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 Rsa1.0_03884.1_g00004.1
Organism
Raphanus sativus
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: 226aa    MW: 25672 Da    PI: 9.6978
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_03884.1_g00004.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.44.6e-17129222199
                              EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                              f  vl ps+  + ++++lp  fae++ +g++ + ++++   +  ++W v++    k gr  +++GW eF  +n++ egD++vF+l 
  Rsa1.0_03884.1_g00004.1 129 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKIQ---LGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELL 208
                              678899********************84442.444555...677*******..666666779***********************9 PP

                              SSSEE..EEEEE-S CS
                       B3  86 grsefelvvkvfrk 99 
                              ++++f l+v++fr 
  Rsa1.0_03884.1_g00004.1 209 STRDFVLKVTAFRV 222
                              99***9***99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.107.7E-23121222IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.89E-22122223IPR015300DNA-binding pseudobarrel domain
CDDcd100173.47E-21127221No hitNo description
PROSITE profilePS5086312.421129223IPR003340B3 DNA binding domain
SMARTSM010192.1E-19129223IPR003340B3 DNA binding domain
PfamPF023621.6E-15129222IPR003340B3 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: 226 aa     Download sequence    Send to blast
MDSANSEFNK RARLFEDHEN KGSKVIHSMI PESTTPLNKG YDASTTTQNL FAESKPEATT  60
TPKVLKKRGR KKKNPNPEET NSSTPGGEDS ENRSKFYESA SARMRTATPE ERERAISAAK  120
TYEPTNPFFR VVLRPSYLYR GCIMYLPSGF AEKYLSGISG FIKIQLGEKQ WPVRCLYKAG  180
RAKFSQGWYE FTLENNIGEG DVCVFELLST RDFVLKVTAF RVNQYV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A7e-899522615146B3 domain-containing transcription factor VRN1
4i1k_B7e-899522615146B3 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
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_03884.1_g00004.1
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018447488.11e-164PREDICTED: B3 domain-containing protein REM19
RefseqXP_018447490.11e-164PREDICTED: B3 domain-containing protein REM19
RefseqXP_018447491.11e-164PREDICTED: B3 domain-containing protein REM19
SwissprotQ9XIB51e-138REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A397Y7E21e-153A0A397Y7E2_BRACM; Uncharacterized protein
STRINGXP_006393253.11e-142(Eutrema salsugineum)
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-129related 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]