PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os12g02870.1
Common NameLOC4351362, Os12g0122000, OsJ_033689, SCR2
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: 661aa    MW: 70394.7 Da    PI: 6.3308
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os12g02870.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS410.31.8e-1252936532374
              GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykal.ppsetseknsseelaalklfsevsPilkf 93 
                        +lLl+cAe v++++l +a+++L ++ ela+p g+++qR+aayf+eA++arl++s+ +ly+ l +ps++  + + +++aa+++f+ +sP++kf
  LOC_Os12g02870.1 293 LTLLLQCAESVNADNLDEAHRALLEIAELATPFGTSTQRVAAYFAEAMSARLVSSCLGLYAPLpSPSPAGARVHGRVAAAFQVFNGISPFVKF 385
                       579************************************************************55555555558899999************* PP

              GRAS  94 shltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrl 186
                       sh+taNqaI ea+e+eervHiiD+di+qGlQWp L++ LasRp+gpp++R+Tg+g+    s e+le+tg+rL++fA++lg+pfef + va++ 
  LOC_Os12g02870.1 386 SHFTANQAIQEAFEREERVHIIDLDIMQGLQWPGLFHILASRPGGPPRVRLTGLGA----SMEALEATGKRLSDFADTLGLPFEFCP-VADKA 473
                       ********************************************************....***************************.7**** PP

              GRAS 187 edleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpres 279
                        +l++e+L v ++Ea+aV++    h+l+d ++s ++    +L+l+++l Pkvv++veq+++h s+sFl+rf+ea++yysalfdsl+a+++++s
  LOC_Os12g02870.1 474 GNLDPEKLGVTRREAVAVHWLR--HSLYDVTGSDSN----TLWLIQRLAPKVVTMVEQDLSH-SGSFLARFVEAIHYYSALFDSLDASYSEDS 559
                       ********************99..999999999999....**********************.899*************************** PP

              GRAS 280 eerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSa 372
                        er++vE++ll+rei+nv+a  g +r+ + + +++Wre+l ++GF+  +l  +aa+qa lll +++sdgy++ ee+g+l lgWkd  L+++Sa
  LOC_Os12g02870.1 560 PERHVVEQQLLSREIRNVLAVGGPARTGDVK-FGSWREKLAQSGFRVSSLAGSAAAQAALLLGMFPSDGYTLIEENGALKLGWKDLCLLTASA 651
                       *************************999987.************************************************************* PP

              GRAS 373 Wr 374
                       Wr
  LOC_Os12g02870.1 652 WR 653
                       *8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098562.042266633IPR005202Transcription factor GRAS
PfamPF035146.1E-123293653IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008356Biological Processasymmetric cell division
GO:0009630Biological Processgravitropism
GO:0009956Biological Processradial pattern formation
GO:0048366Biological Processleaf development
GO:0051457Biological Processmaintenance of protein location in nucleus
GO:0090610Biological Processbundle sheath cell fate specification
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009049anatomyinflorescence
PO:0001083developmental stageinflorescence development stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
Sequence ? help Back to Top
Protein Sequence    Length: 661 aa     Download sequence    Send to blast
MGSSSLLLFP SSSSSATHSS YSPSSSSHAI TSLLPPLPSD HHLLLYLDHQ EQHHLAAAMV  60
RKRPASDMDL PPPRRHVTGD LSDVTAAAAG APTLSASAQL PALPTQLPAF HHTDMDLAAP  120
APPAPQQVAA GEGGPPSTAW VDGIIRDIIA SSGAAVSVAQ LIHNVREIIR PCNPDLASIL  180
ELRLRSLLNS DPAPPPPPPS HPALLPPDAT APPPPPTSVA ALPPPPPAQP DKRRREPQCQ  240
EQEPNQPQSP KPPTAEETAA AAAAAAAAAA AAAKERKEEQ RRKQRDEEGL HLLTLLLQCA  300
ESVNADNLDE AHRALLEIAE LATPFGTSTQ RVAAYFAEAM SARLVSSCLG LYAPLPSPSP  360
AGARVHGRVA AAFQVFNGIS PFVKFSHFTA NQAIQEAFER EERVHIIDLD IMQGLQWPGL  420
FHILASRPGG PPRVRLTGLG ASMEALEATG KRLSDFADTL GLPFEFCPVA DKAGNLDPEK  480
LGVTRREAVA VHWLRHSLYD VTGSDSNTLW LIQRLAPKVV TMVEQDLSHS GSFLARFVEA  540
IHYYSALFDS LDASYSEDSP ERHVVEQQLL SREIRNVLAV GGPARTGDVK FGSWREKLAQ  600
SGFRVSSLAG SAAAQAALLL GMFPSDGYTL IEENGALKLG WKDLCLLTAS AWRPIQASGR  660
*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_A0.02766543380Protein SCARECROW
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1160124960.0
Expression AtlasQ2QYF3-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In the basal portion of the P3 leaf primordium, expressed continuously within the stomatal row. At later stages, expressed in guard mother cell (GMC)-forming cells and in subsidiary mother cell (SMC) just before asymmetric division. {ECO:0000269|PubMed:12974810}.
UniprotTISSUE SPECIFICITY: Expressed in the root endodermis, in the cortex/endodermal initial and in the quiescent center. Not expressed in the shoot apical meristem itself, but strongly in the L1 layer. {ECO:0000269|PubMed:12974810}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in asmmetric cell division in the cortex/endodermis progenitor cell and in the process of stomata and ligule formation in leaves. {ECO:0000250}.
UniProtProbable transcription factor involved in asmmetric cell division in the cortex/endodermis progenitor cell and in the process of stomata and ligule formation in leaves. {ECO:0000269|PubMed:12974810}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os12g02870.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDLOC_Os03g31880
IntActSearch Q2QYF3
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs12g02870
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2431310.0AK243131.1 Oryza sativa Japonica Group cDNA, clone: J100030A12, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015620600.10.0protein SCARECROW 2
SwissprotA2ZHL00.0SCR2_ORYSI; Protein SCARECROW 2
SwissprotQ2QYF30.0SCR2_ORYSJ; Protein SCARECROW 2
TrEMBLA0A0E0RD240.0A0A0E0RD24_ORYRU; Uncharacterized protein
STRINGORUFI12G01460.10.0(Oryza rufipogon)
STRINGOS12T0122000-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP137138122
Representative plantOGRP21831437
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G54220.10.0GRAS family protein
Publications ? help Back to Top
  1. Kamiya N,Itoh J,Morikami A,Nagato Y,Matsuoka M
    The SCARECROW gene's role in asymmetric cell divisions in rice plants.
    Plant J., 2003. 36(1): p. 45-54
    [PMID:12974810]
  2. Kamiya N, et al.
    Rice globular embryo 4 (gle4) mutant is defective in radial pattern formation during embryogenesis.
    Plant Cell Physiol., 2003. 44(9): p. 875-83
    [PMID:14519768]
  3. 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]
  4. Lim J, et al.
    Conservation and diversification of SCARECROW in maize.
    Plant Mol. Biol., 2005. 59(4): p. 619-30
    [PMID:16244911]
  5. Cui H, et al.
    An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants.
    Science, 2007. 316(5823): p. 421-5
    [PMID:17446396]
  6. Kaur P, et al.
    Genes controlling plant growth habit in Leymus (Triticeae): maize barren stalk1 (ba1), rice lax panicle, and wheat tiller inhibition (tin3) genes as possible candidates.
    Funct. Integr. Genomics, 2008. 8(4): p. 375-86
    [PMID:18543009]
  7. Sazuka T, et al.
    A rice tryptophan deficient dwarf mutant, tdd1, contains a reduced level of indole acetic acid and develops abnormal flowers and organless embryos.
    Plant J., 2009. 60(2): p. 227-41
    [PMID:19682283]
  8. Wu S, et al.
    A plausible mechanism, based upon Short-Root movement, for regulating the number of cortex cell layers in roots.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(45): p. 16184-9
    [PMID:25352666]
  9. Fan T, et al.
    Rice osa-miR171c Mediates Phase Change from Vegetative to Reproductive Development and Shoot Apical Meristem Maintenance by Repressing Four OsHAM Transcription Factors.
    PLoS ONE, 2015. 10(5): p. e0125833
    [PMID:26023934]
  10. Yi J, et al.
    OsMPK6 plays a critical role in cell differentiation during early embryogenesis in Oryza sativa.
    J. Exp. Bot., 2016. 67(8): p. 2425-37
    [PMID:26912801]
  11. Li S, et al.
    Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa.
    Plant Cell, 2016. 28(5): p. 1025-34
    [PMID:27081181]