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_Os06g40780.1
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: 667aa    MW: 69779.1 Da    PI: 6.1484
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os06g40780.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS300.73.6e-922766622374
              GRAS   2 velLlecAeavssgdlelaqalLarlsel.aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkf 93 
                       ++lLl+cA+ ++ gdl +a+++ + +    asp+gd+  Rla +f++ALa r+  +  +  + +    ++      +  a+ +f+++ P+l+f
  LOC_Os06g40780.1 276 RDLLLACADLLQRGDLPAARRAAEIVLAAaASPRGDAADRLAYHFARALALRVDAK-AGHGHVVVGGGAA---RPASSGAYLAFNQIAPFLRF 364
                       689*****************9999876665***********************993.3334444333333...4566778999********** PP

              GRAS  94 shltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRp...egppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvl.. 181
                       +hltaNqaIleav+g++rvHi+D+d+ +G+QWp+Llqa+a+R+    gpp++R+Tg g+    ++++l +tg+rL+ fA+++++pf+f++l  
  LOC_Os06g40780.1 365 AHLTANQAILEAVDGARRVHILDLDAVHGVQWPPLLQAIAERAdpaLGPPEVRVTGAGA----DRDTLLRTGNRLRAFARSIHLPFHFTPLll 453
                       *******************************************66666***********....9***************************99 PP

              GRAS 182 .................vakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse...... 251
                                        +a + ++     L+++p+E+laVn+v+ lh+l       ++e  ++Lk vk +sP vv+++e+ea  +++      
  LOC_Os06g40780.1 454 scattaphhvagtstgaAAAASTAAAATGLEFHPDETLAVNCVMFLHNLA-----GHDELAAFLKWVKAMSPAVVTIAEREAGGGGGggdhid 541
                       999999888777776644445555578889*******************8.....2233567*******************999665578888 PP

              GRAS 252 sFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkv 344
                       ++ +r+  a+++ysa+f++lea++p+ s+er  vE+e+lgrei+ +v  +g +     +  e+W  + ++aGF + pls +a++qa+lllr +
  LOC_Os06g40780.1 542 DLPRRVGVAMDHYSAVFEALEATVPPGSRERLAVEQEVLGREIEAAVGPSGGR---WWRGIERWGGAARAAGFAARPLSAFAVSQARLLLRLH 631
                       9***********************************************99998...78899******************************** PP

              GRAS 345 k.sdgyrveeesgslvlgWkdrpLvsvSaWr 374
                       + s+gy v+e +g+ +lgW++rpL+svSaW+
  LOC_Os06g40780.1 632 YpSEGYLVQEARGACFLGWQTRPLLSVSAWQ 662
                       ******************************6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098552.577249641IPR005202Transcription factor GRAS
PfamPF035141.2E-89276662IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010014Biological Processmeristem initiation
GO:0010223Biological Processsecondary shoot formation
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: 667 aa     Download sequence    Send to blast
MHESDELLLL VAFLTLGISL SPSCPLLALC EGWKQGISAC CGCMTQMHMS LLVGNDGVQV  60
EVMIDCLIWG LRHSIQGCPM PCPHIHSQLV ELSPSPPLFA IFHLFANVLY QDALDYMQCE  120
TLTQLDQVWG VCLFLLQGSY LEAIINEDPT KGQNMRWLET WEAAIASPDV GRARSPSLLN  180
PPSSDAPSPP PPSPPPPPPS PAAHRRCSSS GGGGGDDDGY GGGDGMLRSL HSSSSSDTDN  240
NSGGCKNNGG GGGEAAAAVE GGGDQRAVAA AAPSTRDLLL ACADLLQRGD LPAARRAAEI  300
VLAAAASPRG DAADRLAYHF ARALALRVDA KAGHGHVVVG GGAARPASSG AYLAFNQIAP  360
FLRFAHLTAN QAILEAVDGA RRVHILDLDA VHGVQWPPLL QAIAERADPA LGPPEVRVTG  420
AGADRDTLLR TGNRLRAFAR SIHLPFHFTP LLLSCATTAP HHVAGTSTGA AAAASTAAAA  480
TGLEFHPDET LAVNCVMFLH NLAGHDELAA FLKWVKAMSP AVVTIAEREA GGGGGGGDHI  540
DDLPRRVGVA MDHYSAVFEA LEATVPPGSR ERLAVEQEVL GREIEAAVGP SGGRWWRGIE  600
RWGGAARAAG FAARPLSAFA VSQARLLLRL HYPSEGYLVQ EARGACFLGW QTRPLLSVSA  660
WQPSSS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A4e-4929766223375GRAS family transcription factor containing protein, expressed
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.513581e-72stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329726531e-72
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in a small number of epidermal or subepidermal cells at the leaf axils, in axillary meristems and the entire tiller buds. Undetected in the shoot apical meristem. {ECO:0000269|PubMed:12687001}.
Functional Description ? help Back to Top
Source Description
UniProtPutative transcription regulator that controls rice tillering by initiating axillary buds and promoting their outgrowth. Rice tiller is a specialized grain-bearing branch that is formed on the unelongated basal internode and grows independently of the mother stem (culm) by means of its own adventitious roots. {ECO:0000269|PubMed:12687001}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os06g40780.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs06g40780
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0036160.0AP003616.4 Oryza sativa Japonica Group genomic DNA, chromosome 6, PAC clone:P0490F09.
GenBankAP0149620.0AP014962.1 Oryza sativa Japonica Group DNA, chromosome 6, cultivar: Nipponbare, complete sequence.
GenBankAY2420580.0AY242058.1 Oryza sativa (japonica cultivar-group) MONOCULM 1 (MOC1) gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015642672.10.0protein MONOCULM 1
SwissprotQ84MM90.0MOC_ORYSJ; Protein MONOCULM 1
TrEMBLA0A0E0HTD60.0A0A0E0HTD6_ORYNI; Uncharacterized protein
STRINGONIVA06G24530.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP36533479
Representative plantOGRP54911421
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G55580.14e-65GRAS family protein
Publications ? help Back to Top
  1. Li X, et al.
    Control of tillering in rice.
    Nature, 2003. 422(6932): p. 618-21
    [PMID:12687001]
  2. Sun F, et al.
    Identification and functional analysis of the MOC1 interacting protein 1.
    J Genet Genomics, 2010. 37(1): p. 69-77
    [PMID:20171579]
  3. Sanyal A, et al.
    Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum.
    Mol. Biol. Evol., 2010. 27(11): p. 2487-506
    [PMID:20522726]
  4. Yan WH, et al.
    A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice.
    Mol Plant, 2011. 4(2): p. 319-30
    [PMID:21148627]
  5. Xu C, et al.
    Degradation of MONOCULM 1 by APC/C(TAD1) regulates rice tillering.
    Nat Commun, 2012. 3: p. 750
    [PMID:22434193]
  6. Lin Q, et al.
    Rice APC/C(TE) controls tillering by mediating the degradation of MONOCULM 1.
    Nat Commun, 2012. 3: p. 752
    [PMID:22434195]
  7. Liang WH,Shang F,Lin QT,Lou C,Zhang J
    Tillering and panicle branching genes in rice.
    Gene, 2014. 537(1): p. 1-5
    [PMID:24345551]
  8. Zhang B, et al.
    Novel function of a putative MOC1 ortholog associated with spikelet number per spike in common wheat.
    Sci Rep, 2015. 5: p. 12211
    [PMID:26197925]