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_scaffold00066.229
Common NameAMTR_s00066p00182770
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: 416aa    MW: 45621.9 Da    PI: 6.1963
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00066.229genomeTAGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS290.64.2e-89504143374
                                      GRAS   3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetse 71 
                                               +l+l cA+a++++d+++ ++lL+ l+elasp+gd  qR aa f++AL  + ++s+++++++l+  +++ 
  evm_27.model.AmTr_v1.0_scaffold00066.229  50 DLILGCAKAITEKDAARSNHLLWMLNELASPYGDRDQRKAAAFLQALFCKASGSGDRCSRILAIVAEKA 118
                                               57899**********************************************************999998 PP

                                      GRAS  72 knsseelaalklfsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegpp 140
                                               ++ +++  +   f+evsP+ +f+h++aN aIlea+eg + +HiiD++ + ++QWpaLl+aLa+R+e++p
  evm_27.model.AmTr_v1.0_scaffold00066.229 119 QTFDSARRVILRFQEVSPWTTFGHVAANGAILEAFEGVHDLHIIDISNTLCTQWPALLEALANRSEDTP 187
                                               777777777777********************************************************* PP

                                      GRAS 141 slRiTgvgspesg...skeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnl 206
                                               +lR+T+++++      +   l e+++r++k+A+ ++vpfef+++        ++ + rv   E++aVnl
  evm_27.model.AmTr_v1.0_scaffold00066.229 188 RLRLTTLVDEGDLggpHGAVLIEVRQRMEKYARLMRVPFEFEAV---GGGLGSIGSVRVTDSEVVAVNL 253
                                               *********665599999*************************6...6666677*************** PP

                                      GRAS 207 vlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleakl 275
                                               v +l r++       ++r++ ++ +  l P+vv+vve+ead+++++++ r++e++++y + +++l++++
  evm_27.model.AmTr_v1.0_scaffold00066.229 254 VGALRRVP------VDARPSAVHGIAALGPRVVTVVEEEADLTGGEWAGRVSECMRFYGTYYEMLDEGF 316
                                               *******9......445789************************************************* PP

                                      GRAS 276 preseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkv 344
                                               +r seer  +Er+  gre+v    ce ae    +e+  +W+er+++aGF+p++++ +a +++++ll+++
  evm_27.model.AmTr_v1.0_scaffold00066.229 317 GRVSEERLALERQ-CGRELVHTMGCESAE--GGRERSLRWSERMRNAGFGPAAFNFDAIDDVRALLKRY 382
                                               *************.8*************9..77778899****************************** PP

                                      GRAS 345 ksdgyrve..eesgslvlgWkdrpLvsvSaWr 374
                                               +++   v     +  l+l Wkd+p+v++SaW+
  evm_27.model.AmTr_v1.0_scaffold00066.229 383 AGRWSVVSgeVPDTGLYLSWKDQPVVWASAWK 414
                                               *66444443255999****************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098542.9922392IPR005202Transcription factor GRAS
PfamPF035141.4E-8650414IPR005202Transcription 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: 416 aa     Download sequence    Send to blast
MSLGTLKPTF IKPNCHDQTM HHTCKDRIDA ASTSQLSESG DLAAGKWVFD LILGCAKAIT  60
EKDAARSNHL LWMLNELASP YGDRDQRKAA AFLQALFCKA SGSGDRCSRI LAIVAEKAQT  120
FDSARRVILR FQEVSPWTTF GHVAANGAIL EAFEGVHDLH IIDISNTLCT QWPALLEALA  180
NRSEDTPRLR LTTLVDEGDL GGPHGAVLIE VRQRMEKYAR LMRVPFEFEA VGGGLGSIGS  240
VRVTDSEVVA VNLVGALRRV PVDARPSAVH GIAALGPRVV TVVEEEADLT GGEWAGRVSE  300
CMRFYGTYYE MLDEGFGRVS EERLALERQC GRELVHTMGC ESAEGGRERS LRWSERMRNA  360
GFGPAAFNFD AIDDVRALLK RYAGRWSVVS GEVPDTGLYL SWKDQPVVWA SAWKP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_B1e-1183041568474Protein SHORT-ROOT
5b3h_B1e-1193041514420Protein SHORT-ROOT
5b3h_E1e-1193041514420Protein SHORT-ROOT
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 both cell division and cell specification. Regulates the radial organization of the shoot axial organs and is required for normal shoot gravitropism. Directly controls the transcription of SCR, and when associated with SCR, of MGP, RLK, TRI, NUC and SCL3. {ECO:0000269|PubMed:10850497, ECO:0000269|PubMed:12569126, ECO:0000269|PubMed:15314023, ECO:0000269|PubMed:16640459, ECO:0000269|PubMed:17446396, ECO:0000269|PubMed:9670559}.
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_006858846.30.0protein SHORT-ROOT
SwissprotQ9SZF71e-119SHR_ARATH; Protein SHORT-ROOT
TrEMBLU5DIA70.0U5DIA7_AMBTC; Uncharacterized protein
STRINGERN203130.0(Amborella trichopoda)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP27551332
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G37650.11e-121GRAS family protein
Publications ? help Back to Top
  1. Amborella Genome Project
    The Amborella genome and the evolution of flowering plants.
    Science, 2013. 342(6165): p. 1241089
    [PMID:24357323]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. Muraro D, et al.
    Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(2): p. 857-62
    [PMID:24381155]
  4. 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]
  5. 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]
  6. Ahrazem O, et al.
    Ectopic expression of a stress-inducible glycosyltransferase from saffron enhances salt and oxidative stress tolerance in Arabidopsis while alters anchor root formation.
    Plant Sci., 2015. 234: p. 60-73
    [PMID:25804810]
  7. 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]
  8. 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]
  9. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  10. Miguel A,Milhinhos A,Novák O,Jones B,Miguel CM
    The SHORT-ROOT-like gene PtSHR2B is involved in Populus phellogen activity.
    J. Exp. Bot., 2016. 67(5): p. 1545-55
    [PMID:26709311]
  11. 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]
  12. Kim ES, et al.
    HAWAIIAN SKIRT regulates the quiescent center-independent meristem activity in Arabidopsis roots.
    Physiol Plant, 2016. 157(2): p. 221-33
    [PMID:26968317]
  13. 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]
  14. 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]
  15. Clark NM, et al.
    Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.
    Elife, 2017.
    [PMID:27288545]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. Henry S, et al.
    SHR overexpression induces the formation of supernumerary cell layers with cortex cell identity in rice.
    Dev. Biol., 2017. 425(1): p. 1-7
    [PMID:28263767]
  22. Möller BK, et al.
    Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539
    [PMID:28265057]
  23. 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]
  24. 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]
  25. 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]
  26. Yu Q, et al.
    Cell-Fate Specification in Arabidopsis Roots Requires Coordinative Action of Lineage Instruction and Positional Reprogramming.
    Plant Physiol., 2017. 175(2): p. 816-827
    [PMID:28821591]
  27. Spiegelman Z,Lee CM,Gallagher KL
    KinG Is a Plant-Specific Kinesin That Regulates Both Intra- and Intercellular Movement of SHORT-ROOT.
    Plant Physiol., 2018. 176(1): p. 392-405
    [PMID:29122988]
  28. 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]