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 GSBRNA2T00113430001
Common NameGSBRNA2T00113430001
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: 785aa    MW: 85777.5 Da    PI: 7.5737
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00113430001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B360.52.8e-19288387198
                          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++++
  GSBRNA2T00113430001 288 FEKTLSASDAGRIGRLVLPKACAEAYfpPISQSEGIPLKVQDVRGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMRLQAGDTVTFSRVD 376
                          99**************************666678889***************9989999999***9.********************766 PP

                          SSEE..EEEEE- CS
                   B3  87 rsefelvvkvfr 98 
                            +++l +++++
  GSBRNA2T00113430001 377 -PGGKLIMGARK 387
                          .88888888776 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.83E-20285383IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.6E-29285388IPR015300DNA-binding pseudobarrel domain
CDDcd100171.23E-24286387No hitNo description
PROSITE profilePS5086310.884288389IPR003340B3 DNA binding domain
SMARTSM010199.5E-23288389IPR003340B3 DNA binding domain
PfamPF023622.1E-16288387IPR003340B3 DNA binding domain
PROSITE profilePS5105013.561535585IPR011124Zinc finger, CW-type
PfamPF074963.6E-9541582IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:2000034Biological Processregulation of seed maturation
GO:0005634Cellular Componentnucleus
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 785 aa     Download sequence    Send to blast
MFEVKMGSKM CMNASCGSTS SVEWKKGWPL RSGALADLCF RCGSAYETSR FCETFHMEQS  60
GWRECYLCNK RLHCGCIASK LMVEFMDYGG VGCTSCTNSH SKRGENPGVF SRLPMNMQQT  120
NGERSEANLF SQPLVSGDDK REEFTPHRGF GNLMKPDNNV TTTVYTHDSS SSSPSQPSLN  180
MALATLPYSP SFATPVVDGN KLMAAGGASS SQSHLFQCSA SSILQKPSKT VLGTPPPGTS  240
KSAQARIGRP PVEGRGKGHL LPRYWPKYTD KELQQISGNL NLNIVPLFEK TLSASDAGRI  300
GRLVLPKACA EAYFPPISQS EGIPLKVQDV RGKEWTFQFR FWPNNNSRMY VLEGVTPCIQ  360
SMRLQAGDTV TFSRVDPGGK LIMGARKATY TVDMQGCGFA NGASNEDTSS SGVTENLTSI  420
NASSCPSQIL EGLPEHLGSP HGGNGLKKSE INGGDDPSRG KEKKRTRTLG AKNKRLLLHS  480
EESMELRVTW EEAQELLRPS ANAKPTVVVI EEHEFEEFDE PPVFGKRTIL TSRPSGEQER  540
WGSCDDCSKW RRLPLDALLP AKWTCSDNVW DSSRCSCSAP EESLKELENV LRAGKEYKKR  600
RIGVSQTARN EQEPSGLDAL ASAAVLGDAL DDSSEVATTT RHPRHRVGCS CIVCIQPPSG  660
KGRHKPTCGC TVCSTVKRRF KTLMMRRKKR QLERDGTAAV DEENKEGVEP EKNEGEKEGR  720
IDLNSDPYNR EDAEAVAVEK GEESKKSEEG VCWGVSQGGG VLGETEVRGG EAEKTTSEEQ  780
KVAS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A7e-822663962132B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1676688KRRFKTLMMRRKK
2676689KRRFKTLMMRRKKR
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
PlantRegMapGSBRNA2T00113430001
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_013636698.10.0PREDICTED: B3 domain-containing transcription repressor VAL1
RefseqXP_013636699.10.0PREDICTED: B3 domain-containing transcription repressor VAL1
RefseqXP_013636700.10.0PREDICTED: B3 domain-containing transcription repressor VAL1
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLA0A3P6CG840.0A0A3P6CG84_BRAOL; Uncharacterized protein
STRINGBo4g058460.10.0(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]