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 KFK36008.1
Organism
Arabis alpina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Arabideae; Arabis
Family B3
Protein Properties Length: 222aa    MW: 25360.7 Da    PI: 9.6973
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KFK36008.1genomeMPIPBRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.93.2e-17125218199
                 EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS
          B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 
                 f  vl ps+  + ++++lp  fae++ +g++ + ++++   +  ++W v++    k gr  +++GW eF  +n++ egD++vF+l ++++f l+v++fr
  KFK36008.1 125 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKIQ---LGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLRTRDFVLKVTAFR 217
                 678899********************84442.444555...677*******..666666779************************99*******9998 PP

                 S CS
          B3  99 k 99 
                  
  KFK36008.1 218 V 218
                 5 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.105.1E-23117218IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.9E-22118219IPR015300DNA-binding pseudobarrel domain
CDDcd100174.95E-21123217No hitNo description
PfamPF023621.3E-15125218IPR003340B3 DNA binding domain
SMARTSM010194.6E-20125219IPR003340B3 DNA binding domain
PROSITE profilePS5086312.421125219IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009409Biological Processresponse to cold
GO:0034613Biological Processcellular protein localization
GO:0005634Cellular Componentnucleus
GO:0005886Cellular Componentplasma membrane
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 222 aa     Download sequence    Send to blast
MDSAHNPFNK RARLFEDPED KDAEVIYPSI PESTEPVNKG YGGSTTIQSL FVETKPEATP  60
KVLKKRGRKK KNPNPDDSST PRGDESENRS KFYESASARK RTVTAEERER AISAAKTFEP  120
TNPFFRVVLR PSYLYRGCIM YLPSGFAEKY LSGISGFIKI QLGEKQWPVR CLYKAGRAKF  180
SQGWYEFTLE NNIGEGDVCV FELLRTRDFV LKVTAFRVNQ YV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A6e-929122215146B3 domain-containing transcription factor VRN1
4i1k_B6e-929122215146B3 domain-containing transcription factor VRN1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtInvolved in the regulation of vernalization (By similarity). Binds to DNA in vitro in a non-sequence-specific manner. XLG2 promotes the DNA binding activity of RTV1 specifically to promoter regions of FT and SOC1 in vivo and thus leads to the activation of floral integrator genes. {ECO:0000250, ECO:0000269|PubMed:22232549}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00192DAPTransfer from AT1G49480Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapKFK36008.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By cold. {ECO:0000269|PubMed:22232549}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0428680.0AY042868.1 Arabidopsis thaliana Unknown protein (F13F21.8) mRNA, complete cds.
GenBankBT0156820.0BT015682.1 Arabidopsis thaliana At1g49480 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002894192.11e-147B3 domain-containing protein REM19
SwissprotQ9XIB51e-147REM19_ARATH; B3 domain-containing protein REM19
TrEMBLA0A087H1K61e-163A0A087H1K6_ARAAL; B3 domain-containing transcription factor vrn1
STRINGA0A087H1K61e-164(Arabis alpina)
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
AT1G49480.11e-138related to vernalization1 1
Publications ? help Back to Top
  1. Conte MG,Gaillard S,Droc G,Perin C
    Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.
    BMC Genomics, 2008. 9: p. 183
    [PMID:18426584]
  2. 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]