PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os12g06540.1
Common NameOsJ_35316
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family GRAS
Protein Properties Length: 463aa    MW: 50587.6 Da    PI: 4.2822
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os12g06540.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS92.28e-291753063132
              GRAS   3 elLlecAeavssgdlelaqalLarlsel.aspdgd.......pmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsev 87 
                       +lLl+ A av++gd+  a+a+++rl +l a  +g+       p+  la yf+++L+ r+++      +a p+s+ ++     +  a+++++e+
  LOC_Os12g06540.1 175 DLLLAGAMAVDAGDAVHASAIMSRLDDLlADIAGRrsceatsPVDHLAYYFARGLKLRISG------AATPASSPPPPAANWSSPAYRMLQEL 261
                       689999*******************998766666456666679******************......3344444444445667789******* PP

              GRAS  88 sPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaL 132
                       +P++kf+h+taNqaIlea++ +  vH++Df++++G+QW +L+ +L
  LOC_Os12g06540.1 262 TPFVKFAHFTANQAILEATADDLDVHVVDFNVGEGVQWSSLMLKL 306
                       ******************************************776 PP
2GRAS43.64.7e-14308459227373
              GRAS 227 vLklvkslsPkvvvvveqeadh.nse..........sFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrer 308
                       +L ++  l+Pk+v+++e e+++ +++          +F e f++a+ +++a+++s+++ l + ++e ++++ + +g+e   vv  + ++ + r
  LOC_Os12g06540.1 308 LLGTITILQPKLVILIEDELSRiSKNppspslaappPFPEFFSDAVAHFTAVMESTASCLVSYDDE-AWLSLRRVGEE---VVGPRVEDAVGR 396
                       6899999************999544489****************************8776554433.33332223433...344555555556 PP

              GRAS 309 hetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrve.eesgslvlgWkdrpLvsvSaW 373
                         +l+   +++e  G+++ ++s + ++q k+l   ++  g+ v  +e+g l l+Wk+rpL+svS W
  LOC_Os12g06540.1 397 YGSLAGGAQMME--GLRAREVSGFSVAQGKMLAGLFG-GGFGVVhQEKGRLALCWKSRPLISVSLW 459
                       666677778876..***********************.67876638899999************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098518.766147462IPR005202Transcription factor GRAS
PfamPF035142.8E-26175306IPR005202Transcription factor GRAS
PfamPF035141.6E-11308459IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
Sequence ? help Back to Top
Protein Sequence    Length: 463 aa     Download sequence    Send to blast
METMSYPCSL LIPFSTQFEE ISSSSLLLWS PQAEENPHEN ANMYEFDADH SHDQIHQDHQ  60
FLDMMVIQES ANEFDGNHSH DQIHQDHEFL ETMVIQESAN EFDGDHSHDQ IHQDHEFLEM  120
MAIQESANDL LQLQDDFSVP NADPLAASFE FDERLAVAGH ENGNVVATQE ESAGDLLLAG  180
AMAVDAGDAV HASAIMSRLD DLLADIAGRR SCEATSPVDH LAYYFARGLK LRISGAATPA  240
SSPPPPAANW SSPAYRMLQE LTPFVKFAHF TANQAILEAT ADDLDVHVVD FNVGEGVQWS  300
SLMLKLLLLG TITILQPKLV ILIEDELSRI SKNPPSPSLA APPPFPEFFS DAVAHFTAVM  360
ESTASCLVSY DDEAWLSLRR VGEEVVGPRV EDAVGRYGSL AGGAQMMEGL RAREVSGFSV  420
AQGKMLAGLF GGGFGVVHQE KGRLALCWKS RPLISVSLWC PK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A2e-1420430624131GRAS family transcription factor containing protein, expressed
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ2QXC1
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os12g06540.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs12g06540
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAL7139060.0AL713906.3 Oryza sativa chromosome 12, . BAC OJ1587_D05 of library Monsanto from chromosome 12 of cultivar Nipponbare of ssp. japonica of Oryza sativa (rice), complete sequence.
GenBankAP0149680.0AP014968.1 Oryza sativa Japonica Group DNA, chromosome 12, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025809511.14e-67nodulation-signaling pathway 2 protein-like isoform X2
TrEMBLA0A0E0RE570.0A0A0E0RE57_ORYRU; Uncharacterized protein
TrEMBLQ2QXC10.0Q2QXC1_ORYSJ; GRAS family transcription factor containing protein
STRINGORUFI12G04390.10.0(Oryza rufipogon)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP171141111
Representative plantOGRP8945915
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G50650.12e-12GRAS family protein
Publications ? help Back to Top
  1. Rice Chromosomes 11 and 12 Sequencing Consortia
    The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications.
    BMC Biol., 2005. 3: p. 20
    [PMID:16188032]