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 RrC21251_p1
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: 36555.5 Da    PI: 6.592
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC21251_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding47.15.4e-153380148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     +g W+++Ede+l+ +    G g+W+ Iar  g+ R++k+c++rw +yl
      RrC21251_p1 33 KGLWSPDEDEKLISYMLTNGQGCWNVIARNAGLLRCGKSCRLRWINYL 80
                     678*****************************99************97 PP
2Myb_DNA-binding32.52e-1086139147
                      TSSS-HHHHHHHHHHHHHTTTT........-HHHHHHHHTTTS-HHHHHHHHHHH CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGgg........tWktIartmgkgRtlkqcksrwqky 47 
                      rg++++eE+ l+v+++ +            +W+ Ia  ++ gRt++++k++w++ 
      RrC21251_p1  86 RGPFSPEEEYLIVHLHSMIVLYlftlkhftRWSQIATQLP-GRTDNEIKNFWNTT 139
                      89**************998866999999999*********.************87 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129421.2812884IPR017930Myb domain
SuperFamilySSF466891.05E-2330136IPR009057Homeodomain-like
SMARTSM007175.3E-123282IPR001005SANT/Myb domain
PfamPF002491.1E-133380IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.608.3E-223487IPR009057Homeodomain-like
CDDcd001673.68E-103680No hitNo description
SMARTSM007173.7E-885142IPR001005SANT/Myb domain
PROSITE profilePS5129414.07985144IPR017930Myb domain
PfamPF002496.8E-986139IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.606.6E-2288144IPR009057Homeodomain-like
CDDcd001678.17E-988140No 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
MMSNSAITKI IDKNKPKHAC GGTGNNNKPK LRKGLWSPDE DEKLISYMLT NGQGCWNVIA  60
RNAGLLRCGK SCRLRWINYL RPDLKRGPFS PEEEYLIVHL HSMIVLYLFT LKHFTRWSQI  120
ATQLPGRTDN EIKNFWNTTL KKRLENNISN TSSGSLPTNI ICNFFDPKDQ HVDMGGKSNL  180
MMDSYHHHDD MMVVGNTMRI DCSSFSFAPV VSGVDLNQLD PLISVPDHNS YQQMGNMGNL  240
FNVNGLRYCG NAILDPTSKR ASIESEWFLP PSEDDTNVIA CTTSNNLNML GIDNGSLEIE  300
NPKIGDWDLD GLIDNSPPFT FPYF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A4e-22291453109B-MYB
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that acts as molecular switch in the NAC012/SND1-mediated transcriptional network regulating secondary wall biosynthesis. Is directly activated by NAC012/SND1 and its close homologs, including NAC043/NST1, NAC066/NST2, NAC101/VND6 and NAC030/VND7. Is required for functional expression of a number of secondary wall-associated transcription factors and secondary wall biosynthetic genes involved in cellulose, xylan and lignin synthesis. Functions redundantly with MYB46 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). {ECO:0000269|PubMed:19808805, ECO:0000269|PubMed:22197883}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1893682e-93AC189368.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB047A09, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018438573.10.0PREDICTED: transcription factor MYB46-like
SwissprotQ9C6U11e-138MYB83_ARATH; Transcription factor MYB83
TrEMBLA0A078JYG51e-152A0A078JYG5_BRANA; BnaCnng68780D protein
TrEMBLA0A3P6AK701e-152A0A3P6AK70_BRAOL; Uncharacterized protein
STRINGBo3g061630.11e-152(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM70772642
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08500.11e-132myb domain protein 83
Publications ? help Back to Top
  1. 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]
  2. Piya S,Kihm C,Rice JH,Baum TJ,Hewezi T
    Cooperative Regulatory Functions of miR858 and MYB83 during Cyst Nematode Parasitism.
    Plant Physiol., 2017. 174(3): p. 1897-1912
    [PMID:28512179]