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

Sp_058490_wiju.t1

Common Name

SOVF_058490

Organism

Spinacia oleracea

Taxonomic ID

3562

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Chenopodiaceae; Chenopodioideae; Anserineae; Spinacia

Family

GRAS

Protein Properties

Length: 836aa MW: 91147.8 Da PI: 6.0233

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sp_058490_wiju.t1	genome	TBVR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	404.4	1.1e-123	466	821	2	374
GRAS 2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkf 93 +lLl+cAeavs+++ e a+++L ++se a+p g++ qR+aayf eA++arl+ s+ ++ +lp+ + ++ ++a+++f+ +sP++kf Sp_058490_wiju.t1 466 LTLLLQCAEAVSADKYEDANKMLVEISEWATPFGTAAQRVAAYFSEAMSARLVTSCLGIHTSLPSIPHY----QKLVSAFQVFNGISPFVKF 553 579******************************************************9999998885....89999********** PP GRAS 94 shltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakr 185 sh+taNqaI ea+++eervHiiD+di+qGlQWp L++ LasRp+gpp +R+Tg+g s e+le+tg+rL++fAe+lg+pfef + va++ Sp_058490_wiju.t1 554 SHFTANQAIQEAFQREERVHIIDLDIMQGLQWPGLFHILASRPGGPPFVRLTGLGT----SMETLEATGKRLSDFAEKLGLPFEFIP-VAEK 640 ****************************************************....***********************.7* PP GRAS 186 ledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpr 277 + +l+le+L+v+++Ea+aV++ h+l+d ++s ++ +L+l+++l Pkvv+vveq++++ ++sFl rf+ea++yysalfdsl a++++ Sp_058490_wiju.t1 641 VGNLDLERLHVSKREAVAVHWLQ--HSLYDVTGSDTN----TLWLLQRLAPKVVTVVEQDLSR-TGSFLGRFVEAIHYYSALFDSLGASYGE 725 ********************9..999999999999....****************99.889********************* PP GRAS 278 eseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvs 369 +seer++vE++ll+rei+nv+a g +r + + +++Wre+++++GF+ ++l +aa+qa lll +++sdgy++ e++g+l lgWkd L++ Sp_058490_wiju.t1 726 DSEERHVVEQQLLSREIRNVLAVGGPSRSGEPK-FASWREKMQQSGFRGISLAGNAAAQATLLLGMFPSDGYTLVEDNGTLKLGWKDLCLLT 816 ***********************888877.****************************************************** PP GRAS 370 vSaWr 374 +SaWr Sp_058490_wiju.t1 817 ASAWR 821 **8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50985	61.453	439	801	IPR005202	Transcription factor GRAS
Pfam	PF03514	3.9E-121	466	821	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
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: 836 aa Download sequence Send to blast
MAASSSFFPD PNILLPPFLY SSPSPSPYYD NNINNNNNNT IINNNNYINS HPSFSNYSPF 60 LSPPLPPLMS NNIPQSTPPT PPESSKMVRK RTASEMERAS NVSNHDTIDH RLVSRQQPHQ 120 QFTSVNDPGV FNLAEGSLMD RGSGGVEQQP LVCGFSGLPL FPPVVDRSND NRNTSMSMTT 180 FSGSGSGSGL VSSSVVGGTS IEDPGWVDGI IKDLIQSSNS ISIPQLIQNV REIIYPCNPN 240 LGAVIEFRLR SLADPLIAPP LQPPQQPPPP PHPHAISHYH KQQNHQQAGF SRVNNNNNNI 300 NTSSSSQPGL QNKAYYNLSD IEYFSALGAP ECSANISWGG DQTAPPQSLP RASQPPPPPV 360 NEGCVGSGND SNANSIPIPN QNPPQSEMIS HAVEGNSNQN TENPNSRDSD PVVGSSRKEE 420 SPSATVSPPA PSPPPPPPQQ ITAVAKARER EEFRQRQRDE EGLHLLTLLL QCAEAVSADK 480 YEDANKMLVE ISEWATPFGT AAQRVAAYFS EAMSARLVTS CLGIHTSLPS IPHYQKLVSA 540 FQVFNGISPF VKFSHFTANQ AIQEAFQREE RVHIIDLDIM QGLQWPGLFH ILASRPGGPP 600 FVRLTGLGTS METLEATGKR LSDFAEKLGL PFEFIPVAEK VGNLDLERLH VSKREAVAVH 660 WLQHSLYDVT GSDTNTLWLL QRLAPKVVTV VEQDLSRTGS FLGRFVEAIH YYSALFDSLG 720 ASYGEDSEER HVVEQQLLSR EIRNVLAVGG PSRSGEPKFA SWREKMQQSG FRGISLAGNA 780 AAQATLLLGM FPSDGYTLVE DNGTLKLGWK DLCLLTASAW RPSHAHTMST VCTRSQ

Sequence ? help Back to Top

Protein Sequence Length: 836 aa Download sequence Send to blast

MAASSSFFPD PNILLPPFLY SSPSPSPYYD NNINNNNNNT IINNNNYINS HPSFSNYSPF  60
LSPPLPPLMS NNIPQSTPPT PPESSKMVRK RTASEMERAS NVSNHDTIDH RLVSRQQPHQ  120
QFTSVNDPGV FNLAEGSLMD RGSGGVEQQP LVCGFSGLPL FPPVVDRSND NRNTSMSMTT  180
FSGSGSGSGL VSSSVVGGTS IEDPGWVDGI IKDLIQSSNS ISIPQLIQNV REIIYPCNPN  240
LGAVIEFRLR SLADPLIAPP LQPPQQPPPP PHPHAISHYH KQQNHQQAGF SRVNNNNNNI  300
NTSSSSQPGL QNKAYYNLSD IEYFSALGAP ECSANISWGG DQTAPPQSLP RASQPPPPPV  360
NEGCVGSGND SNANSIPIPN QNPPQSEMIS HAVEGNSNQN TENPNSRDSD PVVGSSRKEE  420
SPSATVSPPA PSPPPPPPQQ ITAVAKARER EEFRQRQRDE EGLHLLTLLL QCAEAVSADK  480
YEDANKMLVE ISEWATPFGT AAQRVAAYFS EAMSARLVTS CLGIHTSLPS IPHYQKLVSA  540
FQVFNGISPF VKFSHFTANQ AIQEAFQREE RVHIIDLDIM QGLQWPGLFH ILASRPGGPP  600
FVRLTGLGTS METLEATGKR LSDFAEKLGL PFEFIPVAEK VGNLDLERLH VSKREAVAVH  660
WLQHSLYDVT GSDTNTLWLL QRLAPKVVTV VEQDLSRTGS FLGRFVEAIH YYSALFDSLG  720
ASYGEDSEER HVVEQQLLSR EIRNVLAVGG PSRSGEPKFA SWREKMQQSG FRGISLAGNA  780
AAQATLLLGM FPSDGYTLVE DNGTLKLGWK DLCLLTASAW RPSHAHTMST VCTRSQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_A	0.0	450	822	3	379	Protein SCARECROW
5b3h_D	0.0	450	822	3	379	Protein SCARECROW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Putative transcription factor involved in asymmetric cell division. {ECO:0000250}.
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_021860776.1	0.0	protein SCARECROW 1
Swissprot	Q9AVK4	0.0	SCR_PEA; Protein SCARECROW
Swissprot	Q9M384	0.0	SCR_ARATH; Protein SCARECROW
TrEMBL	A0A0K9RLQ2	0.0	A0A0K9RLQ2_SPIOL; Uncharacterized protein
STRING	XP_010691407.1	0.0	(Beta vulgaris)

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]