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_013623665.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family GRAS
Protein Properties Length: 532aa    MW: 59395.3 Da    PI: 5.46
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013623665.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS380.62e-1161485303374
            GRAS   3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetsekn.sseelaalkl.fsevsPilkfsh 95 
                     + Lle+A+a+s++d+++aq++L++l+e++sp+gd+ q+l +yf++AL +r+++s++++y+++ + +++ek+ s e++  + l f+evsP+ +f+h
  XP_013623665.1 148 SILLEAARAFSDKDTTRAQQILWTLNEISSPYGDTEQKLSSYFLQALVNRMTGSGERCYRTMVTAAATEKTcSFEQTRKTMLkFQEVSPWATFGH 242
                     689***********************************************************999999888533443333337************ PP

            GRAS  96 ltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg......skeeleetgerLakfAeelgvpfefnvlvak 184
                     ++aN aIleav+ge ++Hi+D++ + ++QWp+Ll+aLa+R++++p+lR+T+++ +++       s++ ++e+g+r++kfA+ +gvpf fn++++ 
  XP_013623665.1 243 VAANGAILEAVDGEAKIHIVDISSTFCTQWPTLLEALATRSDDTPHLRLTTIVVANKYvndqtaSHRVMKEIGHRMEKFARLMGVPFTFNIIHHA 337
                     ****************************************************9987778999999***************************777 PP

            GRAS 185 .rledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh.nse....sFlerflealeyysalfdslea 273
                      +l+++++++L++k++E+laVn+v ++h ++    +  ++rd++++ +++l+P+++++ve+ead+ ++e    +Fl+ f e+l+++ ++f sle+
  XP_013623665.1 338 gDLSEFDPNKLDIKSDEVLAVNCVGAMHGIV----PRGNPRDALISKFRRLRPRIMTIVEEEADLvGEEgfddEFLRLFGESLRWFRVCFGSLEE 428
                     7*****************************8....888899************************776677778999999*************** PP

            GRAS 274 klpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdg..yrve.eesgslvlgWkdr 365
                     ++pr+s er ++Er+  gr+iv+vvace ++++er+et++kW++r+++ GF +v +s+++a+++k+llr++k +g   +v+ ++s+ ++l+W+d+
  XP_013623665.1 429 SFPRTSTERLTLERA-AGRAIVDVVACEPSDSTERRETARKWSMRMRNGGFDAVGYSDEVADDVKALLRRYK-EGvwSMVQcSDSAGIFLCWRDQ 521
                     ***************.********************************************************.4444778834566677****** PP

            GRAS 366 pLvsvSaWr 374
                     p+v++SaWr
  XP_013623665.1 522 PVVWASAWR 530
                     ********8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098551.176120508IPR005202Transcription factor GRAS
PfamPF035146.8E-114148530IPR005202Transcription factor GRAS
Sequence ? help Back to Top
Protein Sequence    Length: 532 aa     Download sequence    Send to blast
MDTLFTLVSL QQQQSDSIIT NKSSQSRTST TTTGSPQIAD HYNFPQSDVV EECLNFFMDE  60
EDLSSSNSSQ HNHHHNNNPS NYYSPFTTPT QYHPATSPTP SSTAAAVAAS ASLASPYSSG  120
HHPDPSDFSI SQTPPSFDFS ANAKWADSIL LEAARAFSDK DTTRAQQILW TLNEISSPYG  180
DTEQKLSSYF LQALVNRMTG SGERCYRTMV TAAATEKTCS FEQTRKTMLK FQEVSPWATF  240
GHVAANGAIL EAVDGEAKIH IVDISSTFCT QWPTLLEALA TRSDDTPHLR LTTIVVANKY  300
VNDQTASHRV MKEIGHRMEK FARLMGVPFT FNIIHHAGDL SEFDPNKLDI KSDEVLAVNC  360
VGAMHGIVPR GNPRDALISK FRRLRPRIMT IVEEEADLVG EEGFDDEFLR LFGESLRWFR  420
VCFGSLEESF PRTSTERLTL ERAAGRAIVD VVACEPSDST ERRETARKWS MRMRNGGFDA  480
VGYSDEVADD VKALLRRYKE GVWSMVQCSD SAGIFLCWRD QPVVWASAWR PT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_B0.0585323475Protein 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
PlantRegMapXP_013623665.1
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_013623665.10.0PREDICTED: protein SHORT-ROOT-like
SwissprotQ9SZF70.0SHR_ARATH; Protein SHORT-ROOT
TrEMBLA0A0D3BJT20.0A0A0D3BJT2_BRAOL; Uncharacterized protein
TrEMBLA0A3P6BR420.0A0A3P6BR42_BRAOL; Uncharacterized protein
STRINGBo3g153360.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM61042547
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. 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]