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 Lj6g3v0886420.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
Family GRAS
Protein Properties Length: 512aa    MW: 57269.4 Da    PI: 6.503
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lj6g3v0886420.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS345.68.1e-1061495051374
             GRAS   1 lvelLlecAeavssgdlelaqalLarlselaspdg.dpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkf 93 
                      l++lL+ecA a+s ++l +a+++L +l + asp++ +  +R++ayf++A+a+r+++s+ ++++ l         + +  +al++f+++sP++kf
  Lj6g3v0886420.1 149 LITLLMECAVAISVENLIEAHKMLLELTQVASPYKpSCAERVVAYFAKAMASRVMNSMLGVCSPLID-------HRTIHSALQVFNNMSPFIKF 235
                      5789*******************************8999*****************77776654433.......344568999*********** PP

             GRAS  94 shltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrle 187
                      +h+t NqaIleav+++  +HiiD+di+qGlQWp++++ La+R egpp++R+Tg+gs    s e l etg++L++fA++lg++++fn+ v++++ 
  Lj6g3v0886420.1 236 AHFTSNQAILEAVNRCGSIHIIDLDIMQGLQWPPFFHILATRIEGPPEVRMTGMGS----SMELLVETGKNLTNFARRLGISLKFNP-VVTKFG 324
                      ********************************************************....***************************.7999** PP

             GRAS 188 dleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpresee 281
                      +++++ L+ +pgE+laV++    h+l+d +++  +    +L+l+ +l+P+++++veq+++h ++ Fl+rf+ +l+yys+lfdsl a l+++++ 
  Lj6g3v0886420.1 325 EVDVSILKARPGETLAVHWLQ--HSLYDATGPDWK----TLRLLEELEPRIITLVEQDVNH-GGAFLDRFVGSLHYYSTLFDSLGACLHSDDDR 411
                      ********************9..999999999888....**********************.678***************************** PP

             GRAS 282 rikvErellgreivnvvacegaerrerhetlekWrerlee.aGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaW 373
                      r++vE+ ll+rei n++a  g +r  +  ++++Wr+ l + + F +vp+s + ++qa+l+l++++   gy++ + +g+l lgWkd +L+++SaW
  Lj6g3v0886420.1 412 RHSVEHGLLSREINNILAIGGPARSGED-KFRQWRSELARnCCFVQVPMSVNSMAQAQLILNMFSpALGYSLAQVDGTLRLGWKDTSLYTASAW 504
                      ***********************77665.5*****9987559**************************************************** PP

             GRAS 374 r 374
                      +
  Lj6g3v0886420.1 505 T 505
                      6 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098547.428123484IPR005202Transcription factor GRAS
PfamPF035142.8E-103149505IPR005202Transcription factor GRAS
Sequence ? help Back to Top
Protein Sequence    Length: 512 aa     Download sequence    Send to blast
MMKLGFEVLH ANPNIMIRPH MHETWDYPNI ADHHLPPPPT PSNPPYPKPS STENHCINFT  60
QNNEVCDWVE HITKHLVEDI PDTTSDSNLL PNNLFPSQLS HNFNPRKSTC VYDPTSSSNN  120
FNLIQTNTII PVLDHNNHSN IAHDHELTLI TLLMECAVAI SVENLIEAHK MLLELTQVAS  180
PYKPSCAERV VAYFAKAMAS RVMNSMLGVC SPLIDHRTIH SALQVFNNMS PFIKFAHFTS  240
NQAILEAVNR CGSIHIIDLD IMQGLQWPPF FHILATRIEG PPEVRMTGMG SSMELLVETG  300
KNLTNFARRL GISLKFNPVV TKFGEVDVSI LKARPGETLA VHWLQHSLYD ATGPDWKTLR  360
LLEELEPRII TLVEQDVNHG GAFLDRFVGS LHYYSTLFDS LGACLHSDDD RRHSVEHGLL  420
SREINNILAI GGPARSGEDK FRQWRSELAR NCCFVQVPMS VNSMAQAQLI LNMFSPALGY  480
SLAQVDGTLR LGWKDTSLYT ASAWTCGGGA SR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_A1e-13515550524378Protein SCARECROW
5b3h_D1e-13515550524378Protein SCARECROW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Detected in the ground tissue of late heart-stage embryos. After germination, expressed also in the L1 layer throughout the shoot apical meristem including the peripheral zone. Detected in most tissues of young leaf primordia, except in the presumptive vasculature. In mature leaves, expressed in bundle sheath cells. Detected in inflorescence stems in a single internal cell layer corresponding to the starch sheath. {ECO:0000269|PubMed:10631180, ECO:0000269|PubMed:8756724}.
UniprotTISSUE SPECIFICITY: Expressed in siliques, leaves and roots. Detected in the initial daughter cell before its asymmetric division and remains expressed only in the endodermal cell layer after the division. Expressed in the endodermis or starch sheath of the seedling hypocotyl, in the leaf bundle sheath cells and the root quiescent center. {ECO:0000269|PubMed:10631180, ECO:0000269|PubMed:10850497, ECO:0000269|PubMed:11565032, ECO:0000269|PubMed:8756724, ECO:0000269|PubMed:9375406}.
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
PlantRegMapLj6g3v0886420.1
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_029128720.10.0protein SCARECROW
SwissprotQ9M3841e-131SCR_ARATH; Protein SCARECROW
TrEMBLA0A151U4G70.0A0A151U4G7_CAJCA; Protein SCARECROW
STRINGGLYMA13G18680.10.0(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF117873138
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G54220.11e-125GRAS 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]