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 479415
Common NameARALYDRAFT_479415
Organism
Arabidopsis lyrata
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: 342aa    MW: 39242.6 Da    PI: 9.5175
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
479415genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B356.64.5e-18595197
            EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
      B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97
            ff +l+ s++ +++rl++p kf+++++ +   s+ + l+ ++g +W+v l  rk ++++++++GW+eFv+   ++ g  ++F+++g+s f   v +f
  479415  5 FFHKLIFSSTIQEKRLRVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGL--RKADNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAF--SVYIF 95
            899999*****************999755..99*****************..**********************************9999..88777 PP
2B355.11.4e-17244337199
             EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
      B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 
             f  vl ps+  + ++++lp  fae++ +g++ + ++++   +  ++W v++    k gr  +++GW eF  +n+L egD++vF+l ++++f l+v++fr 
  479415 244 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKVQ---LAEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRV 337
             677899********************84442.444555...567*******..666666779************************99*******99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.107.6E-23397IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.1E-22397IPR015300DNA-binding pseudobarrel domain
CDDcd100175.77E-19596No hitNo description
PfamPF023623.0E-15596IPR003340B3 DNA binding domain
PROSITE profilePS5086314.663598IPR003340B3 DNA binding domain
SMARTSM010192.7E-17598IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.104.3E-23236337IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.32E-22237338IPR015300DNA-binding pseudobarrel domain
CDDcd100172.21E-20242336No hitNo description
PfamPF023625.2E-16244337IPR003340B3 DNA binding domain
PROSITE profilePS5086312.619244338IPR003340B3 DNA binding domain
SMARTSM010198.1E-22244338IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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: 342 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSKF KDELSVAVAL TVPDGHVWRV GLRKADNKIW  60
FQDGWQEFVD RYSIRIGYLL IFRYEGNSAF SVYIFNLSHS EINYHSTGLM DSAHNHFKRA  120
RLFEDLEDED AEFIFPSSVY PSPLPESTVP ANKGYAGSAI QSLFTGSVKA EEATPTPKIP  180
KKRGRKKKNA DPEEINSSAP RDDDPENRSK FYESASARKR TVTAEERERA INAAKTFEPT  240
NPFFRVVLRP SYLYRGCIMY LPSGFAEKYL SGISGFIKVQ LAEKQWPVRC LYKAGRAKFS  300
QGWYEFTLEN NLGEGDVCVF ELLRTRDFVL KVTAFRVNEY V*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A2e-9420734112146B3 domain-containing transcription factor VRN1
4i1k_B2e-9420734112146B3 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
PlantRegMap479415
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
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_020887459.10.0B3 domain-containing transcription factor VRN1
SwissprotQ8L3W10.0VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLD7L9670.0D7L967_ARALL; Uncharacterized protein
STRINGfgenesh2_kg.3__2116__AT3G18990.10.0(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
AT3G18990.10.0B3 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]