PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_013603082.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family MYB
Protein Properties Length: 279aa    MW: 32183.4 Da    PI: 4.6268
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013603082.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding52.11.5e-161663148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     rg+W+++Ed++l+  ++++G ++W++ ++  g+ R++k+c++rw +yl
   XP_013603082.1 16 RGPWSQDEDLKLISFIHKYGHENWRSLPKQAGLLRCGKSCRLRWINYL 63
                     89******************************99************97 PP

2Myb_DNA-binding52.61.1e-1669114148
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                      rg++T eE+e ++++++ +G++ W++Ia++++ gRt++++k+ w+++l
   XP_013603082.1  69 RGNFTLEEEETIIKLHQSFGNK-WSKIASKLP-GRTDNEIKNVWHTHL 114
                      89********************.*********.************986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.604.2E-24766IPR009057Homeodomain-like
PROSITE profilePS5129415.3411163IPR017930Myb domain
SuperFamilySSF466892.6E-2914110IPR009057Homeodomain-like
SMARTSM007172.4E-131565IPR001005SANT/Myb domain
PfamPF002491.5E-151663IPR001005SANT/Myb domain
CDDcd001671.11E-91863No hitNo description
PROSITE profilePS5129425.52964118IPR017930Myb domain
Gene3DG3DSA:1.10.10.604.5E-2767118IPR009057Homeodomain-like
SMARTSM007171.0E-1468116IPR001005SANT/Myb domain
PfamPF002494.7E-1569114IPR001005SANT/Myb domain
CDDcd001677.60E-1071114No 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 SLPKQAGLLR CGKSCRLRWI  60
NYLRPDLKRG NFTLEEEETI IKLHQSFGNK WSKIASKLPG RTDNEIKNVW HTHLKKRLNS  120
YINHNASDEA ASKGSLNKEE TSQESSPNAS RSFGGSNIVS KEEEDDVQIG ETFEYFQDYS  180
ELAGLLQEVD KPELLEIPFD IDPDVWNFLE GFQQPENSLT PKDHQESEED EVDKWFKNLE  240
SELGLEEDDS QQQQEQNNEA KEDSPSPSLL ESYEVLINH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A2e-25161207110B-MYB
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: In nonelongating internodes, highly expressed in interfascicular fibers and xylem cells but not in parenchymatous pith cells. In elongating internodes, predominantly expressed in protoxylem vessels. {ECO:0000269|PubMed:19122102}.
UniprotTISSUE SPECIFICITY: Expressed in leaves (PubMed:9839469). Specifically expressed in fibers and vessels undergoing secondary wall thickening, especially in inflorescence stems (PubMed:19122102). {ECO:0000269|PubMed:19122102, ECO:0000269|PubMed:9839469}.
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
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_013603082.1
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_013603082.10.0PREDICTED: myb-related protein Myb4
RefseqXP_013710348.10.0transcription factor MYB58
SwissprotQ9SA471e-152MYB58_ARATH; Transcription factor MYB58
TrEMBLA0A078D0J50.0A0A078D0J5_BRANA; MYB transcription factor 58.1
TrEMBLA0A0D3DWZ90.0A0A0D3DWZ9_BRAOL; Uncharacterized protein
TrEMBLA0A3P6GFV00.0A0A3P6GFV0_BRAOL; Uncharacterized protein
STRINGBo8g105490.10.0(Brassica oleracea)
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-144myb 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]