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 Rsa1.0_05821.1_g00001.1
Organism
Raphanus sativus
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: 868aa    MW: 95411.6 Da    PI: 7.4105
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_05821.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS423.51.7e-1291314882361
                     GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsev 87 
                              +  L++cA+a+s++dl +a++++++l++++s +g+p+qRl ay++e+L a+la+s+s++yk+l+  +++   s+e l+++++++ev
  Rsa1.0_05821.1_g00001.1 131 RADLVSCAQALSENDLMMAHSMMEKLRQMVSVSGEPIQRLGAYLLEGLVAKLASSGSSIYKSLNRFPEP--ASTELLSYMNILYEV 214
                              678************************************************************988887..599************ PP

                     GRAS  88 sPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg..skeeleetgerLakfAee 171
                              +P+lkf+++ aN aI ea+++e+rvHiiDf+i qG QW++L+qa+a+Rp+gpp +RiTgv++ +s   +   l+ +g+rLak+A++
  Rsa1.0_05821.1_g00001.1 215 CPYLKFGYMSANGAIAEAMKEENRVHIIDFQICQGSQWVTLIQAFAARPGGPPWIRITGVDDTTSAyaRGGGLSIVGNRLAKLAKQ 300
                              **************************************************************998899999*************** PP

                     GRAS 172 lgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerf 257
                              ++vpfefn  v+ + +++el++L v+pgE+laVn+++ lh+++desvs+e++rd++L++vkslsPkvv++veqe+++n++sF+ rf
  Rsa1.0_05821.1_g00001.1 301 FNVPFEFNS-VSVSASEVELKDLGVRPGESLAVNFAFVLHHMPDESVSTENHRDRLLRMVKSLSPKVVTLVEQESNTNTASFFPRF 385
                              *********.7999************************************************************************ PP

                     GRAS 258 lealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrk 343
                               e+++yy a+f+s++++lpr++++ri+vE+++l+r++vn++acega+r+erhe l+kW++r+e+aGF+++pls  +++++k+llr+
  Rsa1.0_05821.1_g00001.1 386 KETMDYYDAMFESIDVTLPRNHKQRINVEQHCLARDLVNIIACEGADRVERHELLGKWKARFEMAGFTSYPLSPLVNSTIKSLLRN 471
                              ************************************************************************************** PP

                     GRAS 344 vksdgyrveeesgslvlg 361
                              ++++ yr+ee++g+l+lg
  Rsa1.0_05821.1_g00001.1 472 YSDK-YRLEERDGALYLG 488
                              **55.**********997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098569.171104482IPR005202Transcription factor GRAS
PfamPF035145.9E-127131488IPR005202Transcription factor GRAS
SuperFamilySSF511262.51E-102489860IPR011050Pectin lyase fold/virulence factor
Gene3DG3DSA:2.160.20.102.4E-108492863IPR012334Pectin lyase fold
PfamPF002951.1E-110518846IPR000743Glycoside hydrolase, family 28
SMARTSM00710640641667IPR006626Parallel beta-helix repeat
SMARTSM00710320668689IPR006626Parallel beta-helix repeat
SMARTSM007108900691711IPR006626Parallel beta-helix repeat
PROSITE patternPS005020698711IPR000743Glycoside hydrolase, family 28
SMARTSM007105.7721742IPR006626Parallel beta-helix repeat
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005975Biological Processcarbohydrate metabolic process
GO:0004650Molecular Functionpolygalacturonase activity
Sequence ? help Back to Top
Protein Sequence    Length: 868 aa     Download sequence    Send to blast
MYKHPRQEIE AYSLPPVGNL RYIPVHNSLK RYCMLEPSSS SSSSSSSSSL VSPAYTVLSN  60
AKVNSSAYED TSGSCVTDDF NDKIKELETV MMGPDSLDLV FTYNDSSDST SCQETNSWRS  120
TLEAISRHDL RADLVSCAQA LSENDLMMAH SMMEKLRQMV SVSGEPIQRL GAYLLEGLVA  180
KLASSGSSIY KSLNRFPEPA STELLSYMNI LYEVCPYLKF GYMSANGAIA EAMKEENRVH  240
IIDFQICQGS QWVTLIQAFA ARPGGPPWIR ITGVDDTTSA YARGGGLSIV GNRLAKLAKQ  300
FNVPFEFNSV SVSASEVELK DLGVRPGESL AVNFAFVLHH MPDESVSTEN HRDRLLRMVK  360
SLSPKVVTLV EQESNTNTAS FFPRFKETMD YYDAMFESID VTLPRNHKQR INVEQHCLAR  420
DLVNIIACEG ADRVERHELL GKWKARFEMA GFTSYPLSPL VNSTIKSLLR NYSDKYRLEE  480
RDGALYLGLS ANAKDFTVTA PPGSDITSLL LKTFNEACQF PTKSSVLIPK GEYKLRPIEM  540
MGPCKAPIRI TLQGTVKADG NVNGNDYWVA FRRINGFKLN GGGIFDGEGN AAWRANNCHK  600
MALTKCKKLP ISIRFDFVTD AKIRGITSLD SKNFHINVLG ARNMTMEEIT IIAPDESPNT  660
DGIHIGRSDG VQIINSIIKT GDDCISIGDG TKNLLVQGVT CGPGHGISIG SLGLYGKEED  720
VTGIRVVNCT LTNTDNGVRI KTWPSSACST TASGIHFENI FLRNVTNPIL IDQEYCPWNQ  780
CNKNKPSSIK LVDISFKNIR GTSANKDAVK LLCSKGFPCK NVEIGDINIR YNGADGPATF  840
QCSNLSPKLM GIQVPRACSS PVTKLPGQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A6e-581344778348GRAS 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_05821.1_g00001.1
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
TrEMBLA0A3P5Z5D70.0A0A3P5Z5D7_BRACM; Uncharacterized protein
STRINGBra037509.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM35022
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]