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 GSBRNA2T00105140001
Common NameGSBRNA2T00105140001
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: 764aa    MW: 83712.4 Da    PI: 6.7574
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00105140001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B355.79.1e-18277376198
                          EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                          f+k+l+ sd+++ grlvlpk +ae++   +++ e++ l+++d +g++W +++++  +++s++yvl+ G     ++  L++gD+v+F++++
  GSBRNA2T00105140001 277 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKIQDVRGKEWIFQFRFwpNNNSRMYVLE-GVTPCIQSMMLQAGDTVTFSRVD 365
                          99**************************666678889***************9989999999***9.********************776 PP

                          SSEE..EEEEE- CS
                   B3  87 rsefelvvkvfr 98 
                            +++l +++++
  GSBRNA2T00105140001 366 -PGGKLIMGFRK 376
                          .77777777776 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.96E-19274378IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.6E-29274386IPR015300DNA-binding pseudobarrel domain
CDDcd100171.02E-22275376No hitNo description
PROSITE profilePS5086310.644277378IPR003340B3 DNA binding domain
SMARTSM010194.3E-21277377IPR003340B3 DNA binding domain
PfamPF023623.3E-15277376IPR003340B3 DNA binding domain
PROSITE profilePS5105013.939521571IPR011124Zinc finger, CW-type
PfamPF074965.2E-10527568IPR011124Zinc finger, CW-type
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
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 764 aa     Download sequence    Send to blast
MCMNASCGST STVEWKKGWP LRSGALADLC FRCGSAYETS LFCETFHLDQ SGWRECYLCN  60
KRLHCGCIAS KLVVEFMDYG GVGCSTCTNC HQPNLGKIGE NPGLFSRLPM NRQHTNGENG  120
MNVGKADLFS QPLVQGDDKR EEFMPHRGFS NLIKTDRLDG GEILESSSTP SQPPSLNMPL  180
AALPYSLNFA TATKKLMDAS SQPHAVQSSS SSILQTPSKS VLGTPPGTSK SAQARIGRPP  240
NEGRGRSHLL PRYWPKYTDK ELQQISGNLN LNIVPLFEKT LSASDAGRIG RLVLPKACAE  300
AYFPPISQSE GIPLKIQDVR GKEWIFQFRF WPNNNSRMYV LEGVTPCIQS MMLQAGDTVT  360
FSRVDPGGKL IMGFRKATHT KDIQGCGLTN GTLNEDTSSS GVTETPTSIN ASSCPSQNPE  420
ELKGLPEHLN SNHGGSSLKK SEVNGVKDKK RTRTVGAKSK RLLLHSEESM EVRITWEETQ  480
ELIRPSPSEK PTVVVIEEHE FEEFYEPPVF GKRTIITSKP SGEQERWASC DDCSKWRKLP  540
VEALLPAKWT CSDNVWDESR CSCSAPEESL KELENVLRMS KEYKKRRTGV SQTVRTEEEL  600
TGLDALASAA ALGDTLGEEE EPATTTRHPR HRVGCSCIVC IQPPSGKGRH NSSCLCTVCS  660
TVKRRFKTLM MRRKKKQLER EEIEAAAAAD QENKEDGKTG RIDLNSDPCN RGEVEAVGVE  720
EKDESGKGEA GECLGVAQAG DVVGVTELEG EGEKIGEESK GSS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A3e-822553852132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1662674KRRFKTLMMRRKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.148770.0seed
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in flowers and at lower levels in roots, stems and leaves. {ECO:0000269|PubMed:15894743}.
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL2/HSL1. {ECO:0000269|PubMed:15894743, ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00105140001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3535020.0AK353502.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-47-G20.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013743580.10.0B3 domain-containing transcription repressor VAL1-like isoform X2
RefseqXP_022557045.10.0B3 domain-containing transcription repressor VAL1-like isoform X2
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A0D3C3320.0A0A0D3C332_BRAOL; Uncharacterized protein
STRINGBo4g173060.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69232440
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G30470.10.0high-level expression of sugar-inducible gene 2
Publications ? help Back to Top
  1. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  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. Schneider A, et al.
    Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos.
    Plant J., 2016. 85(2): p. 305-19
    [PMID:26678037]
  4. Chhun T, et al.
    HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth.
    Plant Cell Physiol., 2016. 57(8): p. 1689-706
    [PMID:27335347]
  5. Qüesta JI,Song J,Geraldo N,An H,Dean C
    Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization.
    Science, 2016. 353(6298): p. 485-8
    [PMID:27471304]
  6. Yuan W, et al.
    A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis.
    Nat. Genet., 2016. 48(12): p. 1527-1534
    [PMID:27819666]
  7. Merini W, et al.
    The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development.
    Plant Physiol., 2017. 173(1): p. 627-641
    [PMID:27837089]
  8. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  9. Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD
    HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 600-619
    [PMID:29475938]
  10. Sasnauskas G,Kauneckaite K,Siksnys V
    Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
    Nucleic Acids Res., 2018. 46(8): p. 4316-4324
    [PMID:29660015]
  11. Wu B, et al.
    Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
    Biochem. Biophys. Res. Commun., 2018. 501(2): p. 415-422
    [PMID:29733847]