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 GSVIVT01036802001
Common NameVIT_19s0085g00050
Organism
Vitis vinifera
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
Family MYB
Protein Properties Length: 365aa    MW: 41332.1 Da    PI: 4.9956
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01036802001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding46.96.2e-151663148
                       TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
    Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                       rg+W++ Ed +lv  +++ G ++W++ ++  g+ R++k+c++rw +yl
  GSVIVT01036802001 16 RGPWSPAEDMRLVSFIQKNGHENWRSLPKQAGLLRCGKSCRLRWINYL 63
                       89******************************99************97 PP
2Myb_DNA-binding53.17.3e-1769114148
                        TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
    Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                        rg++++eE++ ++++++ lG++ W++Ia++++ gRt++++k+ w+++l
  GSVIVT01036802001  69 RGNFSKEEEDAIIKLHQTLGNK-WSKIASHFP-GRTDNEIKNVWNTHL 114
                        89********************.*********.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.606.2E-22766IPR009057Homeodomain-like
PROSITE profilePS5129414.2171163IPR017930Myb domain
SuperFamilySSF466892.53E-2914110IPR009057Homeodomain-like
SMARTSM007174.2E-111565IPR001005SANT/Myb domain
PfamPF002491.4E-131663IPR001005SANT/Myb domain
CDDcd001673.94E-81863No hitNo description
PROSITE profilePS5129425.24564118IPR017930Myb domain
Gene3DG3DSA:1.10.10.602.3E-2767119IPR009057Homeodomain-like
SMARTSM007176.1E-1668116IPR001005SANT/Myb domain
PfamPF002491.1E-1569114IPR001005SANT/Myb domain
CDDcd001674.31E-1171114No 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: 365 aa     Download sequence    Send to blast
MGRGRAPCCD KSKVKRGPWS PAEDMRLVSF IQKNGHENWR SLPKQAGLLR CGKSCRLRWI  60
NYLRPDVKRG NFSKEEEDAI IKLHQTLGNK WSKIASHFPG RTDNEIKNVW NTHLKKRLVA  120
QKNDKLYSSS SNTNPISNSP NPSPSTNNEP KEPSSSSTNS SPNIETQVDS IIFDFVGTYG  180
MLDEVNKPGE ELEIPLETDT SFWEMLDSLG SFQYNNEVEG SQSSIIIADH EQGNDNGDAA  240
HESRSWLRYI ENELGLEETS DETMETCTKI QLNGDEQPAS EIISFLEDDG GKLEDNPSII  300
ILISSNLWYD DDPFVYLKIN LLNFMKLESG LVKFSTYHHR TIQFCDTQFL SVPTLGKNER  360
IKVY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1mse_C4e-25161184105C-Myb DNA-Binding Domain
1msf_C4e-25161184105C-Myb DNA-Binding Domain
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.302700.0bud
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
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
GenBankAM4430470.0AM443047.2 Vitis vinifera contig VV78X076804.3, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010645152.10.0PREDICTED: myb-related protein Myb4
SwissprotQ9SA471e-88MYB58_ARATH; Transcription factor MYB58
TrEMBLD7T0Y30.0D7T0Y3_VITVI; Uncharacterized protein
STRINGVIT_19s0085g00050.t010.0(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP5171784
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G16490.14e-85myb 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]