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 RrC6_p13
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family MYB
Protein Properties Length: 324aa    MW: 37131.1 Da    PI: 4.9443
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC6_p13genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding46.77.4e-151461148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     rg+W+ +Ed++l+  ++++G ++W++ ++  g+ R++k+c++rw +yl
         RrC6_p13 14 RGPWSYDEDLKLISFINKYGHENWRSLPQQAGLMRCGKSCRLRWINYL 61
                     89********************************************97 PP
2Myb_DNA-binding48.61.9e-1567112148
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                      rg+++ eE+e+++++++  G++ W++Ia++++ gRt++++k+ w+++l
         RrC6_p13  67 RGNFSVEEEEIIIKLHQSIGSK-WSKIASKLP-GRTDNEIKNVWHTHL 112
                      89********************.*********.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.602.5E-23564IPR009057Homeodomain-like
PROSITE profilePS5129413.694961IPR017930Myb domain
SuperFamilySSF466899.9E-2912108IPR009057Homeodomain-like
SMARTSM007174.3E-101363IPR001005SANT/Myb domain
PfamPF002496.5E-141461IPR001005SANT/Myb domain
CDDcd001673.78E-81661No hitNo description
PROSITE profilePS5129424.31762116IPR017930Myb domain
Gene3DG3DSA:1.10.10.605.8E-2665116IPR009057Homeodomain-like
SMARTSM007172.5E-1366114IPR001005SANT/Myb domain
PfamPF002496.1E-1467112IPR001005SANT/Myb domain
CDDcd001676.78E-969112No 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: 324 aa     Download sequence    Send to blast
MGRAPCCDKT KVKRGPWSYD EDLKLISFIN KYGHENWRSL PQQAGLMRCG KSCRLRWINY  60
LRPDVKRGNF SVEEEEIIIK LHQSIGSKWS KIASKLPGRT DNEIKNVWHT HLKKKLSSRT  120
NLNADDETGT KGSLNREKTF QESSPNASMS FAGSKISSKE DGAQIGEMFE YIEGHSKVTR  180
TSEEIDKPEL LEIPFGVDPD HIWSFINGYD SFGGSKISSK EDGAQIGDMF EYLEGHSEVK  240
RTLKEVDKPE LLEIPFGVDP DIWHFINGYD SFQQPENSLA PRDHQDSQED EVDKWFKYLE  300
TELGLEENDS QQQQQNDTNK ESSD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A5e-25141187110B-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}.
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
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018454233.11e-148PREDICTED: myb-related protein Zm1-like
SwissprotQ9SA471e-121MYB58_ARATH; Transcription factor MYB58
TrEMBLA0A0D3CAS71e-138A0A0D3CAS7_BRAOL; Uncharacterized protein
STRINGBo5g021910.11e-139(Brassica oleracea)
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-123myb 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]