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 Solyc02g092370.1.1
Common NameLOC101262675
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family GRAS
Protein Properties Length: 508aa    MW: 57399.1 Da    PI: 5.8462
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc02g092370.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS345.96.8e-1061295063374
                GRAS   3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkf 93 
                         + Lle  +a+++++ +++q+l++ l+el+sp+gd+ q+la+yf++AL +r+++s++++y++l + ++++ + +++ + +  f+evsP+ +f
  Solyc02g092370.1.1 129 DILLETSRAIADKNSTRVQQLMWMLNELSSPYGDTEQKLASYFLQALFSRMTDSGERCYRTLLSASDKTCSFESTRKLVLKFQEVSPWTTF 219
                         6799*********************************************************97777775554444455555********** PP

                GRAS  94 shltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg....skeeleetgerLakfAeelgvpfefnv 180
                         +h++ N aI+ea+ege+++HiiD++ ++++QWp+Ll+aLa+R++++p+lR+T+v++++sg     ++ ++e+g+r++kfA+ +gvpf+fnv
  Solyc02g092370.1.1 220 GHVASNGAIMEALEGESKLHIIDISNTYCTQWPTLLEALATRTDETPHLRLTTVVAAASGgaasVQKVMKEIGSRMEKFARLMGVPFKFNV 310
                         ********************************************************999999999999*********************** PP

                GRAS 181 lvak.rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse....sFlerflealeyysa 266
                         +++  +l++l++ +L++k++Eala+n++ +lh++     +  ++rd +++l+++l+P++v++ve+ead++ +    +F+++f e+l++  +
  Solyc02g092370.1.1 311 IHHVgNLSELDMGALDIKEEEALAINCIGALHSVT----PAGNRRDYLISLFRRLQPRIVTIVEEEADLDVGvdgfDFVNGFQECLKWIRV 397
                         96666*****************************8....778889*********************99865556669************** PP

                GRAS 267 lfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrve...ee 354
                          f+sl+++++++s+er ++Er+  gr+iv+++ac  +e+ er+et +kW++r+++ GF+pv +s+++ +++++llr++k dg+++     +
  Solyc02g092370.1.1 398 YFESLDESFSKTSNERLMLERQ-AGRSIVDLLACPPSESMERRETGAKWSHRMHAGGFSPVLYSDEVCDDVRALLRRYK-DGWSMGqcgGD 486
                         **********************.********************************************************.88877744467 PP

                GRAS 355 sgslvlgWkdrpLvsvSaWr 374
                         s+ ++l Wk++p+v++SaW+
  Solyc02g092370.1.1 487 SAGIFLSWKEQPVVWASAWK 506
                         99999**************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098549.619101484IPR005202Transcription factor GRAS
PfamPF035142.3E-103129506IPR005202Transcription 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:0009956Biological Processradial pattern formation
GO:0045930Biological Processnegative regulation of mitotic cell cycle
GO:0048366Biological Processleaf development
GO:0055072Biological Processiron ion homeostasis
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 508 aa     Download sequence    Send to blast
MDTLFRLVSL QQQQQQQSDQ YSFNSSRTSS SSRSSNKQNS TYNYHPHHNH QDEECFNFFM  60
DEDDFSSSSS KHNNYPPPHY NQYQQISTPT TTSSTPTHQS QSQYDHQFSP ARDLNLEFAS  120
SFSGKWATDI LLETSRAIAD KNSTRVQQLM WMLNELSSPY GDTEQKLASY FLQALFSRMT  180
DSGERCYRTL LSASDKTCSF ESTRKLVLKF QEVSPWTTFG HVASNGAIME ALEGESKLHI  240
IDISNTYCTQ WPTLLEALAT RTDETPHLRL TTVVAAASGG AASVQKVMKE IGSRMEKFAR  300
LMGVPFKFNV IHHVGNLSEL DMGALDIKEE EALAINCIGA LHSVTPAGNR RDYLISLFRR  360
LQPRIVTIVE EEADLDVGVD GFDFVNGFQE CLKWIRVYFE SLDESFSKTS NERLMLERQA  420
GRSIVDLLAC PPSESMERRE TGAKWSHRMH AGGFSPVLYS DEVCDDVRAL LRRYKDGWSM  480
GQCGGDSAGI FLSWKEQPVV WASAWKP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_B0.011850778474Protein SHORT-ROOT
5b3h_B0.011850724420Protein SHORT-ROOT
5b3h_E0.011850724420Protein SHORT-ROOT
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the procambium during embryogenesis. {ECO:0000269|PubMed:10850497}.
UniprotTISSUE SPECIFICITY: Expressed in the stele and the quiescent center. Not detected in the ground tissue cell lineage. The SHR protein moves from the stele to a single layer of adjacent cells, where it enters the nucleus. {ECO:0000269|PubMed:10850497, ECO:0000269|PubMed:11565032, ECO:0000269|PubMed:15142972, ECO:0000269|PubMed:15314023}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc02g092370.1.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2154680.0Solanum lycopersicum chromosome 2 clone C02SLe0132D01, complete sequence
GenBankAC2265960.0Solanum lycopersicum chromosome 2 clone C02HBa0146O16, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004231927.10.0protein SHORT-ROOT
SwissprotQ9SZF70.0SHR_ARATH; Protein SHORT-ROOT
TrEMBLA0A3Q7FD170.0A0A3Q7FD17_SOLLC; Uncharacterized protein
STRINGSolyc02g092370.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA20312464
Representative plantOGRP27551332
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G37650.10.0GRAS family protein
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  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]