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 Lj3g3v3336240.1
Organism
Lotus japonicus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
Family B3
Protein Properties Length: 425aa    MW: 47776.1 Da    PI: 9.5472
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lj3g3v3336240.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3512.6e-16695197
                     EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEE CS
               B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkv 96
                     f k  +ps v +++ l+lp +f++++gg+   s   tl  ++g +W+v l  +k +++ +l +GW+eFv+   + +g  +vF+++g+s+f  +v +
  Lj3g3v3336240.1  6 FYKLVLPSTVQAKQ-LRLPDNFMRKYGGE--LSPFATLSVPDGSVWRVGL--KKADNKSWLVDGWQEFVQRYSIGVGYLLVFRYEGKSSF--NVNI 94
                     56777888888886.***********877..66689999***********..9999999**************************99999..6655 PP

                     E CS
               B3 97 f 97
                     +
  Lj3g3v3336240.1 95 L 95
                     4 PP
2B362.56.8e-20295386499
                      E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEE CS
               B3   4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkv 96 
                      vl ps+  + ++++lp  fae+h +g++     ++l++++gr+W v++ yr+++    l++GW eF+ +n+L egD++vF+l + ++  l v++
  Lj3g3v3336240.1 295 VLRPSYLYRGCIMYLPSCFAEKHlNGVSG---FIKLQTSDGRQWPVRCLYRGGR--AKLSQGWFEFALDNNLGEGDVCVFELLKVKDVALQVTL 383
                      78899******************877744...5***************665555..66***********************9999999999999 PP

                      E-S CS
               B3  97 frk 99 
                      fr 
  Lj3g3v3336240.1 384 FRV 386
                      985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.24E-21396IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.3E-23396IPR015300DNA-binding pseudobarrel domain
CDDcd100171.77E-17495No hitNo description
PROSITE profilePS5086312.943598IPR003340B3 DNA binding domain
SMARTSM010195.8E-16698IPR003340B3 DNA binding domain
PfamPF023621.1E-13794IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.103.9E-25284385IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.35E-25285386IPR015300DNA-binding pseudobarrel domain
CDDcd100171.22E-23290385No hitNo description
PROSITE profilePS5086314.41292387IPR003340B3 DNA binding domain
SMARTSM010191.6E-18292387IPR003340B3 DNA binding domain
PfamPF023624.4E-18295385IPR003340B3 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: 425 aa     Download sequence    Send to blast
MPRPSFYKLV LPSTVQAKQL RLPDNFMRKY GGELSPFATL SVPDGSVWRV GLKKADNKSW  60
LVDGWQEFVQ RYSIGVGYLL VFRYEGKSSF NVNILATSEI NYQPATRSSN EGPYFASRLK  120
FLEEMEDEDS IEILDSSPSH LTPGSTLPNK AFPGSVDKST PGGKSYSPPA LQNLFNGSKL  180
NSINRGEGGN TLSSRSANSQ DKKLSRDIGV QFNAAEFKRS NEEVKLRASM EERIKKTATK  240
KRKSEDQEHE EEVEMRVRFY ESASARKRTV TAEEREKAVN AAKEFEPPNP FCRVVLRPSY  300
LYRGCIMYLP SCFAEKHLNG VSGFIKLQTS DGRQWPVRCL YRGGRAKLSQ GWFEFALDNN  360
LGEGDVCVFE LLKVKDVALQ VTLFRVTEDV GLLSSPLQQN ENAVSAKQLS SPLQHHLTSS  420
KLVRN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-7025839015146B3 domain-containing transcription factor VRN1
4i1k_B1e-7025839015146B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots and at lower levels in aerial parts. {ECO:0000269|PubMed:12114624}.
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
PlantRegMapLj3g3v3336240.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0097100.0AP009710.1 Lotus japonicus genomic DNA, chromosome 3, clone: LjT23H01, TM1768, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027356384.10.0B3 domain-containing transcription factor VRN1-like
SwissprotQ8L3W11e-125VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A151TG430.0A0A151TG43_CAJCA; B3 domain-containing transcription factor VRN1
STRINGXP_007131905.10.0(Phaseolus vulgaris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF21473485
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18990.11e-127B3 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]