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 GSBRNA2T00021429001
Common NameGSBRNA2T00021429001, LOC106381237
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: 328aa    MW: 37994.1 Da    PI: 9.8236
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00021429001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B355.78.8e-18596196
                         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+   + +++++++GW+eFv+   ++ g  +vF+++g+s f  
  GSBRNA2T00021429001  5 FFHKLIFSSTIQEKRLRVPDKFVRRFKDE--LSVAVALTVPDGHVWRVGLRKADNNNKIWFQDGWQEFVHRYSIRIGYLLVFRYEGNSAF-- 92
                         899999********************855..99*****************88888888****************************9999.. PP

                         EEEE CS
                   B3 93 vvkv 96
                          v +
  GSBRNA2T00021429001 93 SVYI 96
                         5544 PP
2B352.68.4e-17230323199
                          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++ F+l ++++
  GSBRNA2T00021429001 230 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTVENNLGEGDVCAFELLRTRD 313
                          677899********************84442.43344...4677*******..666666779************************99** PP

                          E..EEEEE-S CS
                   B3  90 felvvkvfrk 99 
                          f l+v++fr 
  GSBRNA2T00021429001 314 FVLKVTAFRV 323
                          *****99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.5E-22398IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019367.85E-223107IPR015300DNA-binding pseudobarrel domain
PfamPF023621.9E-15596IPR003340B3 DNA binding domain
CDDcd100174.75E-22598No hitNo description
PROSITE profilePS5086314.5515100IPR003340B3 DNA binding domain
SMARTSM010199.4E-175100IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.101.3E-22222323IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.12E-21223324IPR015300DNA-binding pseudobarrel domain
CDDcd100175.36E-20228322No hitNo description
PfamPF023623.2E-15230323IPR003340B3 DNA binding domain
SMARTSM010199.3E-21230324IPR003340B3 DNA binding domain
PROSITE profilePS5086312.421230324IPR003340B3 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: 328 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVRRF KDELSVAVAL TVPDGHVWRV GLRKADNNNK  60
IWFQDGWQEF VHRYSIRIGY LLVFRYEGNS AFSVYIYNLP HSEINYHSTG LMDSANHFKR  120
PRLFEDLEDE DAETLHTTTS AIQSFFTGPV KPEEATPTQT SKVPKKRGRK KKKNADHPEE  180
VNSSAPRDDD PESRSKFYES ASARKRTVNA EERERAINAA KTFEPTNPFF RVVLRPSYLY  240
RGCIMYLPSG FAEKYLSGIS GFIKVQLGEK QWPVRCLYKA GRAKFSQGWY EFTVENNLGE  300
GDVCAFELLR TRDFVLKVTA FRVNEYV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A2e-9019632715146B3 domain-containing transcription factor VRN1
4i1k_B2e-9019632715146B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.61741e-119flower| 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
PlantRegMapGSBRNA2T00021429001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5179290.0AY517929.1 Brassica rapa cultivar Kwonsim reduced vernalization response 1 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013676581.10.0B3 domain-containing transcription factor VRN1
SwissprotQ8L3W10.0VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLA0A078GCA60.0A0A078GCA6_BRANA; BnaC03g40730D protein
TrEMBLA0A3P6AJF10.0A0A3P6AJF1_BRAOL; Uncharacterized protein
STRINGBo3g071890.10.0(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]