTSAVS LLREKKEEMR QQKRDEEGLH LLTLLLKCAE AVSADNFDEA TKILLEISEL 480 STPFGTSAQR VAAYFSEAMS ARLVSSCLGI YASLPRSSVP TTHTQKMVSA FQVFNGISPF 540 VKFSHFTANQ AIQEAFERED RVHIVDLDIM QGLQWPGLFH ILASRPGGPP YVRLTGLGTS 600 MEALEATGKR LSDFADKLGL PFEFFPVAEK VANLDPERLN ISKREAVAVH WLQHSLYDVT 660 GSDSSTLWLL QRLAPKVVTV VEQDLSHAGS FLGRFVEAIH YYSALFDSLG ASYGEESEER 720 HVVEQQLLSR EIRNVLAVGG PSRSGEVKFH NWREKFQQTG FRGISLAGNA ANQAALLLGM 780 FPSDGYTLVE DNGTLKLGWK DLCLLTASAW RPPFHAAANP NLHY*

Sequence ? help Back to Top

Protein Sequence Length: 825 aa Download sequence Send to blast

MATCALLGDN GGDRISGNGS SNNNNSDSLG GGGGNPSYPM NNSTTNSNSS SVGQQPPKMV  60
RKRMASEIEV QTTLTSRTAG SDYFRLSRRG IINNSPPVQP VNQNPNASKV NSSMFYPNHS  120
TMQLPVPSST NFAALTSPGG ALLSXTSPSP SPSSAAXAGT WGPIDPLSFH RPLPVQPTTT  180
SQTTTTPAVC GFSGLPLFPP EKTTPLNTSI TATTPSSVSM EDGSSAATAW IDGIIKDLVH  240
SSTNVSIPQL IHNVREIIFP CNPSLAALLE YRLRSISEPL PPPPLPLPVP SFNPTPIPDI  300
RRRQQGGPGP GAFKLNXDSG ALQDVAIFNP STVENNDLYL QSWSGGAGGG GVXLSLPQPN  360
PTPAPITCNQ TNPHHQSPSF NQAIHQTQDK QLENSSPSSP AAEATTPTXA PAPTTTXATA  420
PPEPTTSAVS LLREKKEEMR QQKRDEEGLH LLTLLLKCAE AVSADNFDEA TKILLEISEL  480
STPFGTSAQR VAAYFSEAMS ARLVSSCLGI YASLPRSSVP TTHTQKMVSA FQVFNGISPF  540
VKFSHFTANQ AIQEAFERED RVHIVDLDIM QGLQWPGLFH ILASRPGGPP YVRLTGLGTS  600
MEALEATGKR LSDFADKLGL PFEFFPVAEK VANLDPERLN ISKREAVAVH WLQHSLYDVT  660
GSDSSTLWLL QRLAPKVVTV VEQDLSHAGS FLGRFVEAIH YYSALFDSLG ASYGEESEER  720
HVVEQQLLSR EIRNVLAVGG PSRSGEVKFH NWREKFQQTG FRGISLAGNA ANQAALLLGM  780
FPSDGYTLVE DNGTLKLGWK DLCLLTASAW RPPFHAAANP NLHY*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	435	812	3	380	Protein SCARECROW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.26311	0.0	leaf

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	Putative transcription factor involved in asymmetric cell division (By similarity). Required for differentiation of endodermis and graviresponses. {ECO:0000250, ECO:0000269\|PubMed:16339910}.
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_008388412.2	0.0	protein SCARECROW 2-like
Swissprot	Q2Z2E9	0.0	SCR_IPONI; Protein SCARECROW
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A498IKT2	0.0	A0A498IKT2_MALDO; Uncharacterized protein
STRING	XP_008388412.1	0.0	(Malus domestica)

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

Link Out ? help Back to Top
Phytozome	MDP0000397638

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]