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 Thhalv10012062m
Organism
Eutrema salsugineum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Eutremeae; Eutrema
Family B3
Protein Properties Length: 225aa    MW: 25322.8 Da    PI: 10.0196
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thhalv10012062mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.73.8e-17127220199
                      EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 
                      f  vl ps+  + ++++lp  fae++ +g++ +   ++  ++  ++W v++    k gr  +++GW eF  +n++ egD++vF+l ++++f l+
  Thhalv10012062m 127 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GF--IK-LQLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLKTRDFVLK 214
                      678899********************85452.33..44.44688*******..666666779************************99****** PP

                      EEEE-S CS
               B3  94 vkvfrk 99 
                      v++fr 
  Thhalv10012062m 215 VTAFRV 220
                      *99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.108.3E-24119220IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.26E-22120221IPR015300DNA-binding pseudobarrel domain
CDDcd100176.19E-22125219No hitNo description
PROSITE profilePS5086312.59127221IPR003340B3 DNA binding domain
SMARTSM010191.9E-20127221IPR003340B3 DNA binding domain
PfamPF023621.1E-15127220IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
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: 225 aa     Download sequence    Send to blast
MDSAHNQLNK RARLFGDLEN KDAKVIYPPI PASTAPLNKG SDGSTATQSL FAESKPEETP  60
KVLKKRGRKK KNPNPEEMNS STPGGDDSEN RSKFYESASA RKRTVTAEER ERAINAAKTF  120
EPTNPFFRVV LRPSYLYRGC IMYLPSGFAE KYLSGISGFI KLQLGEKQWP VRCLYKAGRA  180
KFSQGWYEFT LENNIGEGDV CVFELLKTRD FVLKVTAFRV NQYV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A2e-929322415146B3 domain-containing transcription factor VRN1
4i1k_B2e-929322415146B3 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
PlantRegMapThhalv10012062m
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
GenBankAK3532360.0AK353236.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-22-N21.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006393253.21e-167B3 domain-containing protein REM19
SwissprotQ9XIB51e-149REM19_ARATH; B3 domain-containing protein REM19
TrEMBLE4MXI91e-165E4MXI9_EUTHA; mRNA, clone: RTFL01-22-N21
STRINGXP_006393253.11e-166(Eutrema salsugineum)
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-140related 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]