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 XP_009144977.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family B3
Protein Properties Length: 222aa    MW: 25518 Da    PI: 10.0764
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009144977.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.73.7e-17125218199
                     EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 
                     f  vl ps+  + ++++lp  fae++ +g+ ++   ++  ++  ++W v++    k gr  +++GW eF  +n++ egD++vF+l ++++f l+v
  XP_009144977.1 125 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGI-AGF--IK-LQLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNIGEGDVCVFELLRTRDFVLKV 213
                     678899********************7555.354..44.34677*******..666666779************************99******* PP

                     EEE-S CS
              B3  95 kvfrk 99 
                     ++fr 
  XP_009144977.1 214 TAFRV 218
                     99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.1E-23117217IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.87E-22118217IPR015300DNA-binding pseudobarrel domain
CDDcd100172.34E-21123217No hitNo description
SMARTSM010194.7E-20125219IPR003340B3 DNA binding domain
PROSITE profilePS5086312.478125219IPR003340B3 DNA binding domain
PfamPF023621.3E-15125217IPR003340B3 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: 222 aa     Download sequence    Send to blast
MNMDSAQNEF NKRARLFEDR QKEETRVTHP LIPKSNAPLN EGYEGSTTTQ SLFTDSKPEV  60
ATPKVPKKRG RKKKNPNPEE INSSTPENSS KFYKSASDRK RTVTAEERER AISAAKTYEP  120
TNPFFRVVLR PSYLYRGCIM YLPSGFAEKY LSGIAGFIKL QLGEKQWPVR CLYKAGRAKF  180
SQGWYEFTLE NNIGEGDVCV FELLRTRDFV LKVTAFRVTQ YV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A2e-889122215146B3 domain-containing transcription factor VRN1
4i1k_B2e-889122215146B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.19420.0bud| flower| root| seed
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:22232549}.
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
PlantRegMapXP_009144977.1
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009144977.11e-165PREDICTED: B3 domain-containing protein REM19-like
SwissprotQ9XIB51e-131REM19_ARATH; B3 domain-containing protein REM19
TrEMBLM4EU041e-162M4EU04_BRARP; Uncharacterized protein
STRINGBra032286.1-P1e-162(Brassica rapa)
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-119related 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]