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 RrC6819_p1
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: 31563.4 Da    PI: 6.3591
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC6819_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding45.12.2e-142067148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     +g W++eEd +l ++    G g+W+ +a+  g+ R++k+c++rw +yl
       RrC6819_p1 20 KGLWSPEEDSKLMQYMISNGQGCWSDVAKNAGLQRCGKSCRLRWINYL 67
                     678*******************************************97 PP
2Myb_DNA-binding48.91.5e-1573116146
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                      rg+++++E++l+++ +  lG++ W+ Ia++++ gRt++++k++w++
       RrC6819_p1  73 RGAFSPQEEDLIIRFHSILGNR-WSQIAARLP-GRTDNEIKNFWNS 116
                      89********************.*********.***********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.601.3E-221470IPR009057Homeodomain-like
PROSITE profilePS5129416.011567IPR017930Myb domain
SuperFamilySSF466891.25E-2718114IPR009057Homeodomain-like
SMARTSM007175.9E-111969IPR001005SANT/Myb domain
PfamPF002491.5E-132067IPR001005SANT/Myb domain
CDDcd001678.06E-92367No hitNo description
PROSITE profilePS5129424.44968122IPR017930Myb domain
Gene3DG3DSA:1.10.10.602.5E-2571123IPR009057Homeodomain-like
SMARTSM007172.3E-1572120IPR001005SANT/Myb domain
PfamPF002491.7E-1473116IPR001005SANT/Myb domain
CDDcd001671.76E-1075115No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009751Biological Processresponse to salicylic acid
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0050832Biological Processdefense response to fungus
GO:1901348Biological Processpositive regulation of secondary cell wall biogenesis
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 279 aa     Download sequence    Send to blast
MRKPEVAAIA ATHQAKKMKK GLWSPEEDSK LMQYMISNGQ GCWSDVAKNA GLQRCGKSCR  60
LRWINYLRPD LKRGAFSPQE EDLIIRFHSI LGNRWSQIAA RLPGRTDNEI KNFWNSTIKK  120
RLKKMSDTSN LVNNSSSSPN ASDSSSNSSS SLEFKDIIGS FMSLQEQGFI NPSLTNIPTN  180
NNPFPAPHMI SHLFNDDFTP YADGFCGVNT GLQGELYFPP LECEEGNWYK GEINNHLDEV  240
NTNGAGNVPE SMRMEECWDL DQLMNTEVPS FYFNFKQNI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A1e-27201227108B-MYB
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator. Involved in the regulation of secondary wall biosynthesis in fibers and vessels (PubMed:17890373). Transcription activator of the mannan synthase CSLA9 that recognizes and binds to the DNA consensus sequence 5'-[AG][GT]T[AT]GGT[GA]-3' cis-regulatory element of CSLA9 promoter (PubMed:24243147). Transcription factor that acts as molecular switch in the NAC012/SND1-mediated transcriptional network regulating secondary wall biosynthesis. Is directly activated by NAC012/SND1. Functions redundantly with MYB83 in the transcriptional regulatory cascade leading to secondary wall formation in fibers and vessels (PubMed:19808805). Transcription activator that binds to the DNA consensus sequence 5'-ACC[AT]A[AC][TC]-3', designated as the secondary wall MYB-responsive element (SMRE). Regulates directly numerous transcription factors and a number of genes involved in secondary wall biosynthesis that contain SMRE elements in their promoters (PubMed:22197883). Is an obligate component of the transcriptional regulatory complex toward the commitment of secondary wall cellulose synthesis. Is required for functional expression of the three secondary wall CESA genes, CESA4, CESA7 and CESA8 (PubMed:23726771). {ECO:0000269|PubMed:17890373, ECO:0000269|PubMed:19808805, ECO:0000269|PubMed:22197883, ECO:0000269|PubMed:23726771, ECO:0000269|PubMed:24243147}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00599PBMTransfer from AT5G12870Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Slightly induced by salicylic acid (SA). Positively regulated by SND1 and homolog proteins. {ECO:0000269|PubMed:16463103, ECO:0000269|PubMed:17890373}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKF7382830.0KF738283.1 Brassica napus MYB transcription factor 46 (MYB46.1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018444537.10.0PREDICTED: transcription factor MYB46-like
RefseqXP_018444573.10.0PREDICTED: transcription factor MYB46-like
SwissprotQ9LXV21e-163MYB46_ARATH; Transcription factor MYB46
TrEMBLA0A0D3EFY01e-177A0A0D3EFY0_BRAOL; Uncharacterized protein
STRINGBo9g169270.11e-178(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM61152347
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G12870.11e-161myb domain protein 46
Publications ? help Back to Top
  1. Zhao Q, et al.
    Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis.
    Phytochemistry, 2015. 112: p. 170-8
    [PMID:25107662]
  2. Sakamoto S,Mitsuda N
    Reconstitution of a secondary cell wall in a secondary cell wall-deficient Arabidopsis mutant.
    Plant Cell Physiol., 2015. 56(2): p. 299-310
    [PMID:25535195]
  3. Vargas L, et al.
    Improving total saccharification yield of Arabidopsis plants by vessel-specific complementation of caffeoyl shikimate esterase (cse) mutants.
    Biotechnol Biofuels, 2016. 9: p. 139
    [PMID:27390589]
  4. 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]