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_Os04g50060.1
Common NameLOC4336820, Os04g0590400, OsJ_15968, OSJNBa0086O06.18, OSNPB_040590400
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: 637aa    MW: 71656 Da    PI: 5.466
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g50060.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS370.32.6e-1132626342374
              GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfs 94 
                       ++lL++cA+a + +d+++ ++lL+++++++s +gd+ qRla++f++AL+arla+++s++y++l++++ts   + + l+a+kl++ ++P+ k+s
  LOC_Os04g50060.1 262 TTLLIHCAQAAAIDDHRNSNELLKQIRQRSSAYGDAGQRLAHCFANALEARLAGTGSNIYRSLAAKRTS---VYDILNAFKLYVTACPFKKIS 351
                       689**************************************************************9999...9******************** PP

              GRAS  95 hltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg..skeeleetgerLakfAeelgvpfefnvlvakr 185
                       ++   +aIl+a +g +r+Hi+D++i++G+QWp ++q +++Rp+gpps+RiTgv+ p++g   ++ +e+tg+rL+++A+ ++vpfe+++ +a +
  LOC_Os04g50060.1 352 NFFSIEAILNASKGMTRLHIVDYGIQYGFQWPIFFQRISKRPGGPPSVRITGVDLPQPGfrPAQLIEATGRRLHDYARMFNVPFEYHA-IAAK 443
                       **********************************************************9*999*************************.799* PP

              GRAS 186 ledleleeLrvkp..gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklp 276
                       ++++++e+L++++  +E l+Vn+ +++ +++de v+ +s+r +vLk++++++P+++++   +  +n++ F++rf eal yys+lfd+le++++
  LOC_Os04g50060.1 444 WDTIRVEDLKIDKdkDELLVVNCLFRMRNMMDEMVTDDSPRMQVLKTIRKMNPNLFIHGVVNGTYNAPFFVTRFKEALFYYSSLFDMLETTAS 536
                       ***********9999****************************************************************************** PP

              GRAS 277 reseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvs 369
                       r +e+r  +Er l+gre+ nvvaceg+er+er et+++W+ r  +aGFk++pl+++++k+a++ ++k + + + v+e+++++++gWk+r +++
  LOC_Os04g50060.1 537 RVDENRLLIERDLFGREALNVVACEGTERVERPETYKQWQVRNIRAGFKQLPLNQETVKKARYKVKKSYHRDFLVDEDNKWMLQGWKGRIIFA 629
                       *********************************************************************999********************* PP

              GRAS 370 vSaWr 374
                       +SaW+
  LOC_Os04g50060.1 630 LSAWE 634
                       ****5 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098567.547235614IPR005202Transcription factor GRAS
PfamPF035149.1E-111262634IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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:0009066anatomyanther
PO:0001004developmental stageanther development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 637 aa     Download sequence    Send to blast
MLDSGSYDDV DYGDLFSIPN PPAPHLLNFP LQFFPSNGFI SSADDSHRSP AGMFGSTPSP  60
TSTTTELENS EDLSESADDA VLAYINQFLL EDEEDESCPG TITSVEDSAL LAVEKPFVDI  120
LTASQEACQE NSWIDSCCDF TGNGGLLDTF TTTHAACQPA PCEFEKEKGE CAVHKGRKNP  180
HDDCLLFEEE SRRSKQLAVS EEETVREMFD KVLLCNGECE LRAPLPAEAR NCGVYVKGSG  240
NKRGRKKGKS GASAEDDAVD LTTLLIHCAQ AAAIDDHRNS NELLKQIRQR SSAYGDAGQR  300
LAHCFANALE ARLAGTGSNI YRSLAAKRTS VYDILNAFKL YVTACPFKKI SNFFSIEAIL  360
NASKGMTRLH IVDYGIQYGF QWPIFFQRIS KRPGGPPSVR ITGVDLPQPG FRPAQLIEAT  420
GRRLHDYARM FNVPFEYHAI AAKWDTIRVE DLKIDKDKDE LLVVNCLFRM RNMMDEMVTD  480
DSPRMQVLKT IRKMNPNLFI HGVVNGTYNA PFFVTRFKEA LFYYSSLFDM LETTASRVDE  540
NRLLIERDLF GREALNVVAC EGTERVERPE TYKQWQVRNI RAGFKQLPLN QETVKKARYK  600
VKKSYHRDFL VDEDNKWMLQ GWKGRIIFAL SAWEPN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_A1e-4826763525380Protein SCARECROW
5b3h_A8e-4926763524379Protein SCARECROW
5b3h_D8e-4926763524379Protein SCARECROW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.70580.0callus| flower| leaf| panicle| root| stem| vegetative meristem
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ7XLZ1
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, shoots, flowers and siliques. {ECO:0000269|PubMed:10341448, ECO:0000269|PubMed:18500650}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in plant development. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g50060.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g50060
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAL6629810.0AL662981.3 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0086O06, complete sequence.
GenBankAP0149600.0AP014960.1 Oryza sativa Japonica Group DNA, chromosome 4, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015637021.10.0scarecrow-like protein 9
SwissprotQ9XE581e-165SCL14_ARATH; Scarecrow-like protein 14
TrEMBLA0A0E0H5C80.0A0A0E0H5C8_ORYNI; Uncharacterized protein
TrEMBLA0A0E0PDD20.0A0A0E0PDD2_ORYRU; Uncharacterized protein
TrEMBLQ7XLZ10.0Q7XLZ1_ORYSJ; OSJNBa0086O06.18 protein
STRINGORUFI04G25140.10.0(Oryza rufipogon)
STRINGOS04T0590400-010.0(Oryza sativa)
STRINGONIVA04G22790.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP138412529
Representative plantOGRP26615129
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G07530.11e-155SCARECROW-like 14
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]