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 Sopen03g041180.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family GRAS
Protein Properties Length: 542aa    MW: 60736.4 Da    PI: 6.2704
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopen03g041180.1genomespennView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS2422.5e-741615412374
              GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykal..ppsetseknsseelaalklfsevsPilk 92 
                       ++lL  cA a++ g+++++q+lL  l+elas +gd+++Rlaa+ ++AL ++l++ +s+ +++    +++ s+ n++    +l  f +vsP+++
  Sopen03g041180.1 161 EHLLNPCAAAITVGNMNRVQHLLYVLHELASFTGDANHRLAAHGLRALTHHLSSPGSSSASSGtiGVTNFSSANHKFFRDSLINFIDVSPWFR 253
                       699***************************************************666665555115555555555555555555********* PP

              GRAS  93 fshltaNqaIleavege...ervHiiDfdisqGlQWpaLlqaLasRp.egppslRiTgvgspesg.........skeeleetgerLakfAeel 172
                       + + +aN+ +l+ + ++   + +Hi+D+++s+G+QWp+Ll++L+ R+ ++pp +R+T++ + +++                  ++L  +A+++
  Sopen03g041180.1 254 IPNNIANSSVLQIIGEQdrlKNLHILDIGVSHGFQWPTLLEELTRRSgGPPPLVRLTVITPTTENgeltgtpfvIGPPGYDFSSQLLAYAKAI 346
                       ***************99555556************************55666*********888789999888877888999*********** PP

              GRAS 173 gvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh..ns.esFlerfleale 262
                       ++++++n l    l++l+ + ++ +++E+l+++ +++lh+l    +++++ r+++Lk++ksl Pk +v++e+++++  ns ++F++ f++ +e
  Sopen03g041180.1 347 NINLQINRLDNFPLQNLNSQIINSSSDETLVICAQFRLHNLN---HTIPDDRTDLLKILKSLDPKGLVLSENNTECgcNScGDFATTFSRRVE 436
                       ********8777*****************************8...8899999*******************996663354259********** PP

              GRAS 263 yysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveee 354
                       y + ++ds+++ +    + r + Er++++ e+ +++++ g++    +e++ekW er+++aGF ++ ++e+a + a++llrk++ +++ r+ee+
  Sopen03g041180.1 437 YLWRFLDSTSVAY----KGRESEERRMMEGEAAKALTNMGEM----NERKEKWCERMRSAGFVKAVFGEDAIDGARALLRKYDsNWEIRLEEK 521
                       *********9885....7777888888888899*******99....88888********************************9999****** PP

              GRAS 355 sgslvlgWkdrpLvsvSaWr 374
                       +g++ l Wk++p+ ++S W+
  Sopen03g041180.1 522 DGCVDLWWKGQPISFCSLWK 541
                       *******************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098537.162134520IPR005202Transcription factor GRAS
PfamPF035148.5E-72161541IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0042446Biological Processhormone biosynthetic process
GO:2000032Biological Processregulation of secondary shoot formation
Sequence ? help Back to Top
Protein Sequence    Length: 542 aa     Download sequence    Send to blast
MAIEEPEPNS NSDPISEWLA STLSDVPSFF HEPYSYTDDL NFYAEPWWVP DQEDQIVNHN  60
IIIDNTCNSF NISSPVNTAI NNIPLEPIIL DHPQPVDLSK KRKKSDQNPK ASKKNHKLQV  120
NEAEHAPTIV DQGGVQLKKS IGPKRVTTGN NSNNKEGRWA EHLLNPCAAA ITVGNMNRVQ  180
HLLYVLHELA SFTGDANHRL AAHGLRALTH HLSSPGSSSA SSGTIGVTNF SSANHKFFRD  240
SLINFIDVSP WFRIPNNIAN SSVLQIIGEQ DRLKNLHILD IGVSHGFQWP TLLEELTRRS  300
GGPPPLVRLT VITPTTENGE LTGTPFVIGP PGYDFSSQLL AYAKAININL QINRLDNFPL  360
QNLNSQIINS SSDETLVICA QFRLHNLNHT IPDDRTDLLK ILKSLDPKGL VLSENNTECG  420
CNSCGDFATT FSRRVEYLWR FLDSTSVAYK GRESEERRMM EGEAAKALTN MGEMNERKEK  480
WCERMRSAGF VKAVFGEDAI DGARALLRKY DSNWEIRLEE KDGCVDLWWK GQPISFCSLW  540
KI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_B4e-3215754184473Protein SHORT-ROOT
5b3h_B2e-3215754130419Protein SHORT-ROOT
5b3h_E2e-3215754130419Protein SHORT-ROOT
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
199103KKRKK
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional regulator essential for Nod-factor-induced gene expression. Acts downstream of calcium spiking. May be a target of DMI3, a calcium/calmodulin-dependent protein kinase (CCaMK) (PubMed:15961669). Is essential for Nod factor-elicited expression of ERN1 (PubMed:23077241). {ECO:0000269|PubMed:15961669, ECO:0000269|PubMed:23077241}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not induced after treatment with Sinorhizobium meliloti. {ECO:0000269|PubMed:15961669}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9754420.0HG975442.1 Solanum pennellii chromosome ch03, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015069847.10.0nodulation-signaling pathway 1 protein-like
SwissprotQ4VYC80.0NSP1_MEDTR; Nodulation-signaling pathway 1 protein
TrEMBLA0A3Q7FUJ30.0A0A3Q7FUJ3_SOLLC; Uncharacterized protein
STRINGSolyc03g123400.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49492139
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G13840.11e-141GRAS family protein
Publications ? help Back to Top
  1. Cerri MR, et al.
    Medicago truncatula ERN transcription factors: regulatory interplay with NSP1/NSP2 GRAS factors and expression dynamics throughout rhizobial infection.
    Plant Physiol., 2012. 160(4): p. 2155-72
    [PMID:23077241]
  2. Tang H, et al.
    An improved genome release (version Mt4.0) for the model legume Medicago truncatula.
    BMC Genomics, 2014. 15: p. 312
    [PMID:24767513]