PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Thhalv10010179m
Common NameEUTSA_v10010179mg
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Eutremeae; Eutrema
Family GRAS
Protein Properties Length: 657aa    MW: 71780.1 Da    PI: 6.1751
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thhalv10010179mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS426.42.3e-1302946532374
             GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfsh 95 
                       +lLl+cAeavs+++le+a++lL ++s+l++p+g++ qR+aayf eA++arl++s+ ++y+alp++  ++++s + ++a+++f+ +sP++kfsh
  Thhalv10010179m 294 LTLLLQCAEAVSADNLEEANKLLLEISQLSTPYGTSAQRVAAYFSEAMSARLLNSCLGIYAALPSRWMPQTHSLKMVSAFQVFNGISPLVKFSH 387
                      579******************************************************************************************* PP

             GRAS  96 ltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledl 189
                      +taNqaI ea+e+ee vHiiD+di+qGlQWp L++ LasRp+gpp++R+Tg+g     s e+l++tg+rL++fA++lg+pfef + +a+++ +l
  Thhalv10010179m 388 FTANQAIQEAFEKEESVHIIDLDIMQGLQWPGLFHILASRPGGPPHVRLTGLGT----SMEALQATGKRLSDFADKLGLPFEFCP-LAEKVGNL 476
                      ******************************************************....***************************.59****** PP

             GRAS 190 eleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseeri 283
                      + e+L+v+++Ea+aV++    h+l+d ++s ++    +L+l+++l Pkvv+vveq+++h ++sFl rf+ea++yysalfdsl a++++eseer+
  Thhalv10010179m 477 DAERLNVRKREAVAVHWLQ--HSLYDVTGSDTH----TLWLLQRLAPKVVTVVEQDLSH-AGSFLGRFVEAIHYYSALFDSLGASYGEESEERH 563
                      ******************9..999988888777....**********************.899******************************* PP

             GRAS 284 kvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374
                      +vE++ll++ei+nv+a  g +r  + + +e+Wre+++++GFk ++l  +aa+qa lll +++sdgy++ +++g+l lgWkd +L+++SaW+
  Thhalv10010179m 564 VVEQQLLSKEIRNVLAVGGPSRSGEVK-FESWREKMQQCGFKGISLAGNAATQATLLLGMFPSDGYTLVDDNGTLKLGWKDLSLLTASAWT 653
                      *********************888776.**************************************************************6 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098561.664267633IPR005202Transcription factor GRAS
PfamPF035147.9E-128294653IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008356Biological Processasymmetric cell division
GO:0009630Biological Processgravitropism
GO:0009956Biological Processradial pattern formation
GO:0048366Biological Processleaf development
GO:0051457Biological Processmaintenance of protein location in nucleus
GO:0090610Biological Processbundle sheath cell fate specification
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 657 aa     Download sequence    Send to blast
MADSGDFNGA QPPHSPLRTT SSGSSSAPPP PPPPPVMVRK RLASEMSSSS SLNTPDYTNH  60
RPPRRAPHLL DSTYFMTSPP QPPPPVSAVT VDSTTQPTPP LSVCGFSGLP VFPSDRRTAM  120
SIQTMEQDPS ASSSSSPTVW VDAIIRDLIH SSTSVSIPQL IQNVRDIIFP CNPNLGALLE  180
YRLRSLMLLD PSSSSDPSPP QPFDSITQPL YHHQIPNNPS PPVTQQQQQQ QHHKPPPPPP  240
TIQQQERENS STDAPPPETA VTCTATVTTT AEALRERKEE IKRQKQDEEG LHLLTLLLQC  300
AEAVSADNLE EANKLLLEIS QLSTPYGTSA QRVAAYFSEA MSARLLNSCL GIYAALPSRW  360
MPQTHSLKMV SAFQVFNGIS PLVKFSHFTA NQAIQEAFEK EESVHIIDLD IMQGLQWPGL  420
FHILASRPGG PPHVRLTGLG TSMEALQATG KRLSDFADKL GLPFEFCPLA EKVGNLDAER  480
LNVRKREAVA VHWLQHSLYD VTGSDTHTLW LLQRLAPKVV TVVEQDLSHA GSFLGRFVEA  540
IHYYSALFDS LGASYGEESE ERHVVEQQLL SKEIRNVLAV GGPSRSGEVK FESWREKMQQ  600
CGFKGISLAG NAATQATLLL GMFPSDGYTL VDDNGTLKLG WKDLSLLTAS AWTPRS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_A0.02776563382Protein SCARECROW
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription 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
SourceLink
PlantRegMapThhalv10010179m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: 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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEF1045490.0EF104549.1 Thellungiella halophila clone scr_14 genomic sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006403603.10.0protein SCARECROW
SwissprotQ9M3840.0SCR_ARATH; Protein SCARECROW
TrEMBLV4NG290.0V4NG29_EUTSA; Uncharacterized protein
STRINGXP_006403603.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM81642640
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G54220.10.0GRAS family protein
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. Benfey PN
    Defining the Path from Stem Cells to Differentiated Tissue.
    Curr. Top. Dev. Biol., 2016. 116: p. 35-43
    [PMID:26970612]
  17. 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]
  18. Clark NM, et al.
    Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.
    Elife, 2017.
    [PMID:27288545]
  19. Choi JW,Lim J
    Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation.
    Mol. Cells, 2016. 39(7): p. 524-9
    [PMID:27306644]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. Ercoli MF, et al.
    GIF Transcriptional Coregulators Control Root Meristem Homeostasis.
    Plant Cell, 2018. 30(2): p. 347-359
    [PMID:29352064]
  33. 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]