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 RrC111_p2
Organism
Raphanus raphanistrum
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: 418aa    MW: 48266 Da    PI: 8.8874
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC111_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B352.49.3e-1765155196
                EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTE.EEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEE CS
         B3   1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgr.yvltkGWkeFvkangLkegDfvvFkldgrsefelvvkv 96 
                ff +l+ +++ +++rl++p kfa++++ +   s+ + l+ ++g +W+v l  rk ++  +++++GW+eFv+   ++ g  ++F+++g+s f   v++
  RrC111_p2  65 FFHKLIFPSTIQEKRLRVPDKFASKFKDE--LSVAVALTVPDGHVWRVGL--RKADNNkIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAF--SVSI 155
                78899999999999*********999755..99*****************..66655559***************************9999..6665 PP
2B340.64.6e-133434131792
                E--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
         B3  17 vlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                +lp  fae++ +g++ + +++   ++  ++W v++    k gr  +++GW eF  +n+L egD++vF+l ++++f l
  RrC111_p2 343 YLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTVENNLGEGDVCVFELLRTRDFVL 413
                79999***9974442.43344...4677*******..666666779**********************999888844 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.37E-2160158IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.109.5E-2362158IPR015300DNA-binding pseudobarrel domain
CDDcd100172.10E-1764157No hitNo description
PROSITE profilePS5086314.64965159IPR003340B3 DNA binding domain
PfamPF023625.9E-1465155IPR003340B3 DNA binding domain
SMARTSM010191.0E-1765159IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.105.5E-19286309IPR015300DNA-binding pseudobarrel domain
CDDcd100171.12E-12292415No hitNo description
SuperFamilySSF1019364.32E-15332411IPR015300DNA-binding pseudobarrel domain
SMARTSM010193.9E-10334418IPR003340B3 DNA binding domain
PfamPF023629.1E-12343414IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.105.5E-19343413IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086310.673367418IPR003340B3 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: 418 aa     Download sequence    Send to blast
ITQAKCKRKE RERDYLFDHN QSFYTKLFTD LKGLPSVSVA YSPASFHDLT FCLFSLFTLN  60
MPRPFFHKLI FPSTIQEKRL RVPDKFASKF KDELSVAVAL TVPDGHVWRV GLRKADNNKI  120
WFQDGWQEFV DRYSIRIGYL LIFRYEGNSA FSVSIYNLSH SEINYHSTGL MDSAAHNHFK  180
RPCLFEDLED EDAETTVHAN KEHASSAIQS FFAGPVKAEE ATPTPTLKVT KKRGRKKKNA  240
DPEEVNSSAP RVDDPESRSK FYESASARKR TVTAEERERA INASKTYEPT NPFFRVVLRP  300
SYLYRGCIMV IIITDISELH FFAYIYTMVS KEAFVFFCVF EQYLPSGFAE KYLSGISGFI  360
KVQLGEKQWP VRCLYKAGRA KFSQGWYEFT VENNLGEGDV CVFELLRTRD FVLKFANT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-7526041415136B3 domain-containing transcription factor VRN1
4i1k_B1e-7526041415136B3 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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY3563680.0AY356368.1 Brassica rapa cultivar Samjin reduced vernalization response 1 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018464741.10.0PREDICTED: B3 domain-containing transcription factor VRN1-like isoform X2
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]