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 RrC562_p6
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family GRAS
Protein Properties Length: 493aa    MW: 55293.9 Da    PI: 6.4424
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC562_p6genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS448.93.4e-1371234932374
       GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaNqa 101
                +  L++cA+a+s++dl +a++++++l++++s +g+p+qRl ay++e+L a+la+s+s++yk+l+  +++   s+e l+++++++ev+P+lkf+++ aN a
  RrC562_p6 123 RADLVSCAQALSENDLMMAHSMMEKLRQMVSVSGEPIQRLGAYLLEGLVAKLASSGSSIYKSLNRFPEP--ASTELLSYMNILYEVCPYLKFGYMSANGA 220
                678************************************************************988887..599************************** PP

       GRAS 102 IleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg..skeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpg 199
                I ea+++e+rvHiiDf+i qG QW++L+qa+a+Rp+gpp++RiTgv++ +s   +   l+ +g+rLak+A++++vpfefn  v+ + +++el++L v+pg
  RrC562_p6 221 IAEAMKEENRVHIIDFQICQGSQWVTLIQAFAARPGGPPRIRITGVDDTTSAyaRGGGLSIVGNRLAKLAKQFNVPFEFNS-VSVSASEVELKDLGVRPG 319
                ************************************************998899999************************.7999************** PP

       GRAS 200 EalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvva 299
                Ea aVn+++ lh+++desvs++++rd++L++vkslsPkvv++veqe+++n++sF+ rf e+++yy a+f+s++++lpr++++ri+vE+++l+r++vn++a
  RrC562_p6 320 EAPAVNFAFVLHHMPDESVSTKNHRDRLLRMVKSLSPKVVTLVEQESNTNTASFFPRFKETMDYYDAMFESIDVTLPRNHKQRINVEQHCLARDLVNIIA 419
                **************************************************************************************************** PP

       GRAS 300 cegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374
                cega+r+erhe l+kW++r+e+aGF+++pls  +++++k+llr+++++ yr+ee++g+l+lgW++r Lv+ +aWr
  RrC562_p6 420 CEGADRVERHELLGKWKARFEMAGFTSYPLSPLVNSTIKSLLRNYSDK-YRLEERDGALYLGWMQRDLVASCAWR 493
                **********************************************55.*************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098569.00496474IPR005202Transcription factor GRAS
PfamPF035141.2E-134123493IPR005202Transcription factor GRAS
Sequence ? help Back to Top
Protein Sequence    Length: 493 aa     Download sequence    Send to blast
MYKHPRQEIE AYSLPPVGNL RYIPVHNSLK RYCMLEPSSS SLVSPAYTVL SNAKVNSSAY  60
EDTSGSCVTD DFNDKIKELE TVMMGPDSLD LVFTYNDSSD STSCQETNSW RSTLEAISRH  120
DLRADLVSCA QALSENDLMM AHSMMEKLRQ MVSVSGEPIQ RLGAYLLEGL VAKLASSGSS  180
IYKSLNRFPE PASTELLSYM NILYEVCPYL KFGYMSANGA IAEAMKEENR VHIIDFQICQ  240
GSQWVTLIQA FAARPGGPPR IRITGVDDTT SAYARGGGLS IVGNRLAKLA KQFNVPFEFN  300
SVSVSASEVE LKDLGVRPGE APAVNFAFVL HHMPDESVST KNHRDRLLRM VKSLSPKVVT  360
LVEQESNTNT ASFFPRFKET MDYYDAMFES IDVTLPRNHK QRINVEQHCL ARDLVNIIAC  420
EGADRVERHE LLGKWKARFE MAGFTSYPLS PLVNSTIKSL LRNYSDKYRL EERDGALYLG  480
WMQRDLVASC AWR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A6e-661264938375GRAS family transcription factor containing protein, expressed
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in phytochrome A (phyA) signal transduction. {ECO:0000269|PubMed:10817761}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018482554.10.0PREDICTED: scarecrow-like transcription factor PAT1 isoform X1
RefseqXP_018482555.10.0PREDICTED: scarecrow-like transcription factor PAT1 isoform X1
RefseqXP_018482556.10.0PREDICTED: scarecrow-like transcription factor PAT1 isoform X1
RefseqXP_018482557.10.0PREDICTED: scarecrow-like transcription factor PAT1 isoform X1
RefseqXP_018482558.10.0PREDICTED: scarecrow-like transcription factor PAT1 isoform X1
RefseqXP_018482560.10.0PREDICTED: scarecrow-like transcription factor PAT1 isoform X1
SwissprotQ9LDL70.0PAT1_ARATH; Scarecrow-like transcription factor PAT1
TrEMBLA0A0D3DBQ40.0A0A0D3DBQ4_BRAOL; Uncharacterized protein
STRINGBo7g089080.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM62128141
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G48150.20.0GRAS family protein
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]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. Heyman J, et al.
    The heterodimeric transcription factor complex ERF115-PAT1 grants regeneration competence.
    Nat Plants, 2016. 2(11): p. 16165
    [PMID:27797356]