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 Sopim03g123400.0.1
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: 543aa    MW: 60735.4 Da    PI: 6.3671
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopim03g123400.0.1genomeCSHLView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS243.58.6e-751615412374
                GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykal..ppsetseknsseelaalklfsevsPi 90 
                         ++lL  cA a++ g+++++q+lL  l+elas +gd+++Rlaa+ ++AL ++l++ +s+ +++    +++ s+ n++    +l  f +vsP+
  Sopim03g123400.0.1 161 EHLLNPCAAAITVGNMNRVQHLLYVLHELASFTGDANHRLAAHGLRALTHHLSSPGSSSASSGtiGVTNFSSANHKFFRDSLINFIDVSPW 251
                         699***************************************************666665555115555555555555555555******* PP

                GRAS  91 lkfshltaNqaIleavege...ervHiiDfdisqGlQWpaLlqaLasRp.egppslRiTgvgspesg.........skeeleetgerLakf 168
                         +++ + +aN+ +l+ + ++   + +Hi+D+++s+G+QWp+Ll++L+ R+ ++pp +R+T++ + +++                  ++L  +
  Sopim03g123400.0.1 252 FRIPNNIANSSVLQIIGQQdrlKNLHILDIGVSHGFQWPTLLEELTRRSgGPPPLVRLTVITPTTENgeltgtpfvIGPPGYDFSSQLLAY 342
                         *******************555556************************55666*********888789999888877888999******* PP

                GRAS 169 AeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqe..adhns.esFler 256
                         A+++++++++n l    l++l+ + ++ +++E+l+++ +++lh+l    +++++ r+++Lk++ksl Pk +v++e++  +++ns ++F++ 
  Sopim03g123400.0.1 343 AKAININLQINRLDNFPLQNLNSQIINSSSDETLVICAQFRLHNLN---HTIPDDRTDLLKILKSLDPKGLVLSENNteCSCNScGDFATT 430
                         ************8777*****************************8...8899999*******************983355555269**** PP

                GRAS 257 flealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.s 346
                         f++ +ey + ++ds+++ +    + r + Er++++ e+ +++++ g++    +e++ekW er+++aGF ++ ++e+a + a++llrk++ +
  Sopim03g123400.0.1 431 FSRRVEYLWRFLDSTSVAY----KGRESEERRMMEGEAAKALTNMGEM----NERKEKWCERMRSAGFVKAVFGEDAIDGARALLRKYDsN 513
                         ***************9885....7777888888888899*******99....88888********************************99 PP

                GRAS 347 dgyrveeesgslvlgWkdrpLvsvSaWr 374
                         ++ rvee++g++ l Wk++p+ ++S W+
  Sopim03g123400.0.1 514 WEIRVEEKDGCVDLWWKGQPISFCSLWK 541
                         99*************************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098537.195134520IPR005202Transcription factor GRAS
PfamPF035143.0E-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: 543 aa     Download sequence    Send to blast
MAIEEPEPNS NSDPISEWLA STLSDVPSFF HEPYSYADDL NFYADPWWVP DQEDQIVNHN  60
IIIDNTCNSF NISSPVNTAI NNIPLEPIIL DHPQPVDLSK KRKKSDQNPK ASKKNHKLQI  120
NEAAHAPTIV DQEGVQLKKS IGPKRVTTGN NSNNKEGRWA EHLLNPCAAA ITVGNMNRVQ  180
HLLYVLHELA SFTGDANHRL AAHGLRALTH HLSSPGSSSA SSGTIGVTNF SSANHKFFRD  240
SLINFIDVSP WFRIPNNIAN SSVLQIIGQQ DRLKNLHILD IGVSHGFQWP TLLEELTRRS  300
GGPPPLVRLT VITPTTENGE LTGTPFVIGP PGYDFSSQLL AYAKAININL QINRLDNFPL  360
QNLNSQIINS SSDETLVICA QFRLHNLNHT IPDDRTDLLK ILKSLDPKGL VLSENNTECS  420
CNSCGDFATT FSRRVEYLWR FLDSTSVAYK GRESEERRMM EGEAAKALTN MGEMNERKEK  480
WCERMRSAGF VKAVFGEDAI DGARALLRKY DSNWEIRVEE KDGCVDLWWK GQPISFCSLW  540
KI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_B2e-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}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2469370.0AC246937.1 Solanum lycopersicum chromosome 3 clone HBa0033F13, complete sequence.
GenBankAC2470030.0AC247003.1 Solanum lycopersicum chromosome 3 clone HBa0033F13, complete sequence.
GenBankHG9755150.0HG975515.1 Solanum lycopersicum chromosome ch03, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004235543.10.0nodulation-signaling pathway 1 protein
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-142GRAS 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]