PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Kaladp0069s0091.1.p
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Saxifragales; Crassulaceae; Kalanchoe
Family GRAS
Protein Properties Length: 253aa    MW: 28103.2 Da    PI: 8.9012
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Kaladp0069s0091.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
                 GRAS 120 sqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledl.eleeLrvkpgEalaVnlvl 208
                          +qGlQWpaL++ La+R egpp++R+Tg+g+   gs+e l etg++L+ fA++lg++fef++l a+++ +l +++++++++gEalaV++  
                          69****************************...89**************************7.55555555******************9 PP

                 GRAS 209 qlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvv 298
                            h+l+d +++ ++    +++l++ + Pk++++v+q+++h  +sFl+rf+++l+yys+lfdsl a+lp ++ +r+ vE+ l++rei n+ 
                          ..99*999999999....**********************.789********************************************** PP

                 GRAS 299 acegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374
                          a  g +r  +  ++++Wr+ l++ GF++vp+s + ++qa+l++ +++  +gy++   +g+l lgWk+ +L+++SaW+
                          ******77665.5***************************************************************6 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF035141.1E-671245IPR005202Transcription factor GRAS
PROSITE profilePS5098534.1921224IPR005202Transcription factor GRAS
Sequence ? help Back to Top
Protein Sequence    Length: 253 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_A3e-981245138379Protein SCARECROW
5b3h_A2e-981245137378Protein SCARECROW
5b3h_D2e-981245137378Protein 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}.
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
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017233335.11e-136PREDICTED: protein SCARECROW-like
SwissprotQ9M3849e-95SCR_ARATH; Protein SCARECROW
TrEMBLA0A169WM711e-135A0A169WM71_DAUCS; Uncharacterized protein
STRINGVIT_07s0005g03700.t011e-133(Vitis vinifera)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G54220.14e-97GRAS 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
  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
  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
  4. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
  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
  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
  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.
  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
  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
  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
  11. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
  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
  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
  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
  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
  16. Benfey PN
    Defining the Path from Stem Cells to Differentiated Tissue.
    Curr. Top. Dev. Biol., 2016. 116: p. 35-43
  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
  18. Clark NM, et al.
    Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.
    Elife, 2017.
  19. Choi JW,Lim J
    Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation.
    Mol. Cells, 2016. 39(7): p. 524-9
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  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
  32. Ercoli MF, et al.
    GIF Transcriptional Coregulators Control Root Meristem Homeostasis.
    Plant Cell, 2018. 30(2): p. 347-359
  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