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 RrC21563_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 B3
Protein Properties Length: 233aa    MW: 27113.1 Da    PI: 7.4731
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC21563_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3100.97.4e-3240145199
                  EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                  f+k ltpsdv+k++rlv+pk++ae++           e++  l +ede+g+ W+++++y+++s++yvltkGW+++vk+++L++gD+++F++++ ++++
  RrC21563_p1  40 FEKPLTPSDVGKLNRLVIPKQHAERYfplaaaaADAMEKGLLLCFEDEEGKPWRFRYSYWNSSQSYVLTKGWSRYVKEKQLDAGDVILFHRHRVDGGR 137
                  99*****************************99555568889************************************************87779**9 PP

                  .EEEEE-S CS
           B3  92 lvvkvfrk 99 
                  ++++++r+
  RrC21563_p1 138 FFISWRRR 145
                  *****997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.5E-4034153IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.67E-3137146IPR015300DNA-binding pseudobarrel domain
CDDcd100175.09E-2839144No hitNo description
PfamPF023621.9E-2940145IPR003340B3 DNA binding domain
SMARTSM010195.1E-2440146IPR003340B3 DNA binding domain
PROSITE profilePS5086314.22640146IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0080167Biological Processresponse to karrikin
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 233 aa     Download sequence    Send to blast
MSINQYSSDF NYHALMCQQQ QHQHHHHHRN DVVEEKEALF EKPLTPSDVG KLNRLVIPKQ  60
HAERYFPLAA AAADAMEKGL LLCFEDEEGK PWRFRYSYWN SSQSYVLTKG WSRYVKEKQL  120
DAGDVILFHR HRVDGGRFFI SWRRRGDSSS SSDSYRHLQS NASIQYYPHA GAQAAESQRG  180
NSKTLRLFGV NMECQLDSDW SDPSTPNGST ICPTSHDQFH LYPQQHYPPP YYM
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5os9_A4e-49331451113B3 domain-containing transcription factor NGA1
5os9_B4e-49331451113B3 domain-containing transcription factor NGA1
Search in ModeBase
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2325750.0AC232575.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrS010A05, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018437389.11e-176PREDICTED: B3 domain-containing protein At2g36080-like
SwissprotQ8GYJ21e-137Y2608_ARATH; B3 domain-containing protein At2g36080
TrEMBLA0A397Z9X01e-147A0A397Z9X0_BRACM; Uncharacterized protein
STRINGBra005301.1-P1e-143(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM122028100
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G36080.11e-130B3 family protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Tanaka M, et al.
    The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation.
    Plant Cell, 2016. 28(11): p. 2830-2849
    [PMID:27760805]