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_18666.1_g00001.1
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: 217aa    MW: 24937.2 Da    PI: 9.6975
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_18666.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B352.31.1e-16120213199
                              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_18666.1_g00001.1 120 FRVVLRPSYLYRGCIMYLPSGFAEKYlTGI-AGF--IK-LQLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELL 199
                              678899********************8444.344..44.34677*******..666666779************************ PP

                              SSSEE..EEEEE-S CS
                       B3  86 grsefelvvkvfrk 99 
                              ++++f l+v++fr 
  Rsa1.0_18666.1_g00001.1 200 KTRDFILKVTAFRV 213
                              99***999999985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.7E-23112213IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.53E-22113214IPR015300DNA-binding pseudobarrel domain
CDDcd100171.12E-20118212No hitNo description
SMARTSM010191.8E-18120214IPR003340B3 DNA binding domain
PROSITE profilePS5086312.435120214IPR003340B3 DNA binding domain
PfamPF023623.3E-15120213IPR003340B3 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: 217 aa     Download sequence    Send to blast
MDSAHDVFNN KRARLFEDRQ IEGTRDTQPL IPESNEGYDG SNPTQSLFTD SKPEETPKVP  60
KKRGRKKKNP NPEDMSSSTT PENSSKFYKS ASDRKRTVTA EERERAISAA KTYEPTNPFF  120
RVVLRPSYLY RGCIMYLPSG FAEKYLTGIA GFIKLQLGEK QWPVRCLYKA GRAKFSQGWY  180
EFTLENNIGE GDVCVFELLK TRDFILKVTA FRVNQYV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-888621715146B3 domain-containing transcription factor VRN1
4i1k_B1e-888621715146B3 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_18666.1_g00001.1
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3532361e-175AK353236.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-22-N21.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018492716.11e-162PREDICTED: B3 domain-containing protein REM19-like
SwissprotQ9XIB51e-121REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A078J4Z61e-140A0A078J4Z6_BRANA; BnaC05g51360D protein
TrEMBLA0A0D3CFU51e-140A0A0D3CFU5_BRAOL; Uncharacterized protein
TrEMBLA0A3P6EJG71e-140A0A3P6EJG7_BRAOL; Uncharacterized protein
STRINGBo5g076230.11e-141(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-110related 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]