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 334927
Common NameARALYDRAFT_334927
Organism
Arabidopsis lyrata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family MYB
Protein Properties Length: 277aa    MW: 31814.1 Da    PI: 4.8802
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
334927genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding50.54.7e-161663148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     rg+W+++Ed +l+  ++++G ++W++ ++  g+ R++k+c++rw +yl
           334927 16 RGPWSQDEDFKLISFIHKYGHENWRSLPKQAGLLRCGKSCRLRWINYL 63
                     89******************************99************97 PP
2Myb_DNA-binding54.13.5e-1769114148
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                      rg++T+eE+e ++++++ +G++ W++Ia++++ gRt++++k+ w+++l
           334927  69 RGNFTAEEEETIIKLHQSFGNK-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:1.10.10.602.1E-23766IPR009057Homeodomain-like
PROSITE profilePS5129414.8581163IPR017930Myb domain
SuperFamilySSF466892.53E-2914110IPR009057Homeodomain-like
SMARTSM007177.0E-131565IPR001005SANT/Myb domain
PfamPF002495.6E-151663IPR001005SANT/Myb domain
CDDcd001672.18E-91863No hitNo description
PROSITE profilePS5129425.90764118IPR017930Myb domain
Gene3DG3DSA:1.10.10.601.3E-2767118IPR009057Homeodomain-like
SMARTSM007172.7E-1568116IPR001005SANT/Myb domain
PfamPF002491.7E-1569114IPR001005SANT/Myb domain
CDDcd001672.52E-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: 277 aa     Download sequence    Send to blast
MGKGRAPCCD KSKVKRGPWS QDEDFKLISF IHKYGHENWR SLPKQAGLLR CGKSCRLRWI  60
NYLRPDVKRG NFTAEEEETI IKLHQSFGNK WSKIASKLPG RTDNEIKNVW HTHLKKRLSS  120
KTNLNVDEAA SKGSLNEEEN SQESSPNASM SFAGSNISSK DDDAQISQKT FEHILTFSDF  180
TEMLQEVDKP ELLEMTFDID PDIWSFIDGS DSSFQQPENR ALQESEEDEV DKWFKHLECE  240
LGLEENDNQQ QQQQHKQGTE DENSSSLLES YELLIH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A4e-26161207110B-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
PlantRegMap334927
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_002892910.10.0transcription factor MYB58
SwissprotQ9SA470.0MYB58_ARATH; Transcription factor MYB58
TrEMBLD7KEF90.0D7KEF9_ARALL; AtMYB58
STRINGfgenesh1_pg.C_scaffold_10014920.0(Arabidopsis lyrata)
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-161myb 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]