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 Pp3c7_24880V3.2.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Bryophyta; Bryophytina; Bryopsida; Funariidae; Funariales; Funariaceae; Physcomitrella
Family GRAS
Protein Properties Length: 546aa    MW: 61637.4 Da    PI: 4.8892
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pp3c7_24880V3.2.pgenomeCOSMOSSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS330.92.5e-1011645363374
               GRAS   3 elLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfs 94 
                        +lL+ecA+a++++d +++++l++ l+el sp+gd+ qR+aayf++AL  ++++++s++y+al++ ++++++ ++  ++   ++e+sP+ +f+
  Pp3c7_24880V3.2.p 164 NLLVECARAITANDSARVKNLMWVLNELGSPYGDADQRVAAYFLQALFCKITNTGSSCYRALTAAAERTYSFDTLRKMILDYQEASPWTTFG 255
                        69************************************************************9999997666666555555*********** PP

               GRAS  95 hltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvg.spesgskeeleetgerLakfAeelgvpfefnvlvakr 185
                        h + N a++ea+ege+++Hi+D++ ++++QWp L++aLa+R+eg+p+lR+ +++ spe++  + ++++  rL++fA+ +gvpfe+ v ++ +
  Pp3c7_24880V3.2.p 256 HTAGNGAMMEAFEGETKIHIVDMSSTYCTQWPILFEALATRAEGTPHLRLSTIViSPEESALQVMKQIMTRLERFARLMGVPFEYVVKHEPQ 347
                        **************************************************8876255666999***********************96666* PP

               GRAS 186 ledleleeLrvkpgEalaVnlvlqlhrlldesvsles..erdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleakl 275
                        le+lel +L+++++E+la+ + + lh++ +     e+  +rd +L ++++ +Pk++++ve+e+d++s++F   f+eal++ys lf+sle+++
  Pp3c7_24880V3.2.p 348 LEKLELAALDLRQDEVLAITCNHTLHHVSEIVPRGEQysPRDVLLCTFRNANPKIMILVEEEVDLTSPDFIVCFCEALKFYSLLFESLEENF 439
                        ****************************864433333559**************************************************** PP

               GRAS 276 preseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpL 367
                        pr+s+er  +Er   +r++vn++ c   e +er+et  +W  rl++ GF p p+s+++++++++ll+++k +g+++  +++ l+l Wk++ +
  Pp3c7_24880V3.2.p 440 PRTSNERLILERI-CARNLVNLIGCDPPENVERQETGIQWDLRLKRIGFVPCPFSDDVVDDVRALLKRYK-EGWSLSMNENRLYLAWKEQVV 529
                        ************9.799*****************************************************.9******************** PP

               GRAS 368 vsvSaWr 374
                        + ++aW+
  Pp3c7_24880V3.2.p 530 LCATAWK 536
                        ******8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098550.864136517IPR005202Transcription factor GRAS
PfamPF035148.6E-99164536IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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: 546 aa     Download sequence    Send to blast
MDKLLVKYQE YPQTDQIADL NTSDEAGPTR SSEDSIFEEP RHSARSQLGS GVVSTSLAAR  60
RTPSSEGHQY PNLQSEESRQ SFPSFRLEQH PHEFDSEPRQ LHDQSPRPEW QYYASPVKPS  120
SGKGDLDGNS MIAGFTGLPS EPYRSSTSQT TESSNSSSHQ WAPNLLVECA RAITANDSAR  180
VKNLMWVLNE LGSPYGDADQ RVAAYFLQAL FCKITNTGSS CYRALTAAAE RTYSFDTLRK  240
MILDYQEASP WTTFGHTAGN GAMMEAFEGE TKIHIVDMSS TYCTQWPILF EALATRAEGT  300
PHLRLSTIVI SPEESALQVM KQIMTRLERF ARLMGVPFEY VVKHEPQLEK LELAALDLRQ  360
DEVLAITCNH TLHHVSEIVP RGEQYSPRDV LLCTFRNANP KIMILVEEEV DLTSPDFIVC  420
FCEALKFYSL LFESLEENFP RTSNERLILE RICARNLVNL IGCDPPENVE RQETGIQWDL  480
RLKRIGFVPC PFSDDVVDDV RALLKRYKEG WSLSMNENRL YLAWKEQVVL CATAWKPIAS  540
PSPEP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_B1e-1341365376420Protein SHORT-ROOT
5b3h_E1e-1341365376420Protein 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}.
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_024379763.10.0protein SHORT-ROOT-like
SwissprotQ9SZF71e-133SHR_ARATH; Protein SHORT-ROOT
TrEMBLA0A2K1KCY70.0A0A2K1KCY7_PHYPA; Uncharacterized protein
STRINGPP1S97_39V6.10.0(Physcomitrella patens)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G37650.11e-134GRAS 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]