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_009145836.1
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: 346aa    MW: 39580.9 Da    PI: 9.5581
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009145836.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B355.69.9e-18595194
                    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+++++   e s+ + l+ ++g +W+v l  rk+++  +++++GW+eFv+   ++ g  ++F+++g+s f+ ++
  XP_009145836.1  5 FFHKLIFSSTIQEKRLRVPDKFVSNFKD--ELSVAVALTVPDGHVWRVGL--RKSDNNkIYFQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSVYI 95
                    899999*****************76664..499*****************..7777777****************************99995544 PP
2B353.54.4e-17250342198
                     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_009145836.1 250 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKV 338
                     677899********************84442.43344...4677*******..666666779***********************999***9999 PP

                     EEE- CS
              B3  95 kvfr 98 
                     +++r
  XP_009145836.1 339 TAYR 342
                     8877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.108.0E-22398IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.94E-21398IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086314.931599IPR003340B3 DNA binding domain
CDDcd100172.24E-20597No hitNo description
PfamPF023627.4E-15595IPR003340B3 DNA binding domain
SMARTSM010192.1E-17599IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.101.1E-22242342IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.67E-22243343IPR015300DNA-binding pseudobarrel domain
CDDcd100171.08E-20248342No hitNo description
PROSITE profilePS5086312.52250344IPR003340B3 DNA binding domain
PfamPF023621.7E-15250342IPR003340B3 DNA binding domain
SMARTSM010197.8E-21250344IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 346 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSNF KDELSVAVAL TVPDGHVWRV GLRKSDNNKI  60
YFQDGWQEFV DRYSIRIGYL LIFRYEGNSA FSVYIYNLSH SEINYHSSAL MDTAHTHLKR  120
ARLFEDLEDE DAAEVVYPSS SVYPSSQQHP EVTVAAIKGY ASPAIQSFFA GPPVKAEEAT  180
PTPKVTKKRG RKKKNAVPEE VNSSAPRDDD PESRSKFYES ASARKRTVTA EERERAINAA  240
KTFEPTNPFF RVVLRPSYLY RGCIMYLPSG FAEKYLSGIS GFIKVQLGEK QWPVRCLYKA  300
GRAKFSQGWY EFTLENNLGE GDVCVFELLR TRDFVLKVTA YRVNSI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A8e-9221334412143B3 domain-containing transcription factor VRN1
4i1k_B8e-9221334412143B3 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_009145836.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2325620.0AC232562.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH054E04, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009145836.10.0PREDICTED: B3 domain-containing transcription factor VRN1
SwissprotQ8L3W10.0VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A397ZIW80.0A0A397ZIW8_BRACM; Uncharacterized protein
STRINGBo5g116790.10.0(Brassica oleracea)
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]