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_009135606.1
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: 329aa    MW: 38058.1 Da    PI: 9.4459
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009135606.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B353.64.1e-17596196
                    EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEE CS
              B3  1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkv 96
                    ff +l+ s++ +++rl++p kf+++++ +   s+ + l+ ++g +W+v l+   + +++++++GW+eFv+   ++ g  ++F+++g+s f   v +
  XP_009135606.1  5 FFHKLIFSSTIQEKRLRVPDKFVSRFKDE--LSVAVALTVPDGHVWRVGLRKADNNNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAF--SVCI 96
                    899999*****************999755..99*****************88888888****************************9999..5544 PP
2B354.42.3e-17232324198
                     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_009135606.1 232 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKV---QLGEKQWPVRC--LYKAGRAKFSQGWYEFTVENNLGEGDVCVFELLRTRDFVLKV 320
                     677899********************84442.43344...4677*******..666666779***********************999***9999 PP

                     EEE- CS
              B3  95 kvfr 98 
                     +++r
  XP_009135606.1 321 TAYR 324
                     8877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.9E-21398IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.55E-213107IPR015300DNA-binding pseudobarrel domain
PfamPF023621.4E-14596IPR003340B3 DNA binding domain
CDDcd100171.21E-20598No hitNo description
SMARTSM010197.6E-165100IPR003340B3 DNA binding domain
PROSITE profilePS5086314.3675100IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.106.3E-23224324IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.32E-22225326IPR015300DNA-binding pseudobarrel domain
CDDcd100171.76E-20230324No hitNo description
PROSITE profilePS5086312.534232326IPR003340B3 DNA binding domain
PfamPF023629.7E-16232324IPR003340B3 DNA binding domain
SMARTSM010193.5E-21232326IPR003340B3 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: 329 aa     Download sequence    Send to blast
MPRPFFHKLI FSSTIQEKRL RVPDKFVSRF KDELSVAVAL TVPDGHVWRV GLRKADNNNK  60
IWFQDGWQEF VDRYSIRIGY LLIFRYEGNS AFSVCIYNLP QSEINYHSTG LMDSASHNNH  120
FKRPRLFEDL EDEDAETLHT TASAIQSFFT GPVKPEEATP TQTSKVPKKR GRKKKNADHP  180
EEVNSSAPRD DDPESRSKFY ESASARKRTV NAEERERAVN AAKTFEPTNP FFRVVLRPSY  240
LYRGCIMYLP SGFAEKYLSG ISGFIKVQLG EKQWPVRCLY KAGRAKFSQG WYEFTVENNL  300
GEGDVCVFEL LRTRDFVLKV TAYRVNEYV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A3e-9019832915146B3 domain-containing transcription factor VRN1
4i1k_B3e-9019832915146B3 domain-containing transcription factor VRN1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.22570.0bud
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_009135606.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
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
RefseqNP_001288881.10.0B3 domain-containing transcription factor VRN1-like
RefseqXP_013736461.10.0B3 domain-containing transcription factor VRN1
SwissprotQ8L3W10.0VRN1_ARATH; B3 domain-containing transcription factor VRN1
TrEMBLQ6R2U80.0Q6R2U8_BRACM; Reduced vernalization response 1
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. 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]