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 GSBRNA2T00091101001
Common NameGSBRNA2T00091101001
Organism
Brassica napus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family B3
Protein Properties Length: 226aa    MW: 25820.2 Da    PI: 9.6977
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00091101001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.64.1e-17128221199
                          EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                          f  vl ps+  + ++++lp  fae++ +g+  + ++++   +  ++W v++    k gr  +++GW eF  +n++ egD++vF+l ++++
  GSBRNA2T00091101001 128 FRVVLRPSYLYRGCIMYLPSGFAEKYfSGI-SGFIKIQ---LGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLSTRD 211
                          678899********************7444.3544555...677*******..666666779***********************999** PP

                          E..EEEEE-S CS
                   B3  90 felvvkvfrk 99 
                          f l+v++fr 
  GSBRNA2T00091101001 212 FVLKVTAFRV 221
                          *9***99985 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
SuperFamilySSF1019363.73E-22121222IPR015300DNA-binding pseudobarrel domain
CDDcd100171.16E-20126220No hitNo description
PROSITE profilePS5086312.337128222IPR003340B3 DNA binding domain
PfamPF023629.1E-16128221IPR003340B3 DNA binding domain
SMARTSM010199.5E-20128222IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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: 226 aa     Download sequence    Send to blast
MDSTHSEFNK RARLFEDHQN KDAKVIHPMI PESTTPLDKG YDASTTTQNL FNESKPEVAT  60
PKVLKKRGRK KKNPNPEEVN SSTPRGDDSE NRSKFYESAS ARMRTVTAEE RERAITAAKA  120
YEPTNPFFRV VLRPSYLYRG CIMYLPSGFA EKYFSGISGF 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-889422515146B3 domain-containing transcription factor VRN1
4i1k_B1e-889422515146B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.144860.0seed
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:22232549}.
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
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00091101001
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_013735877.11e-167B3 domain-containing protein REM19-like
SwissprotQ9XIB51e-140REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A078FUJ31e-168A0A078FUJ3_BRANA; BnaA08g02650D protein
STRINGBra014192.1-P1e-157(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-116related 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]
  3. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]