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_009112206.1
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: 342aa    MW: 39558.8 Da    PI: 9.2646
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009112206.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.44.6e-17595194
                    EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTE.EEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS
              B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgr.yvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94
                    ff +l+ s++ +++rl++p kf+++++ +   s+ + l+ ++g +W+v l  rk ++  +++++GW+eFv+   ++ g  ++F+++g+s f+ ++
  XP_009112206.1  5 FFHKLIFSSTIQEKRLRVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGL--RKADNNkIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSVYI 95
                    899999*****************999755..99*****************..66655559***************************99995544 PP
2B354.81.7e-17245338199
                     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+L egD++vF+l ++++f l+v
  XP_009112206.1 245 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENDLGEGDVCVFELLRTRDFVLKV 333
                     677899********************84442.43344...4677*******..666666779************************99******* PP

                     EEE-S CS
              B3  95 kvfrk 99 
                     ++fr 
  XP_009112206.1 334 TAFRV 338
                     99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.9E-21398IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.8E-22398IPR015300DNA-binding pseudobarrel domain
PfamPF023623.5E-14595IPR003340B3 DNA binding domain
PROSITE profilePS5086314.649599IPR003340B3 DNA binding domain
CDDcd100175.18E-19597No hitNo description
SMARTSM010191.0E-17599IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.106.2E-23237338IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.53E-22238339IPR015300DNA-binding pseudobarrel domain
CDDcd100171.69E-20243337No hitNo description
PfamPF023627.6E-16245338IPR003340B3 DNA binding domain
SMARTSM010194.7E-21245339IPR003340B3 DNA binding domain
PROSITE profilePS5086312.562245339IPR003340B3 DNA binding domain
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: 342 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSKF KDELSVAVAL TVPDGHVWRV GLRKADNNKI  60
WFQDGWQEFV DRYSIRIGYL LIFRYEGNSA FSVYIYNLSH SEINYHSTGL MDSAHNHFKR  120
ARLFEDLEDE DVEVVHPSSL YPLQHPETTG HANKGHTSSA IQSFFAEPVK AEETTPTPKV  180
PKKRGRKKKN ADPEEINSSA PRDDDPENRS KFYESASARK RTVTAEERER AINAAKTFEP  240
TNPFFRVVLR PSYLYRGCIM YLPSGFAEKY LSGISGFIKV QLGEKQWPVR CLYKAGRAKF  300
SQGWYEFTLE NDLGEGDVCV FELLRTRDFV LKVTAFRVNE YV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-9121134215146B3 domain-containing transcription factor VRN1
4i1k_B1e-9121134215146B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.40880.0leaf
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots and at lower levels in aerial parts. {ECO:0000269|PubMed:12114624}.
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
PlantRegMapXP_009112206.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3532690.0AK353269.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-34-E14.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009112206.10.0PREDICTED: B3 domain-containing transcription factor VRN1
RefseqXP_013694026.10.0B3 domain-containing transcription factor VRN1
RefseqXP_013721398.10.0B3 domain-containing transcription factor VRN1
SwissprotQ8L3W10.0VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLM4F8Y20.0M4F8Y2_BRARP; Uncharacterized protein
STRINGBra037544.1-P0.0(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
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]