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 Cagra.1535s0018.1.p
Organism
Capsella grandiflora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family MYB
Protein Properties Length: 288aa    MW: 32451.3 Da    PI: 5.9641
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.1535s0018.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding44.34.1e-142168148
                         TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
      Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                         +g W++eEd +l ++    G g+W+ +a+  g+ R++k+c++rw +yl
  Cagra.1535s0018.1.p 21 KGLWSPEEDSKLMQYMLSNGQGCWSDVAKNAGLQRCGKSCRLRWINYL 68
                         678*******************************************97 PP
2Myb_DNA-binding48.81.6e-1574117146
                          TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
      Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                          rg+++++E++l+++ +  lG++ W+ Ia++++ gRt++++k++w++
  Cagra.1535s0018.1.p  74 RGAFSPQEEDLIIRFHSILGNR-WSQIAARLP-GRTDNEIKNFWNS 117
                          89********************.*********.***********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129414.8421668IPR017930Myb domain
SuperFamilySSF466899.94E-2819115IPR009057Homeodomain-like
SMARTSM007172.0E-102070IPR001005SANT/Myb domain
PfamPF002492.2E-132168IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.601.3E-222275IPR009057Homeodomain-like
CDDcd001671.70E-82468No hitNo description
PROSITE profilePS5129424.44969123IPR017930Myb domain
SMARTSM007172.3E-1573121IPR001005SANT/Myb domain
PfamPF002491.7E-1474117IPR001005SANT/Myb domain
CDDcd001671.07E-1076116No hitNo description
Gene3DG3DSA:1.10.10.602.6E-2576124IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009751Biological Processresponse to salicylic acid
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0050832Biological Processdefense response to fungus
GO:1901348Biological Processpositive regulation of secondary cell wall biogenesis
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 288 aa     Download sequence    Send to blast
MRKPEVAIAA STTHQVKKMK KGLWSPEEDS KLMQYMLSNG QGCWSDVAKN AGLQRCGKSC  60
RLRWINYLRP DLKRGAFSPQ EEDLIIRFHS ILGNRWSQIA ARLPGRTDNE IKNFWNSTIK  120
KRLKKMSDTS NLINNSSSSP ANTASDTSSN STSSLELKDI IGSFMSLQEQ GFVNPNSLTH  180
HMPTNNPFPA PNMISHPCND DFITYADGIY GVNAGVQGEL YFPPLECDQE SDWYNANINN  240
HIEELNTNGS GNEPDQGMIR PVEEFWDIDQ LMNTEVPSFY FNFKQSI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A1e-27211237108B-MYB
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator. Involved in the regulation of secondary wall biosynthesis in fibers and vessels (PubMed:17890373). Transcription activator of the mannan synthase CSLA9 that recognizes and binds to the DNA consensus sequence 5'-[AG][GT]T[AT]GGT[GA]-3' cis-regulatory element of CSLA9 promoter (PubMed:24243147). Transcription factor that acts as molecular switch in the NAC012/SND1-mediated transcriptional network regulating secondary wall biosynthesis. Is directly activated by NAC012/SND1. Functions redundantly with MYB83 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). Is an obligate component of the transcriptional regulatory complex toward the commitment of secondary wall cellulose synthesis. Is required for functional expression of the three secondary wall CESA genes, CESA4, CESA7 and CESA8 (PubMed:23726771). {ECO:0000269|PubMed:17890373, ECO:0000269|PubMed:19808805, ECO:0000269|PubMed:22197883, ECO:0000269|PubMed:23726771, ECO:0000269|PubMed:24243147}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00599PBMTransfer from AT5G12870Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.1535s0018.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Slightly induced by salicylic acid (SA). Positively regulated by SND1 and homolog proteins. {ECO:0000269|PubMed:16463103, ECO:0000269|PubMed:17890373}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5196210.0AY519621.1 Arabidopsis thaliana MYB transcription factor (At5g12870) mRNA, complete cds.
GenBankBT0004550.0BT000455.1 Arabidopsis thaliana putative transcription factor (MYB46) (At5g12870) mRNA, complete cds.
GenBankBT0025490.0BT002549.1 Arabidopsis thaliana putative transcription factor (MYB46) (At5g12870) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006288326.20.0transcription factor MYB46
SwissprotQ9LXV21e-170MYB46_ARATH; Transcription factor MYB46
TrEMBLR0GWC90.0R0GWC9_9BRAS; Uncharacterized protein (Fragment)
STRINGCagra.1535s0018.1.p0.0(Capsella grandiflora)
STRINGXP_006288326.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM61152347
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G12870.11e-170myb domain protein 46
Publications ? help Back to Top
  1. Zhao Q, et al.
    Pinoresinol reductase 1 impacts lignin distribution during secondary cell wall biosynthesis in Arabidopsis.
    Phytochemistry, 2015. 112: p. 170-8
    [PMID:25107662]
  2. Sakamoto S,Mitsuda N
    Reconstitution of a secondary cell wall in a secondary cell wall-deficient Arabidopsis mutant.
    Plant Cell Physiol., 2015. 56(2): p. 299-310
    [PMID:25535195]
  3. 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]
  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]