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 XP_009107297.1
Organism
Brassica rapa
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: 213aa    MW: 24380.6 Da    PI: 9.4499
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009107297.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B347.14.4e-15128208186
                     EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                     f  vl ps+  + ++++lp  fae++ +g++ + ++++   +  ++W v++    k gr  +++GW eF  +n++ egD++vF+l +
  XP_009107297.1 128 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKIQ---LGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLS 208
                     678899********************84442.444555...677*******..666666779**********************865 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.4E-21120209IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.77E-20121208IPR015300DNA-binding pseudobarrel domain
CDDcd100173.90E-19126206No hitNo description
PfamPF023622.2E-13128209IPR003340B3 DNA binding domain
PROSITE profilePS5086312.167128213IPR003340B3 DNA binding domain
SMARTSM010192.5E-12128212IPR003340B3 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: 213 aa     Download sequence    Send to blast
MDSTHSEFNK RARLFEDHQN KDAKVIHPMI PESTTPLDKG YDASTTTQNL FNESKPEVAT  60
PKVLKKRGRK KKNPNPEEVN SSTPRGDDSE NRSKFYESAS ARMRTVTAEE RERAITAAKA  120
YEPTNPFFRV VLRPSYLYRG CIMYLPSGFA EKYLSGISGF IKIQLGEKQW PVRCLYKAGR  180
AKFSQGWYEF TLENNIGEGD VCVFELLSTR DLF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A2e-799421215133B3 domain-containing transcription factor VRN1
4i1k_B2e-799421215133B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.109540.0flower
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
PlantRegMapXP_009107297.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009107297.11e-160PREDICTED: B3 domain-containing protein REM19
SwissprotQ9XIB51e-131REM19_ARATH; B3 domain-containing protein REM19
TrEMBLM4DCH81e-158M4DCH8_BRARP; Uncharacterized protein
STRINGBra014192.1-P1e-159(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]