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 RrC8235_p2
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: 225aa    MW: 25687.1 Da    PI: 9.9014
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC8235_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3536.3e-17128221199
                 EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS
          B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 
                 f  vl ps+  + ++++lp  fae++  g+ ++   ++  ++  ++W v++    k gr  +++GW eF  +n++ egD++vF+l ++++f l+v++fr
  RrC8235_p2 128 FRVVLRPSYLYRGCIMYLPSGFAEKYlTGI-AGF--IK-LQLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLKTRDFVLKVTAFR 220
                 678899********************8444.344..44.34677*******..666666779************************99*******9998 PP

                 S CS
          B3  99 k 99 
                  
  RrC8235_p2 221 V 221
                 5 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.0E-23120221IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.55E-22121222IPR015300DNA-binding pseudobarrel domain
CDDcd100172.08E-21126220No hitNo description
PfamPF023621.8E-15128221IPR003340B3 DNA binding domain
SMARTSM010191.1E-19128222IPR003340B3 DNA binding domain
PROSITE profilePS5086312.506128222IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 225 aa     Download sequence    Send to blast
MNMDSAAHNE FNNKRARLFE DRLKEGTRGV TQPLIPESNA PLNEGYDGSN PTQSLFTDSK  60
PEETPKVPKK RGRKKKNPNP EDLSSSTTPE NSSKFYKSAS DRKRTVTAEE RERAISAAKT  120
YEPTNPFFRV VLRPSYLYRG CIMYLPSGFA EKYLTGIAGF IKLQLGEKQW PVRCLYKAGR  180
AKFSQGWYEF TLENNIGEGD VCVFELLKTR DFVLKVTAFR VNQYV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-889422515146B3 domain-containing transcription factor VRN1
4i1k_B1e-889422515146B3 domain-containing transcription factor VRN1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtInvolved in the regulation of vernalization (By similarity). Binds to DNA in vitro in a non-sequence-specific manner. XLG2 promotes the DNA binding activity of RTV1 specifically to promoter regions of FT and SOC1 in vivo and thus leads to the activation of floral integrator genes. {ECO:0000250, ECO:0000269|PubMed:22232549}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By cold. {ECO:0000269|PubMed:22232549}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3532361e-159AK353236.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-22-N21.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018492716.11e-150PREDICTED: B3 domain-containing protein REM19-like
SwissprotQ9XIB51e-123REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A078J4Z61e-147A0A078J4Z6_BRANA; BnaC05g51360D protein
TrEMBLA0A0D3CFU51e-147A0A0D3CFU5_BRAOL; Uncharacterized protein
TrEMBLA0A3P6EJG71e-147A0A3P6EJG7_BRAOL; Uncharacterized protein
STRINGBo5g076230.11e-147(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM112428103
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G49480.11e-112related to vernalization1 1
Publications ? help Back to Top
  1. Conte MG,Gaillard S,Droc G,Perin C
    Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.
    BMC Genomics, 2008. 9: p. 183
    [PMID:18426584]
  2. Mantegazza O, et al.
    Analysis of the arabidopsis REM gene family predicts functions during flower development.
    Ann. Bot., 2014. 114(7): p. 1507-15
    [PMID:25002525]