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 RrC1476_p4
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 MYB
Protein Properties Length: 242aa    MW: 27996.6 Da    PI: 9.8938
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1476_p4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding56.56.2e-18550147
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47
                     rg W + Ede+l ++v+q+G+++W++Ia+++  gR++k+c++rw++ 
       RrC1476_p4  5 RGHWRPAEDEKLRELVQQFGPHNWNAIAQKLS-GRSGKSCRLRWFNQ 50
                     899*****************************.***********996 PP
2Myb_DNA-binding55.61.2e-1757100146
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                      r+++T+eE+e+l+  ++ +G++ W+ Iar ++ gRt++ +k++w+ 
       RrC1476_p4  57 RNPFTEEEEERLLASHRIHGNR-WSVIARFFP-GRTDNAVKNHWHV 100
                      789*******************.*********.***********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129424.726155IPR017930Myb domain
SMARTSM007171.4E-14453IPR001005SANT/Myb domain
PfamPF002496.8E-17550IPR001005SANT/Myb domain
SuperFamilySSF466894.12E-30598IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.602.9E-27658IPR009057Homeodomain-like
CDDcd001672.07E-13849No hitNo description
PROSITE profilePS5129418.71356106IPR017930Myb domain
SMARTSM007171.3E-1556104IPR001005SANT/Myb domain
PfamPF002491.7E-145799IPR001005SANT/Myb domain
CDDcd001672.87E-125999No hitNo description
Gene3DG3DSA:1.10.10.606.6E-2159104IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009737Biological Processresponse to abscisic acid
GO:2000652Biological Processregulation of secondary cell wall biogenesis
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 242 aa     Download sequence    Send to blast
MMCSRGHWRP AEDEKLRELV QQFGPHNWNA IAQKLSGRSG KSCRLRWFNQ LDPRINRNPF  60
TEEEEERLLA SHRIHGNRWS VIARFFPGRT DNAVKNHWHV IMARRGRERS KVRPRSLGHD  120
GTAVGPGMMG YKDTDKKRRL GTTTAINYPY SFSHINHFQI LKEFLTGKIG FCNNTTPINE  180
GAVDQTKRPL EFYNFLQVKT DSKKPEVIHN SRKDEEEEDV DSCVPFFDFL SVGNSASHQG  240
LC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1mse_C1e-3121051104C-Myb DNA-Binding Domain
1msf_C1e-3121051104C-Myb DNA-Binding Domain
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that confers sensitivity to abscisic acid (ABA) and salt, but tolerance to drought (PubMed:21399993). Regulates secondary cell wall (SCW) biosynthesis, especially in interfascicular and xylary fibers (PubMed:18952777, PubMed:23781226). {ECO:0000269|PubMed:18952777, ECO:0000269|PubMed:21399993, ECO:0000269|PubMed:23781226}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00145DAPTransfer from AT1G17950Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By abscisic acid (PubMed:16463103, PubMed:21399993). Accumulates in response to salt (PubMed:21399993). Triggered by MYB46 and MYB83 in the regulation of secondary cell wall biosynthesis (PubMed:19674407, PubMed:22197883). {ECO:0000269|PubMed:16463103, ECO:0000269|PubMed:19674407, ECO:0000269|PubMed:21399993, ECO:0000269|PubMed:22197883}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5195540.0AY519554.1 Arabidopsis thaliana MYB transcription factor (At1g17950) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018449713.11e-179PREDICTED: transcriptional activator Myb-like isoform X1
SwissprotQ6R0C41e-156MYB52_ARATH; Transcription factor MYB52
TrEMBLA0A0D3DQ451e-162A0A0D3DQ45_BRAOL; Uncharacterized protein
TrEMBLA0A3P6GAB31e-162A0A3P6GAB3_BRAOL; Uncharacterized protein
STRINGBo8g067590.11e-163(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM28182769
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G17950.11e-159myb domain protein 52
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. Cassan-Wang H, et al.
    Identification of novel transcription factors regulating secondary cell wall formation in Arabidopsis.
    Front Plant Sci, 2013. 4: p. 189
    [PMID:23781226]
  3. Shi D, et al.
    MYB52 Negatively Regulates Pectin Demethylesterification in Seed Coat Mucilage.
    Plant Physiol., 2018. 176(4): p. 2737-2749
    [PMID:29440562]