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

XP_008244193.1

Organism

Prunus mume

Taxonomic ID

102107

Taxonomic Lineage

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

Family

GRAS

Protein Properties

Length: 849aa MW: 92089 Da PI: 6.8304

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_008244193.1	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	415.2	5.9e-127	477	836	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshl 96 +lLl+cAeavs++++ +a+++L ++sel++p g++ qR+aayf eA++arl++s+ ++y++lpps + +++++ ++a+++f+ +sP++kfsh+ XP_008244193.1 477 LTLLLQCAEAVSADNFDEATKILLEISELSTPFGTSAQRVAAYFSEAMSARLVSSCLGIYASLPPSYVPISHTQKMVSAFQVFNGISPFVKFSHF 571 579****************************************************************************************** PP GRAS 97 taNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledlel 191 taNqaI ea+e+e+rvHi+D+di+qGlQWp L++ LasRp+gpp +R+Tg+g s e+le+tg+rL++fA++lg+pfef + va+++ +l++ XP_008244193.1 572 TANQAIQEAFEREDRVHIVDLDIMQGLQWPGLFHILASRPGGPPYVRLTGLGT----SMEALEATGKRLSDFADKLGLPFEFFP-VAEKVGSLDP 661 *************************************************....***********************.7***** PP GRAS 192 eeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvE 286 e+L+++++Ea+aV++ h+l+d ++s ++ +L+l+++l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl a++++eseer++vE XP_008244193.1 662 ERLNISKREAVAVHWLQ--HSLYDVTGSDSN----TLWLLQRLAPKVVTVVEQDLSH-AGSFLGRFVEAIHYYSALFDSLGASYGEESEERHVVE 749 ************9..999999999999....******************.899****************************** PP GRAS 287 rellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 ++ll+rei+nv+a g +r + + +++Wre+++++GF+ ++l +aa+qa lll +++sdgy++ e++g+l lgWkd L+++SaWr XP_008244193.1 750 QQLLSREIRNVLAVGGPSRSGEVK-FHNWREKFQQSGFRGISLAGNAATQATLLLGMFPSDGYTLVEDHGTLKLGWKDLCLLTASAWR 836 **************888776.************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	61.909	450	816	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.0E-124	477	836	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: 849 aa Download sequence Send to blast
MAACALLGDH NGEHISGNGS SNNISHGGGS PSCPMTSTTN SNSQGSSVEQ QPPRQHQNQQ 60 QQQRQSTEGS KMVRKRMACE IEVQNYPTSR NTSASDYMRL SRRSSSIINN NPNPNATKVN 120 NNSMVYPNYS TMLLPVPSST NLTTLTSAGG ALSPASASAS SAAASAANWG PIDPLSLHHH 180 HQSGALPPHQ LQLQPKTLTP AVCGFSGLPL FPPEKTTPSN QSTATPSSIS ISMEDSSSAT 240 AWIDGIIKDL IHSSTNVSIP QLIHNVREII FPCNPNLASL LEYRLRSISE PPPPPPPIPN 300 FNPTTVPELR RRRETLQLQQ QQNQHHHHHH QGPGALKLNL DSAALHDVAI FTNPTTVETA 360 SVATHVMNSN DLYLHSWTGG GGGAGPTPIT CSQTNPHHPN SPFNQAIHHT QDKQLENSSS 420 SSPAAESTTP TAAPATTTAT TTPTPPPTTP SAAVSLIRER KEEMRQQKRD EEGLHLLTLL 480 LQCAEAVSAD NFDEATKILL EISELSTPFG TSAQRVAAYF SEAMSARLVS SCLGIYASLP 540 PSYVPISHTQ KMVSAFQVFN GISPFVKFSH FTANQAIQEA FEREDRVHIV DLDIMQGLQW 600 PGLFHILASR PGGPPYVRLT GLGTSMEALE ATGKRLSDFA DKLGLPFEFF PVAEKVGSLD 660 PERLNISKRE AVAVHWLQHS LYDVTGSDSN TLWLLQRLAP KVVTVVEQDL SHAGSFLGRF 720 VEAIHYYSAL FDSLGASYGE ESEERHVVEQ QLLSREIRNV LAVGGPSRSG EVKFHNWREK 780 FQQSGFRGIS LAGNAATQAT LLLGMFPSDG YTLVEDHGTL KLGWKDLCLL TASAWRPPFH 840 ATTNPNLHY

Sequence ? help Back to Top

Protein Sequence Length: 849 aa Download sequence Send to blast

MAACALLGDH NGEHISGNGS SNNISHGGGS PSCPMTSTTN SNSQGSSVEQ QPPRQHQNQQ  60
QQQRQSTEGS KMVRKRMACE IEVQNYPTSR NTSASDYMRL SRRSSSIINN NPNPNATKVN  120
NNSMVYPNYS TMLLPVPSST NLTTLTSAGG ALSPASASAS SAAASAANWG PIDPLSLHHH  180
HQSGALPPHQ LQLQPKTLTP AVCGFSGLPL FPPEKTTPSN QSTATPSSIS ISMEDSSSAT  240
AWIDGIIKDL IHSSTNVSIP QLIHNVREII FPCNPNLASL LEYRLRSISE PPPPPPPIPN  300
FNPTTVPELR RRRETLQLQQ QQNQHHHHHH QGPGALKLNL DSAALHDVAI FTNPTTVETA  360
SVATHVMNSN DLYLHSWTGG GGGAGPTPIT CSQTNPHHPN SPFNQAIHHT QDKQLENSSS  420
SSPAAESTTP TAAPATTTAT TTPTPPPTTP SAAVSLIRER KEEMRQQKRD EEGLHLLTLL  480
LQCAEAVSAD NFDEATKILL EISELSTPFG TSAQRVAAYF SEAMSARLVS SCLGIYASLP  540
PSYVPISHTQ KMVSAFQVFN GISPFVKFSH FTANQAIQEA FEREDRVHIV DLDIMQGLQW  600
PGLFHILASR PGGPPYVRLT GLGTSMEALE ATGKRLSDFA DKLGLPFEFF PVAEKVGSLD  660
PERLNISKRE AVAVHWLQHS LYDVTGSDSN TLWLLQRLAP KVVTVVEQDL SHAGSFLGRF  720
VEAIHYYSAL FDSLGASYGE ESEERHVVEQ QLLSREIRNV LAVGGPSRSG EVKFHNWREK  780
FQQSGFRGIS LAGNAATQAT LLLGMFPSDG YTLVEDHGTL KLGWKDLCLL TASAWRPPFH  840
ATTNPNLHY

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	0.0	460	837	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_008244193.1

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_008244193.1	0.0	PREDICTED: protein SCARECROW-like
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A251NXN6	0.0	A0A251NXN6_PRUPE; Uncharacterized protein
STRING	XP_008244193.1	0.0	(Prunus mume)

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]