PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID evm_27.model.AmTr_v1.0_scaffold00032.155
Common NameAMTR_s00032p00179410
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella
Family GRAS
Protein Properties Length: 466aa    MW: 50150.9 Da    PI: 6.0519
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00032.155genomeTAGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS3764.8e-115874483374
                                      GRAS   3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetse 71 
                                                lLl+cAeav+ +dl la+ lL ++ +lasp g+p  R+aayf+ AL+arl++s+ ++y+ +p+ + + 
  evm_27.model.AmTr_v1.0_scaffold00032.155  87 GLLLQCAEAVAMDDLDLASCLLPEITHLASPFGSPAVRVAAYFADALQARLVSSWLGVYAPVPSHALE- 154
                                               58*********************************************************999988886. PP

                                      GRAS  72 knsseelaalklfsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegpp 140
                                               + s++ l+a+++++ +sP++kfsh+taNqaI++av++++r+HiiD+di+qGlQWp L++ L++R+++pp
  evm_27.model.AmTr_v1.0_scaffold00032.155 155 RFSQRLLHAFQAYNAISPLVKFSHFTANQAIVQAVSQASRIHIIDLDIMQGLQWPGLFHLLSTRSSSPP 223
                                               679999*************************************************************** PP

                                      GRAS 141 slRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlq 209
                                               s+RiTg+gs     +++l +tg+rL++fA +lg+ fe++ l++++ e  +l +L+++ gE+++V++ + 
  evm_27.model.AmTr_v1.0_scaffold00032.155 224 SVRITGLGS----CTRTLAATGDRLSEFAGSLGLAFEYTGLACRAGEVGDLARLKLRAGETVVVHWLH- 287
                                               *********....9***************************99999999*****************99. PP

                                      GRAS 210 lhrlldesvsleserdevLklvkslsPkvvvvveqeadh.nsesFlerflealeyysalfdsleaklpr 277
                                                h l+d ++s +     +Lkl+ s++P+++++veq+ +h +++ Fl rf+eal+yysalfd+l +   +
  evm_27.model.AmTr_v1.0_scaffold00032.155 288 -HCLYDVTGSDAG----LLKLLHSTKPRLITMVEQDFNHgGGGGFLGRFVEALHYYSALFDALGSMQDS 351
                                               .888888888888....**********************9999********************99999* PP

                                      GRAS 278 eseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk. 345
                                               ++++r+ vE+++lgrei+n+va  g +r+ +   +e+W + l++ GF+ v+l  +aa+qa lll +++ 
  evm_27.model.AmTr_v1.0_scaffold00032.155 352 TNQDRHIVEQQVLGREIKNIVAVGGPKRTGEVV-VERWPAELGKLGFRGVSLAGSAADQAGLLLGMYPw 419
                                               ***************************998887.9********************************** PP

                                      GRAS 346 sdgyrveeesgslvlgWkdrpLvsvSaWr 374
                                               ++gy++ ee g+l lgWkd pL+++SaW+
  evm_27.model.AmTr_v1.0_scaffold00032.155 420 QEGYTLVEEGGCLRLGWKDLPLLTASAWE 448
                                               ****************************5 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098555.43659427IPR005202Transcription factor GRAS
PfamPF035141.6E-11287448IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
Sequence ? help Back to Top
Protein Sequence    Length: 466 aa     Download sequence    Send to blast
MDETPPWIHL LAPPAGIQPP SPESGAGTKR HHPNLPESST GRHDEDAGEA ETSLSENKRK  60
QRKSETGKEA PNYAIEDEES SGLRLLGLLL QCAEAVAMDD LDLASCLLPE ITHLASPFGS  120
PAVRVAAYFA DALQARLVSS WLGVYAPVPS HALERFSQRL LHAFQAYNAI SPLVKFSHFT  180
ANQAIVQAVS QASRIHIIDL DIMQGLQWPG LFHLLSTRSS SPPSVRITGL GSCTRTLAAT  240
GDRLSEFAGS LGLAFEYTGL ACRAGEVGDL ARLKLRAGET VVVHWLHHCL YDVTGSDAGL  300
LKLLHSTKPR LITMVEQDFN HGGGGGFLGR FVEALHYYSA LFDALGSMQD STNQDRHIVE  360
QQVLGREIKN IVAVGGPKRT GEVVVERWPA ELGKLGFRGV SLAGSAADQA GLLLGMYPWQ  420
EGYTLVEEGG CLRLGWKDLP LLTASAWEPS LKDAPFSPST LTEAT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_A1e-147684493379Protein SCARECROW
5b3h_D1e-147684493379Protein SCARECROW
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtPutative transcription factor involved in asymmetric cell division. {ECO:0000250}.
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
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006853441.20.0protein SCARECROW
SwissprotQ9AVK41e-144SCR_PEA; Protein SCARECROW
SwissprotQ9M3841e-144SCR_ARATH; Protein SCARECROW
TrEMBLU5D3G50.0U5D3G5_AMBTC; Uncharacterized protein
STRINGERN149080.0(Amborella trichopoda)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP21831437
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G54220.11e-145GRAS 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. Amborella Genome Project
    The Amborella genome and the evolution of flowering plants.
    Science, 2013. 342(6165): p. 1241089
    [PMID:24357323]
  5. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. Benfey PN
    Defining the Path from Stem Cells to Differentiated Tissue.
    Curr. Top. Dev. Biol., 2016. 116: p. 35-43
    [PMID:26970612]
  18. 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]
  19. Clark NM, et al.
    Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.
    Elife, 2017.
    [PMID:27288545]
  20. Choi JW,Lim J
    Control of Asymmetric Cell Divisions during Root Ground Tissue Maturation.
    Mol. Cells, 2016. 39(7): p. 524-9
    [PMID:27306644]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. Ercoli MF, et al.
    GIF Transcriptional Coregulators Control Root Meristem Homeostasis.
    Plant Cell, 2018. 30(2): p. 347-359
    [PMID:29352064]
  34. 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]