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 RrC3_p9
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: 279aa    MW: 32025.4 Da    PI: 4.754
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC3_p9genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding513.3e-161663148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     rg+W+++Ed++l+  ++++G ++W++ ++  g+ R++k+c++rw +yl
          RrC3_p9 16 RGPWSQDEDLKLISFIHKYGHENWRSLPNQAGLLRCGKSCRLRWINYL 63
                     89******************************99************97 PP
2Myb_DNA-binding47.73.6e-1569116148
                      TSSS-HHHHHHHHHHHHHTTTT.-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGgg.tWktIartmgkgRtlkqcksrwqkyl 48 
                      rg++T eE+e ++++++ +G++  W++Ia++++ gRt++++k+ w+++l
          RrC3_p9  69 RGNFTLEEEETIIKLHQSFGNKsMWSKIASKLP-GRTDNEIKNVWHTHL 116
                      89*******************************.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.608.4E-24766IPR009057Homeodomain-like
PROSITE profilePS5129414.991163IPR017930Myb domain
SuperFamilySSF466891.27E-2714112IPR009057Homeodomain-like
SMARTSM007176.9E-131565IPR001005SANT/Myb domain
PfamPF002493.1E-151663IPR001005SANT/Myb domain
CDDcd001671.90E-91863No hitNo description
PROSITE profilePS5129423.71164120IPR017930Myb domain
Gene3DG3DSA:1.10.10.607.5E-2567120IPR009057Homeodomain-like
SMARTSM007175.0E-1168118IPR001005SANT/Myb domain
PfamPF002491.2E-1369116IPR001005SANT/Myb domain
CDDcd001671.13E-971116No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009809Biological Processlignin biosynthetic process
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:2000652Biological Processregulation of secondary cell wall biogenesis
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 279 aa     Download sequence    Send to blast
MGKGRAPCCD KTKVKRGPWS QDEDLKLISF IHKYGHENWR SLPNQAGLLR CGKSCRLRWI  60
NYLRPDLKRG NFTLEEEETI IKLHQSFGNK SMWSKIASKL PGRTDNEIKN VWHTHLKKRL  120
SSYINHNASD EAATKGSLNR EETSQESSPN ASRSFGGSNI VSKEDDDVQI GETFECFQDY  180
SELAGMLQEV DKPELLEIPF DIDPDVWNFI DGFQQPENSL TPRAHQESEE AEVDKWFKNL  240
ESELGLEEDN SQQQEQPNEA KEESPSPSLL ESYELLINH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A5e-23161227110B-MYB
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional activator that binds DNA to the AC cis-elements 5'-ACCTACC-3', 5'-ACCAACC-3' and 5'-ACCTAAC-3' of promoters and specifically activates lignin biosynthetic genes during secondary wall formation mediated by SND1. {ECO:0000269|PubMed:19122102}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00144DAPTransfer from AT1G16490Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Slightly induced by light (PubMed:9839469). Regulated by the SND1 close homologs NST1, NST2, VND6, and VND7 and their downstream targets MYB46 and MYB83 (PubMed:19122102, PubMed:22197883). {ECO:0000269|PubMed:19122102, ECO:0000269|PubMed:22197883, ECO:0000269|PubMed:9839469}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKM9756540.0KM975654.1 Brassica napus MYB transcription factor 58.1 (MYB58.1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018436893.10.0PREDICTED: myb-related protein Zm1-like isoform X2
SwissprotQ9SA471e-149MYB58_ARATH; Transcription factor MYB58
TrEMBLA0A397YCH71e-180A0A397YCH7_BRACM; Uncharacterized protein
STRINGBra026720.1-P1e-180(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM4282646
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G16490.11e-145myb domain protein 58
Publications ? help Back to Top
  1. Fernández-Pérez F,Vivar T,Pomar F,Pedreño MA,Novo-Uzal E
    Peroxidase 4 is involved in syringyl lignin formation in Arabidopsis thaliana.
    J. Plant Physiol., 2015. 175: p. 86-94
    [PMID:25506770]
  2. Noda S, et al.
    The expression of a rice secondary wall-specific cellulose synthase gene, OsCesA7, is directly regulated by a rice transcription factor, OsMYB58/63.
    Planta, 2015. 242(3): p. 589-600
    [PMID:26070439]
  3. Takeuchi M,Kegasa T,Watanabe A,Tamura M,Tsutsumi Y
    Expression analysis of transporter genes for screening candidate monolignol transporters using Arabidopsis thaliana cell suspensions during tracheary element differentiation.
    J. Plant Res., 2018. 131(2): p. 297-305
    [PMID:28921082]