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 Sopim10g005550.0.1
Organism
Solanum pimpinellifolium
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; Lycopersicon
Family MYB
Protein Properties Length: 244aa    MW: 28037.3 Da    PI: 8.3753
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopim10g005550.0.1genomeCSHLView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding53.45.9e-171663148
                        TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
     Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                        +g+WT+ Ed++l+  ++++G g+W++ ++  g+ R++k+c++rw +yl
  Sopim10g005550.0.1 16 KGPWTPSEDLKLISFIQKHGHGNWRALPKQAGLLRCGKSCRLRWINYL 63
                        79******************************99************97 PP
2Myb_DNA-binding537.9e-1769114148
                         TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
     Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                         rg++T++E++ ++++++ +G++ W++Ia++++ gRt++++k+ w+++l
  Sopim10g005550.0.1  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:1.10.10.602.9E-25866IPR009057Homeodomain-like
PROSITE profilePS5129416.231163IPR017930Myb domain
SuperFamilySSF466894.12E-3114110IPR009057Homeodomain-like
SMARTSM007177.2E-141565IPR001005SANT/Myb domain
PfamPF002494.3E-161663IPR001005SANT/Myb domain
CDDcd001671.90E-101863No hitNo description
PROSITE profilePS5129424.94964118IPR017930Myb domain
Gene3DG3DSA:1.10.10.601.1E-2767118IPR009057Homeodomain-like
SMARTSM007171.3E-1568116IPR001005SANT/Myb domain
PfamPF002491.0E-1569114IPR001005SANT/Myb domain
CDDcd001671.35E-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: 244 aa     Download sequence    Send to blast
MGKGRTACCD KSKVKKGPWT PSEDLKLISF IQKHGHGNWR ALPKQAGLLR CGKSCRLRWI  60
NYLRPDVKRG NFTPQEEDTI INLHRAFGNR WSKIASHLPG RTDNEIKNVW NTHLKKRLVV  120
MKKEECKSSS SSTSTSSHQG QYMDNNNNNN SNTLESFSPT SSKANDQVMD FWEYMLDTSS  180
TTTSINNLDH LDSYSKLDIT SEHHPQQLVD EYECQKWLTY LEIELGLTTN NQQEDHQNNF  240
MQL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A5e-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
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}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2448030.0AC244803.1 Solanum lycopersicum strain Heinz 1706 chromosome 10 clone hba-8f2 map 10, complete sequence.
GenBankAC2449370.0AC244937.1 Solanum lycopersicum strain Heinz 1706 chromosome 10 clone sle-8f2 map 10, complete sequence.
GenBankHG9755220.0HG975522.1 Solanum lycopersicum chromosome ch10, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010327227.10.0transcription factor MYB58
SwissprotQ9SA471e-77MYB58_ARATH; Transcription factor MYB58
TrEMBLM1ASG51e-161M1ASG5_SOLTU; Uncharacterized protein
STRINGSolyc10g005550.1.10.0(Solanum lycopersicum)
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
AT1G16490.15e-76myb 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]