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 PGSC0003DMP400013034
Common NameLOC102604248
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: 352aa    MW: 39232.5 Da    PI: 6.5078
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400013034genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding46.58.3e-153178148
                          TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
       Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                          +g W++eEde+l ++    G g+W+ +ar  g+ R++k+c++rw +yl
  PGSC0003DMP400013034 31 KGLWSPEEDEKLMHYMLTNGQGCWSDVARNAGLQRCGKSCRLRWINYL 78
                          678*******************************************97 PP
2Myb_DNA-binding50.26e-1684128147
                           TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
       Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 
                           rg+++++E+e +++++  lG++ W+ Ia++++ gRt++++k++w++ 
  PGSC0003DMP400013034  84 RGAFSPQEEEHIIHLHSILGNR-WSQIAARLP-GRTDNEIKNFWNST 128
                           89********************.*********.***********986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129416.5862678IPR017930Myb domain
SuperFamilySSF466895.86E-2829125IPR009057Homeodomain-like
SMARTSM007171.4E-103080IPR001005SANT/Myb domain
PfamPF002491.7E-133178IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.601.2E-223285IPR009057Homeodomain-like
CDDcd001675.32E-93478No hitNo description
PROSITE profilePS5129424.88279133IPR017930Myb domain
SMARTSM007171.1E-1483131IPR001005SANT/Myb domain
PfamPF002491.6E-1484128IPR001005SANT/Myb domain
CDDcd001672.31E-1086129No hitNo description
Gene3DG3DSA:1.10.10.605.6E-2686134IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
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: 352 aa     Download sequence    Send to blast
MRKPEFSSSS SSSTKNSNNN NNNNTNVKLR KGLWSPEEDE KLMHYMLTNG QGCWSDVARN  60
AGLQRCGKSC RLRWINYLRP DLKRGAFSPQ EEEHIIHLHS ILGNRWSQIA ARLPGRTDNE  120
IKNFWNSTLK KRLKNSSSSS TPSPNASDSS SDHPSKELNM GVTQQGFMPM LKHNLMSMYM  180
DSTSPSSPSI ALNTINIDPL PTLEHTLISI PNGFNVPSFL STTQPCMVQG GNSVSTNGGS  240
LFYGNNHGIF GGNLSMEGHE LYVPPLENVS IEYQNVENGN FSHHQNNNNP NNMTNLINTS  300
HNFNTCSNIK VENFGGIGNY WEGDDVKVGE WDLEELMKDV SPFPFLDFQV E*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A5e-26291335108B-MYB
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that acts as molecular switch in the NAC012/SND1-mediated transcriptional network regulating secondary wall biosynthesis. Is directly activated by NAC012/SND1 and its close homologs, including NAC043/NST1, NAC066/NST2, NAC101/VND6 and NAC030/VND7. Is required for functional expression of a number of secondary wall-associated transcription factors and secondary wall biosynthetic genes involved in cellulose, xylan and lignin synthesis. Functions redundantly with MYB46 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). {ECO:0000269|PubMed:19808805, ECO:0000269|PubMed:22197883}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00336DAPTransfer from AT3G08500Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPGSC0003DMP400013034
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9754500.0HG975450.1 Solanum pennellii chromosome ch11, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006361760.10.0PREDICTED: transcription factor MYB46
SwissprotQ9C6U11e-87MYB83_ARATH; Transcription factor MYB83
TrEMBLM1ABG80.0M1ABG8_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000189950.0(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
AT3G08500.12e-83myb domain protein 83
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. 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]
  3. Piya S,Kihm C,Rice JH,Baum TJ,Hewezi T
    Cooperative Regulatory Functions of miR858 and MYB83 during Cyst Nematode Parasitism.
    Plant Physiol., 2017. 174(3): p. 1897-1912
    [PMID:28512179]