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 XP_009127989.1
Organism
Brassica rapa
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: 234aa    MW: 27333.8 Da    PI: 9.6836
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009127989.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding59.38.7e-19449147
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47
                     rg W + Ede+l+d+v+q+G+++W++Ia +++ gR++k+c++rw++ 
   XP_009127989.1  4 RGHWRPAEDEKLKDLVEQYGPHNWNAIALKLP-GRSGKSCRLRWFNQ 49
                     899*****************************.***********996 PP
2Myb_DNA-binding60.63.3e-195699146
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46
                     r+++T+eE+e+l+ a++ +G++ W+ Iar ++ gRt++ +k++w+ 
   XP_009127989.1 56 RNPFTEEEEERLLAAHRIHGNR-WSIIARLFP-GRTDNAVKNHWHV 99
                     789*******************.*********.***********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129419.673150IPR017930Myb domain
SMARTSM007171.1E-15352IPR001005SANT/Myb domain
PfamPF002491.9E-17449IPR001005SANT/Myb domain
SuperFamilySSF466893.29E-30497IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.602.4E-27557IPR009057Homeodomain-like
CDDcd001671.02E-14748No hitNo description
PROSITE profilePS5129426.37951105IPR017930Myb domain
SMARTSM007171.9E-1655103IPR001005SANT/Myb domain
PfamPF002497.6E-165698IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.601.0E-2158104IPR009057Homeodomain-like
CDDcd001671.37E-75898No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 234 aa     Download sequence    Send to blast
MCSRGHWRPA EDEKLKDLVE QYGPHNWNAI ALKLPGRSGK SCRLRWFNQL DPRINRNPFT  60
EEEEERLLAA HRIHGNRWSI IARLFPGRTD NAVKNHWHVI MARRTRRQTS KPRILTSTTS  120
SLLETEQIMM ASGDRKRILG DGISYPYQFS HINHLQLLKE FFTEKIAFNT KDAMVANQSK  180
KPMEFYNFLQ VDMDSNKSEI VDQDSDQSNP HDSDNKNESR VPFFDFLSVK NSTS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A1e-3141057108B-MYB
1mse_C8e-3211051105C-Myb DNA-Binding Domain
1msf_C8e-3211051105C-Myb DNA-Binding Domain
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: In elongating stem internodes, expressed in developing protoxylem and elongating interfascicular fiber cells. In non-elongating internodes, expressed in developing metaxylem cells and interfascicular fibers. In roots, expressed in developing secondary xylem. {ECO:0000269|PubMed:18952777}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates secondary cell wall (SCW) biosynthesis, especially in interfascicular and xylary fibers. {ECO:0000269|PubMed:18952777}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009127989.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF0628901e-123AF062890.1 Arabidopsis thaliana putative transcription factor (MYB54) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009127989.11e-177PREDICTED: transcription factor WER-like isoform X1
SwissprotQ9FX361e-131MYB54_ARATH; Transcription factor MYB54
TrEMBLA0A078J0051e-176A0A078J005_BRANA; BnaA02g16430D protein
TrEMBLA0A398AIA31e-176A0A398AIA3_BRACM; Uncharacterized protein
TrEMBLM4CV501e-176M4CV50_BRARP; Uncharacterized protein
STRINGBra008096.1-P1e-177(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM28182769
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G73410.11e-129myb domain protein 54
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]