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 RrC19093_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: 225aa    MW: 25753.1 Da    PI: 9.7063
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC19093_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.44.6e-17128221199
                  EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97 
                  f  vl ps+  + ++++lp  fae++ +g++ + ++++   +  ++W v++    k gr  +++GW eF  +n++ egD++vF+l ++++f l+v++f
  RrC19093_p1 128 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKIQ---LGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLSTRDFVLKVTAF 219
                  678899********************84442.444555...677*******..666666779***********************999***9***999 PP

                  -S CS
           B3  98 rk 99 
                  r 
  RrC19093_p1 220 RV 221
                  85 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.107.6E-23120221IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.89E-22121222IPR015300DNA-binding pseudobarrel domain
CDDcd100172.94E-21126220No hitNo description
PfamPF023621.6E-15128221IPR003340B3 DNA binding domain
PROSITE profilePS5086312.421128222IPR003340B3 DNA binding domain
SMARTSM010192.1E-19128222IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009409Biological Processresponse to cold
GO:0034613Biological Processcellular protein localization
GO:0005634Cellular Componentnucleus
GO:0005886Cellular Componentplasma membrane
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 225 aa     Download sequence    Send to blast
MNMDSANSEF NKRARLFEDR ENKDSKVIHS MIPESTTPRY DASTTTQNLF AESKPEATTP  60
KVLKKRGRKK KNPNPEEQTN SSTPGGEDSE NRSKFYESAS ARMRTATAEE RERAITAAKT  120
YEPTNPFFRV VLRPSYLYRG CIMYLPSGFA EKYLSGISGF IKIQLGEKQW PVRCLYKAGR  180
AKFSQGWYEF TLENNIGEGD VCVFELLSTR DFVLKVTAFR VNQYV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-899422515146B3 domain-containing transcription factor VRN1
4i1k_B1e-899422515146B3 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00192DAPTransfer from AT1G49480Download
Motif logo
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018447488.11e-156PREDICTED: B3 domain-containing protein REM19
RefseqXP_018447490.11e-156PREDICTED: B3 domain-containing protein REM19
RefseqXP_018447491.11e-156PREDICTED: B3 domain-containing protein REM19
SwissprotQ9XIB51e-134REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A397Y7E21e-149A0A397Y7E2_BRACM; Uncharacterized protein
STRINGBra014192.1-P1e-139(Brassica rapa)
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-107related 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]