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 XP_009785856.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
Family GRAS
Protein Properties Length: 441aa    MW: 50420.2 Da    PI: 5.2764
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009785856.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS324.22.7e-99574303374
            GRAS   3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlt 97 
                     +lL ecA+a+s++d +++++lL+ l+elasp+gd +q+la+yf++AL  + ++++ ++yk+l++ ++++k+ +++ +    f+evsP+ +f+h++
  XP_009785856.1  57 RLLRECATAISEKDSTKIHHLLWMLNELASPYGDCNQKLAFYFLQALFCKATDTGLRCYKTLTSAAEKSKSFDSSRKLILKFQEVSPWTTFGHVA 151
                     7899**********************************************************9999987666666566666************** PP

            GRAS  98 aNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvl.vakrledlel 191
                      N aIlea++ge+++HiiD++ + ++QWp+Ll+aLa+R++++p+l++T+v+ +++  k  ++e+++r++kfA+ +gvpfefnv+   ++l++l+ 
  XP_009785856.1 152 SNGAILEALDGESKLHIIDISHTFCTQWPTLLEALATRNDETPHLKLTVVVTESTLVKSVMKEVAQRMEKFARLMGVPFEFNVIgGLNNLKELTK 246
                     ****************************************************9999***************************97788******* PP

            GRAS 192 eeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh..nsesFlerflealeyysalfdsleaklpreseerik 284
                     e+L++k++Ea+aVn++ +l ++      +e+ r +v+++++sl+Pkvv++ve+ead   ++++F++ f e+l++y+  f++l++++p +s+er +
  XP_009785856.1 247 ESLNIKEEEAVAVNCIGALRKVE-----VEE-RGDVIRILQSLNPKVVTIVEHEADFscTRNDFVKCFEECLRFYTLYFEMLDESFPITSNERLV 335
                     ********************997.....444.889*******************98766899********************************* PP

            GRAS 285 vErellgreivnvvace...gaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrve.....eesgslvlgWkdrpLvsvS 371
                     +Ere  +++iv+v+ac    g+   e +e+ ++W+erl+e  F+p pl+++a++++++ll+++k  g+++      +es  ++l+W+d+p+v++S
  XP_009785856.1 336 IERE-CSKSIVKVLACDdqiGDGDGETRERGNQWSERLREL-FSPFPLNDDAVDDVRSLLKRYK-AGWSLVlpqenQESPGIYLTWRDEPVVWAS 427
                     ****.89*********83334457899999*********98.**********************.666665556556688899************ PP

            GRAS 372 aWr 374
                     aW+
  XP_009785856.1 428 AWK 430
                     **8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098546.19329406IPR005202Transcription factor GRAS
PfamPF035149.3E-9757430IPR005202Transcription factor GRAS
Sequence ? help Back to Top
Protein Sequence    Length: 441 aa     Download sequence    Send to blast
MEKSLFFSKP TNNFLVTNYV HHLINMQNPN QQPHENSSRS QSPENGDPVS DAKWASRLLR  60
ECATAISEKD STKIHHLLWM LNELASPYGD CNQKLAFYFL QALFCKATDT GLRCYKTLTS  120
AAEKSKSFDS SRKLILKFQE VSPWTTFGHV ASNGAILEAL DGESKLHIID ISHTFCTQWP  180
TLLEALATRN DETPHLKLTV VVTESTLVKS VMKEVAQRME KFARLMGVPF EFNVIGGLNN  240
LKELTKESLN IKEEEAVAVN CIGALRKVEV EERGDVIRIL QSLNPKVVTI VEHEADFSCT  300
RNDFVKCFEE CLRFYTLYFE MLDESFPITS NERLVIEREC SKSIVKVLAC DDQIGDGDGE  360
TRERGNQWSE RLRELFSPFP LNDDAVDDVR SLLKRYKAGW SLVLPQENQE SPGIYLTWRD  420
EPVVWASAWK PQEKSMERYD Q
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_B1e-1414143173474Protein SHORT-ROOT
5b3h_B1e-1414143119420Protein SHORT-ROOT
5b3h_E1e-1414143119420Protein 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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0107850.0AP010785.1 Solanum lycopersicum DNA, chromosome 8, clone: C08HBa0040B24, complete sequence.
GenBankHG9755200.0HG975520.1 Solanum lycopersicum chromosome ch08, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009785856.10.0PREDICTED: protein SHORT-ROOT-like
SwissprotQ9SZF71e-141SHR_ARATH; Protein SHORT-ROOT
TrEMBLA0A1U7X8770.0A0A1U7X877_NICSY; protein SHORT-ROOT-like
STRINGXP_009785856.10.0(Nicotiana sylvestris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA20312464
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G37650.11e-143GRAS family protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. Clark NM, et al.
    Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy.
    Elife, 2017.
    [PMID:27288545]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]