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 PGSC0003DMP400019896
Common NameLOC102579550
Organism
Solanum tuberosum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum
Family MYB
Protein Properties Length: 240aa    MW: 27675.9 Da    PI: 7.6211
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400019896genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding53.45.8e-171663148
                          TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
       Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                          +g+WTt Ed++l+  ++++G g+W++ ++  g+ R++k+c++rw +yl
  PGSC0003DMP400019896 16 KGPWTTSEDLKLISFIQKHGHGNWRALPKQAGLLRCGKSCRLRWINYL 63
                          79******************************99************97 PP
2Myb_DNA-binding537.7e-1769114148
                           TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
       Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                           rg++T++E++ ++++++ +G++ W++Ia++++ gRt++++k+ w+++l
  PGSC0003DMP400019896  69 RGNFTPQEEDTIINLHRAFGNR-WSKIASHLP-GRTDNEIKNVWNTHL 114
                           89********************.*********.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.609.2E-25866IPR009057Homeodomain-like
PROSITE profilePS5129415.4821163IPR017930Myb domain
SuperFamilySSF466899.54E-3114110IPR009057Homeodomain-like
SMARTSM007172.7E-131565IPR001005SANT/Myb domain
PfamPF002491.1E-151663IPR001005SANT/Myb domain
CDDcd001675.66E-101863No hitNo description
PROSITE profilePS5129424.94964118IPR017930Myb domain
Gene3DG3DSA:1.10.10.601.0E-2767118IPR009057Homeodomain-like
SMARTSM007171.3E-1568116IPR001005SANT/Myb domain
PfamPF002491.0E-1569114IPR001005SANT/Myb domain
CDDcd001671.05E-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: 240 aa     Download sequence    Send to blast
MGKGRTACCD KSKVKKGPWT TSEDLKLISF IQKHGHGNWR ALPKQAGLLR CGKSCRLRWI  60
NYLRPDVKRG NFTPQEEDTI INLHRAFGNR WSKIASHLPG RTDNEIKNVW NTHLKKRLVM  120
MKKEEYNSSS SSTSTSSHQG QYMDNNSTTL ESFSPTSSKA NDQVMDFWEY MLDTSSTPTS  180
INNLDHLDSY SNLDTTSEHH PQQLVDEFEC QKWLTYLEIE LELTTNNQQE DHQNNFMQL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A3e-27161187108B-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
Cis-element ? help Back to Top
SourceLink
PlantRegMapPGSC0003DMP400019896
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
GenBankHG9754490.0HG975449.1 Solanum pennellii chromosome ch10, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006352640.10.0PREDICTED: myb-related protein Zm1-like
SwissprotQ9SA478e-76MYB58_ARATH; Transcription factor MYB58
TrEMBLM1ASG51e-180M1ASG5_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000292350.0(Solanum tuberosum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA12242154
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G16490.12e-73myb domain protein 58
Publications ? help Back to Top
  1. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  2. 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]
  3. 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]
  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]