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_Os07g39820.1
Common NameLOC4343753, OJ1047_C01.1, OJ1113_E01.116, Os07g0586900, OsJ_24926, SHR1
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: 603aa    MW: 64709.3 Da    PI: 5.7639
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os07g39820.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS314.62.1e-961936012374
              GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalkl.fsevsPilkf 93 
                        +lLlecA+ v+++d +++q+l++ l+elasp+gd  q+la+yf+++L arl+ s++++ ++l++ +++++ s +++  + l f+e+sP+  f
  LOC_Os07g39820.1 193 SQLLLECARSVAARDSQRVQQLMWMLNELASPYGDVEQKLASYFLQGLFARLTASGPRTLRTLAAASDRNT-SFDSTRRTALrFQELSPWSSF 284
                       589************************************************************99888744.44444444446********** PP

              GRAS  94 shltaNqaIleavege........ervHiiDfdisqGlQWpaLlqaLasRp.egppslRiTgvgspesg.....skeeleetgerLakfAeel 172
                       +h++aN aIle++ +         +r Hi+D++ + ++QWp+Ll+aLa+R+ +++p+l iT+v+s++++      ++ ++e+g+r++kfA+ +
  LOC_Os07g39820.1 285 GHVAANGAILESFLEVaaaassetQRFHILDLSNTFCTQWPTLLEALATRSaDETPHLSITTVVSAAPSaptaaVQRVMREIGQRMEKFARLM 377
                       ***********8754434455567999************************8889**********988889999999**************** PP

              GRAS 173 gvpfefnvlvak.rledleleeLrvkp...gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh.nse......... 251
                       gvpf+f++++++ +l++l+l++L++++     alaVn+v +l  ++  ++  + +rd++   +++l P+vv+vve+ead+   +         
  LOC_Os07g39820.1 378 GVPFRFRAVHHSgDLAELDLDALDLREggaTTALAVNCVNSLRGVV--PGRAR-RRDAFAASLRRLDPRVVTVVEEEADLvA-Sdpdassate 466
                       *********8888**************888889************9..55555.59***********************954.44899***** PP

              GRAS 252 .......sFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqa 337
                               Fl+ f e l+++sa +dsle+++p++s+er  +Er   gr+iv++v+c  +e+ er+et+++W +r+++aGF+pv++se++a+++
  LOC_Os07g39820.1 467 eggdteaAFLKVFGEGLRFFSAYMDSLEESFPKTSNERLALERG-AGRAIVDLVSCPASESMERRETAASWARRMRSAGFSPVAFSEDVADDV 558
                       ********************************************.************************************************ PP

              GRAS 338 klllrkvksdgyrveee.......sgslvlgWkdrpLvsvSaWr 374
                       ++llr++  +g+++ e         + ++l Wk++pLv++SaWr
  LOC_Os07g39820.1 559 RSLLRRYR-EGWSMREAgtddsaaGAGVFLAWKEQPLVWASAWR 601
                       ********.88888866666666455566**************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098552.633166575IPR005202Transcription factor GRAS
PfamPF035147.2E-94193601IPR005202Transcription 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:0009047anatomystem
PO:0007010developmental stagewhole plant fruit ripening stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 603 aa     Download sequence    Send to blast
MDTLFRLVSL QAASEQQQQQ QQSASYNSRS TTSSGSRSSS HQTNASYSYY HHSSNSGGGG  60
GGGGGYYYGG QQPPPSQYYY LEPYQEECGN APHHQLYMDE DFSSSSSSRH FHHGARVQQQ  120
QPPASSTPTG TAPTPPLSTS STAAGAGHGL FEAADLSFPP DLNLDFSSPA SSSGGGTASS  180
GAVGGGGGGR WASQLLLECA RSVAARDSQR VQQLMWMLNE LASPYGDVEQ KLASYFLQGL  240
FARLTASGPR TLRTLAAASD RNTSFDSTRR TALRFQELSP WSSFGHVAAN GAILESFLEV  300
AAAASSETQR FHILDLSNTF CTQWPTLLEA LATRSADETP HLSITTVVSA APSAPTAAVQ  360
RVMREIGQRM EKFARLMGVP FRFRAVHHSG DLAELDLDAL DLREGGATTA LAVNCVNSLR  420
GVVPGRARRR DAFAASLRRL DPRVVTVVEE EADLVASDPD ASSATEEGGD TEAAFLKVFG  480
EGLRFFSAYM DSLEESFPKT SNERLALERG AGRAIVDLVS CPASESMERR ETAASWARRM  540
RSAGFSPVAF SEDVADDVRS LLRRYREGWS MREAGTDDSA AGAGVFLAWK EQPLVWASAW  600
RP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_B1e-16018760228420Protein SHORT-ROOT
5b3h_E1e-16018760228420Protein SHORT-ROOT
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.441710.0callus| flower| root
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO379905820.0
Expression AtlasQ8H2X8-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In P3 leaf primordium, expressed ubiquitously in the L1 layer and in the inner cells at lower levels. Not limited to the developing stomata until the last cell divisions. {ECO:0000269|PubMed:12974810}.
UniprotTISSUE SPECIFICITY: Expressed in leaves and roots. Detected in the stele, the endodermis and part of the cortex. {ECO:0000269|PubMed:12974810, ECO:0000269|PubMed:17446396}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor required for the asymmetric cell division involved in radial pattern formation in roots. Essential for both cell division and cell specification. {ECO:0000269|PubMed:17446396}.
Function -- GeneRIF ? help Back to Top
  1. Arabidopsis thaliana SHR gene, rice OsSHR1 and OsSHR2, could complement the A. thaliana shr mutant.
    [PMID: 28263767]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os07g39820.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDLOC_Os11g03110, LOC_Os12g02870
IntActSearch Q8H2X8
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs07g39820
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0039850.0AP003985.4 Oryza sativa Japonica Group genomic DNA, chromosome 7, BAC clone:OJ1047_C01.
GenBankAP0054370.0AP005437.3 Oryza sativa Japonica Group genomic DNA, chromosome 7, BAC clone:OJ1113_E01.
GenBankAP0149630.0AP014963.1 Oryza sativa Japonica Group DNA, chromosome 7, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015645491.10.0protein SHORT-ROOT 1
SwissprotQ8H2X80.0SHR1_ORYSJ; Protein SHORT-ROOT 1
TrEMBLA0A0E0QAI80.0A0A0E0QAI8_ORYRU; Uncharacterized protein
STRINGORUFI07G21310.10.0(Oryza rufipogon)
STRINGOS07T0586900-010.0(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-144GRAS family protein
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. 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]
  3. 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]
  4. 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]
  5. 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]