PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID GSBRNA2T00107563001
Common NameGSBRNA2T00107563001, LOC106446859
Organism
Brassica napus
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: 347aa    MW: 39559 Da    PI: 9.662
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00107563001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.93.2e-17595194
                         EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
                   B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92
                         ff +l+ s++ +++rl++p kf+++++ +   s+ + l+ ++g +W+v l+ +  s+++++++GW+eFv+   ++ g  ++F+++g+s f+ 
  GSBRNA2T00107563001  5 FFHKLIFSSTIQEKRLRVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGLR-KADSNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAFSV 93
                         899999*****************999755..99*****************3.666677****************************999955 PP

                         EE CS
                   B3 93 vv 94
                         ++
  GSBRNA2T00107563001 94 YI 95
                         44 PP
2B353.54.4e-17250342198
                          EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                          f  vl ps+  + ++++lp  fae++ +g++ + +++   ++  ++W v++    k gr  +++GW eF  +n+L egD++vF+l ++++
  GSBRNA2T00107563001 250 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRD 333
                          677899********************84442.43344...4677*******..666666779***********************999** PP

                          E..EEEEE- CS
                   B3  90 felvvkvfr 98 
                          f l+v+++r
  GSBRNA2T00107563001 334 FVLKVTAYR 342
                          *99998877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.107.6E-22398IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.51E-21398IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086314.649599IPR003340B3 DNA binding domain
CDDcd100172.09E-19597No hitNo description
PfamPF023621.8E-14595IPR003340B3 DNA binding domain
SMARTSM010198.0E-18599IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.101.1E-22242342IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.47E-22243343IPR015300DNA-binding pseudobarrel domain
CDDcd100171.28E-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:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 347 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSKF KDELSVAVAL TVPDGHVWRV GLRKADSNKI  60
WFQDGWQEFV 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 YRVNAI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A9e-9221334412143B3 domain-containing transcription factor VRN1
4i1k_B9e-9221334412143B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.61740.0flower| leaf| microspore-derived embryo| seed
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
PlantRegMapGSBRNA2T00107563001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013744124.10.0B3 domain-containing transcription factor VRN1
SwissprotQ8L3W10.0VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A3P6F0N10.0A0A3P6F0N1_BRAOL; 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. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]
  3. 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]