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.0824s0021.1.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: 280aa    MW: 31739.9 Da    PI: 4.8803
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.0824s0021.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding48.12.8e-151663148
                         TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
      Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                         rg+W+++Ed++l+  +++ G ++W++ ++  g+ R++k+c++rw +yl
  Cagra.0824s0021.1.p 16 RGPWSQDEDLKLISFIHKSGHENWRSLPKQAGLLRCGKSCRLRWINYL 63
                         89******************************99************97 PP
2Myb_DNA-binding52.79.8e-1769114148
                          TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
      Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                          rg++++eE+e ++++++ +G++ W++Ia++++ gRt++++k+ w+++l
  Cagra.0824s0021.1.p  69 RGNFSAEEEETIIKLHQSFGNK-WSKIASKLP-GRTDNEIKNVWHTHL 114
                          89********************.*********.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.603.5E-23766IPR009057Homeodomain-like
PROSITE profilePS5129413.5681163IPR017930Myb domain
SuperFamilySSF466893.41E-2814110IPR009057Homeodomain-like
SMARTSM007175.4E-121565IPR001005SANT/Myb domain
PfamPF002492.5E-141663IPR001005SANT/Myb domain
CDDcd001671.40E-81863No hitNo description
PROSITE profilePS5129425.46564118IPR017930Myb domain
Gene3DG3DSA:1.10.10.603.1E-2767118IPR009057Homeodomain-like
SMARTSM007175.4E-1568116IPR001005SANT/Myb domain
PfamPF002493.7E-1569114IPR001005SANT/Myb domain
CDDcd001673.89E-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: 280 aa     Download sequence    Send to blast
MGKGRAPCCD KTKVKRGPWS QDEDLKLISF IHKSGHENWR SLPKQAGLLR CGKSCRLRWI  60
NYLRPDVKRG NFSAEEEETI IKLHQSFGNK WSKIASKLPG RTDNEIKNVW HTHLKKRLSS  120
DTTNLNADEA ASKDSLNEAE TSQESSPNAS MSFAGSNISS REEDDAQISQ AFEHIQTYSE  180
FTGMLQEVDK PELLEIPFDL DHDIWSFIDG SDSFQHLENS WSSRAPQESE GDEIEKWFKH  240
LESELGLEEN DNQQHEQGTT DGEESSSSSL LEGYKLLIH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A2e-24161207110B-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
PlantRegMapCagra.0824s0021.1.p
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
GenBankAB4934590.0AB493459.1 Arabidopsis thaliana At1g16490 mRNA for hypothetical protein, partial cds, clone: RAAt1g16490.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006304479.10.0transcription factor MYB58
SwissprotQ9SA471e-169MYB58_ARATH; Transcription factor MYB58
TrEMBLR0GN610.0R0GN61_9BRAS; Uncharacterized protein
STRINGCagra.0824s0021.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM4282646
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G16490.11e-166myb 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]