PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Rsa1.0_09250.1_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: 343aa    MW: 39532.8 Da    PI: 9.5179
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_09250.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.44.6e-17595194
                             EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTE.EEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                       B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgr.yvltkGWkeFvkangLkegDfvvFkldgr 87
                             ff +l+ s++ +++rl++p kf+++++ +   s+ + l+ ++g +W+v l  rk ++  +++++GW+eFv+   ++ g  ++F+++g+
  Rsa1.0_09250.1_g00001.1  5 FFHKLIFSSTIQEKRLRVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGL--RKADNNkIWFQDGWQEFVDRYSIRIGYLLIFRYEGN 88
                             899999*****************999755..99*****************..66655559***************************9 PP

                             SEE..EE CS
                       B3 88 sefelvv 94
                             s f+ ++
  Rsa1.0_09250.1_g00001.1 89 SAFSVYI 95
                             9995544 PP
2B354.91.6e-17246339199
                              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+L egD++vF+l 
  Rsa1.0_09250.1_g00001.1 246 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELL 325
                              677899********************84442.43344...4677*******..666666779************************ PP

                              SSSEE..EEEEE-S CS
                       B3  86 grsefelvvkvfrk 99 
                              ++++f l+v++fr 
  Rsa1.0_09250.1_g00001.1 326 RTRDFVLKVTAFRV 339
                              99*******99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.9E-21398IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.8E-22398IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086314.649599IPR003340B3 DNA binding domain
PfamPF023623.5E-14595IPR003340B3 DNA binding domain
CDDcd100174.69E-19597No hitNo description
SMARTSM010191.0E-17599IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.104.0E-23238339IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.55E-22239340IPR015300DNA-binding pseudobarrel domain
CDDcd100171.42E-20244338No hitNo description
PfamPF023626.4E-16246339IPR003340B3 DNA binding domain
SMARTSM010192.7E-21246340IPR003340B3 DNA binding domain
PROSITE profilePS5086312.633246340IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009909Biological Processregulation of flower development
GO:0010048Biological Processvernalization response
GO:0005654Cellular Componentnucleoplasm
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 343 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSKF KDELSVAVAL TVPDGHVWRV GLRKADNNKI  60
WFQDGWQEFV DRYSIRIGYL LIFRYEGNSA FSVYIYNLSH SEINYHSTGL MDSAHNHFKR  120
ARLFEDLEDE DVEVVHPSSL LYPSQHPETT AHASKGHTSS AIQSFFAGPV KAEETTPTPK  180
VPKKRGRKKK NADPEEINSS APRDDDPESR SKFYESASAR KRTVTAEERE RAINAAKTFE  240
PTNPFFRVVL RPSYLYRGCI MYLPSGFAEK YLSGISGFIK VQLGEKQWPV RCLYKAGRAK  300
FSQGWYEFTL ENNLGEGDVC VFELLRTRDF VLKVTAFRVN EYV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A2e-9420934312146B3 domain-containing transcription factor VRN1
4i1k_B2e-9420934312146B3 domain-containing transcription factor VRN1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtInvolved in the regulation of vernalization. Acts as transcriptional repressor of FLC, a major target of the vernalization pathway. Binds DNA in vitro in a non-sequence-specific manner. {ECO:0000269|PubMed:12114624}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_09250.1_g00001.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3532690.0AK353269.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-34-E14.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018433421.10.0PREDICTED: B3 domain-containing transcription factor VRN1
SwissprotQ8L3W10.0VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A078G0N60.0A0A078G0N6_BRANA; BnaA01g26330D protein
STRINGBra037544.1-P0.0(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
AT3G18990.10.0B3 family protein
Publications ? help Back to Top
  1. 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]
  2. Kumar A,Singh A,Panigrahy M,Sahoo PK,Panigrahi KCS
    Carbon nanoparticles influence photomorphogenesis and flowering time in Arabidopsis thaliana.
    Plant Cell Rep., 2018. 37(6): p. 901-912
    [PMID:29541883]