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_Os03g31880.1
Common NameLOC9269685, Os03g0433200, OsJ_010915, OSJNBb0031F05.14, SHR2
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: 604aa    MW: 64247.8 Da    PI: 6.3708
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g31880.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS300.93.1e-921896022374
              GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalkl.fsevsPilkf 93 
                        +lL+ecA+av+ +d +++q+l++ l+elasp+gd  q+la+yf+++L arl+ s++++ ++l++ ++++  s +++  + l f+e+sP+  f
  LOC_Os03g31880.1 189 AQLLMECARAVAGRDSQRVQQLMWMLNELASPYGDVDQKLASYFLQGLFARLTTSGPRTLRTLATASDRNA-SFDSTRRTALkFQELSPWTPF 280
                       589************************************************************99988744.44444444446********** PP

              GRAS  94 shltaNqaIleavege...................ervHiiDfdisqGlQWpaLlqaLasRp.egppslRiTgvgspesg...skeeleetge 163
                       +h++aN aIle++ ++                   +r+Hi+D++ + ++QWp+Ll+aLa+R+ +++p+l iT+v++ ++     ++ ++e+g+
  LOC_Os03g31880.1 281 GHVAANGAILESFLEAaaagaaassssssssstppTRLHILDLSNTFCTQWPTLLEALATRSsDDTPHLSITTVVPTAAPsaaAQRVMREIGQ 373
                       ***********986655666677778888888888899************************8889********996655788999******* PP

              GRAS 164 rLakfAeelgvpfefnvlvak.rledleleeLrvkp...gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnse. 251
                       rL+kfA+ +gvpf+f++++++ +l+dl+l +L++++     alaVn+v +l  +          rd+++  +++l+P+vv+vve+ead+ ++ 
  LOC_Os03g31880.1 374 RLEKFARLMGVPFSFRAVHHSgDLADLDLAALDLREggaTAALAVNCVNALRGVA-------RGRDAFVASLRRLEPRVVTVVEEEADLAAPe 459
                       ******************8888**************8877899********9998.......5589********************9997767 PP

              GRAS 252 ...........sFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplseka 333
                                   F++ f e l+++sa +dsle+++p++s+er ++Er+ +gr+iv++v+c  +++ er+et+++W +r+++aGF+p+++se++
  LOC_Os03g31880.1 460 adasseadtdaAFVKVFGEGLRFFSAYMDSLEESFPKTSNERLSLERA-VGRAIVDLVSCPASQSAERRETAASWARRMRSAGFSPAAFSEDV 551
                       89999999999*************************************.******************************************** PP

              GRAS 334 akqaklllrkvksdgyrveee...........sgslvlgWkdrpLvsvSaWr 374
                       a+++++llr++k +g+++ +             + ++l Wk++p+v++SaW+
  LOC_Os03g31880.1 552 ADDVRSLLRRYK-EGWSMRDAggatddaagaaAAGAFLAWKEQPVVWASAWK 602
                       ************.888988555556667777688899**************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098550.842162572IPR005202Transcription factor GRAS
PfamPF035141.1E-89189602IPR005202Transcription 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:0009956Biological Processradial pattern formation
GO:0045930Biological Processnegative regulation of mitotic cell cycle
GO:0048366Biological Processleaf development
GO:0055072Biological Processiron ion homeostasis
GO:0005634Cellular Componentnucleus
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: 604 aa     Download sequence    Send to blast
MDTLFRLVSL HHHHHHQHAA SPSPPDQPHK SYPSSRGSTS SPSSHHTHNH TYYHHSHSHY  60
NNNSNTNYYY QGGGGGGGGY YYAEEQQPAA YLEECGNGHQ FYMDEDFSSS SSSRQFHSGT  120
GAPSSAPVPP PPSATTSSAG GHGLFEAADF SFPQVDISLD FGGSPAVPSS SGAGAGAGAA  180
PSSSGRWAAQ LLMECARAVA GRDSQRVQQL MWMLNELASP YGDVDQKLAS YFLQGLFARL  240
TTSGPRTLRT LATASDRNAS FDSTRRTALK FQELSPWTPF GHVAANGAIL ESFLEAAAAG  300
AAASSSSSSS SSTPPTRLHI LDLSNTFCTQ WPTLLEALAT RSSDDTPHLS ITTVVPTAAP  360
SAAAQRVMRE IGQRLEKFAR LMGVPFSFRA VHHSGDLADL DLAALDLREG GATAALAVNC  420
VNALRGVARG RDAFVASLRR LEPRVVTVVE EEADLAAPEA DASSEADTDA AFVKVFGEGL  480
RFFSAYMDSL EESFPKTSNE RLSLERAVGR AIVDLVSCPA SQSAERRETA ASWARRMRSA  540
GFSPAAFSED VADDVRSLLR RYKEGWSMRD AGGATDDAAG AAAAGAFLAW KEQPVVWASA  600
WKP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_B1e-1591376034420Protein SHORT-ROOT
5b3h_E1e-1591376034420Protein SHORT-ROOT
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.758480.0panicle| root
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ75I13
Functional Description ? help Back to Top
Source Description
UniProtPutative transcription factor involved in asymmetric cell division. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. Arabidopsis thaliana SHORT ROOT protein SHR gene, rice OsSHR1 and OsSHR2, could complement the A. thaliana shr mutant.
    [PMID: 28263767]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g31880.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g31880
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1338610.0AC133861.5 Oryza sativa chromosome 3 BAC OSJNBb0031F05 genomic sequence, complete sequence.
GenBankAP0149590.0AP014959.1 Oryza sativa Japonica Group DNA, chromosome 3, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015629293.10.0protein SHORT-ROOT 2
SwissprotQ75I130.0SHR2_ORYSJ; Protein SHORT-ROOT 2
TrEMBLA0A0E0GPE20.0A0A0E0GPE2_ORYNI; Uncharacterized protein
TrEMBLA0A0E0NWY00.0A0A0E0NWY0_ORYRU; Uncharacterized protein
STRINGOS03T0433200-000.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP35263781
Representative plantOGRP27551332
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G37650.11e-133GRAS family protein
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. Henry S, et al.
    SHR overexpression induces the formation of supernumerary cell layers with cortex cell identity in rice.
    Dev. Biol., 2017. 425(1): p. 1-7
    [PMID:28263767]