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 Araha.3451s0002.1.p
Organism
Arabidopsis halleri
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family B3
Protein Properties Length: 280aa    MW: 32051.2 Da    PI: 8.5868
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.3451s0002.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B357.23.1e-18595197
                         EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
                   B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92
                         ff +l+ s++ +++rl++p kf+++++ +   s+ + l+ ++g +W+v l  rk ++++++++GW+eFv+   ++ g  ++F+++g+s f  
  Araha.3451s0002.1.p  5 FFHKLIFSSTIQEKRLRVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGL--RKADNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAF-- 90
                         899999*****************999755..99*****************..**********************************9999.. PP

                         EEEEE CS
                   B3 93 vvkvf 97
                          v +f
  Araha.3451s0002.1.p 91 SVYIF 95
                         88777 PP
2B340.26.1e-132202754299
                          TS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
                   B3  42 sgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 
                            ++W v++    k gr  +++GW eF  +n+L egD++vF+l ++++f l+v++fr 
  Araha.3451s0002.1.p 220 AEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRV 275
                          569******..666666779************************99*******99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.53E-22398IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.105.1E-23397IPR015300DNA-binding pseudobarrel domain
CDDcd100174.29E-19596No hitNo description
PfamPF023622.0E-15596IPR003340B3 DNA binding domain
PROSITE profilePS5086314.663598IPR003340B3 DNA binding domain
SMARTSM010192.7E-17598IPR003340B3 DNA binding domain
SMARTSM010195.5E-6164276IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.108.2E-14219275IPR015300DNA-binding pseudobarrel domain
PfamPF023623.6E-11220275IPR003340B3 DNA binding domain
SuperFamilySSF1019361.84E-12221276IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086310.898222276IPR003340B3 DNA binding domain
CDDcd100171.22E-10222274No hitNo description
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: 280 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSKF KDELSVAVAL TVPDGHVWRV GLRKADNKIW  60
FQDGWQEFVD RYSIRIGYLL IFRYEGNSAF SVYIFNLSHS EINYHSTGLM DSAHNHFKRA  120
RLFEDLEDED AEVVFPSSVY PSPLPDSTVP ANKGYAGSAI QSLFTGSVKA EEATPTPKVP  180
KKRGRKKKNA DPEEINSSAP RDDDPENRSK FYESASVQLA EKQWPVRCLY KAGRAKFSQG  240
WYEFTLENNL GEGDVCVFEL LRTRDFVLKV TAFRVNEYV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-3921727984146B3 domain-containing transcription factor VRN1
4i1k_B1e-3921727984146B3 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
PlantRegMapAraha.3451s0002.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4936200.0AB493620.1 Arabidopsis thaliana At3g18990 mRNA for hypothetical protein, partial cds, clone: RAAt3g18990.
GenBankAF2890520.0AF289052.1 Arabidopsis thaliana reduced vernalization response 1 (VRN1) mRNA, VRN1-Ler allele, complete cds.
GenBankAK2303880.0AK230388.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL25-06-L05.
GenBankBT0247310.0BT024731.1 Arabidopsis thaliana At3g18990 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020887459.11e-177B3 domain-containing transcription factor VRN1
SwissprotQ8L3W11e-176VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLD7L9671e-176D7L967_ARALL; Uncharacterized protein
STRINGfgenesh2_kg.3__2116__AT3G18990.11e-176(Arabidopsis lyrata)
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
AT3G18990.11e-142B3 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]