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 GSBRNA2T00073552001
Common NameGSBRNA2T00073552001, LOC106423838
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: 169aa    MW: 19415.3 Da    PI: 10.2165
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00073552001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B349.11e-1571164199
                          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++ e+D++vF+l ++++
  GSBRNA2T00073552001  71 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-SFIK---IQLGEKLWPVRC--PYKAGRAKFSQGWYEFTLENNIGERDVCVFELLSTRD 154
                          678899********************84442.3334...45777*******..777777889***********************999** PP

                          E..EEEEE-S CS
                   B3  90 felvvkvfrk 99 
                          f l+v++fr 
  GSBRNA2T00073552001 155 FVLKVTAFRV 164
                          *****99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.7E-2163164IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.71E-2064165IPR015300DNA-binding pseudobarrel domain
CDDcd100172.61E-1769163No hitNo description
SMARTSM010191.0E-1571165IPR003340B3 DNA binding domain
PROSITE profilePS5086311.1871165IPR003340B3 DNA binding domain
PfamPF023624.1E-1471164IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 169 aa     Download sequence    Send to blast
MATPKILKKR GRKKKNPNPE EVNSSTPRGD DSENRSKFYE SASARMRTVT AEERERGITA  60
AKTYEPTNPF FRVVLRPSYL YRGCIMYLPS GFAEKYLSGI SSFIKIQLGE KLWPVRCPYK  120
AGRAKFSQGW YEFTLENNIG ERDVCVFELL STRDFVLKVT AFRVNQYV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A9e-853716815146B3 domain-containing transcription factor VRN1
4i1k_B9e-853716815146B3 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00073552001
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-176AK353236.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-22-N21.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013604041.11e-122PREDICTED: B3 domain-containing protein REM19
RefseqXP_013720050.11e-122B3 domain-containing protein REM19
SwissprotQ9XIB51e-109REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A078JSI51e-121A0A078JSI5_BRANA; BnaC02g46200D protein
TrEMBLA0A0D3DJK41e-121A0A0D3DJK4_BRAOL; Uncharacterized protein
STRINGBo8g011550.11e-121(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-100related 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]