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 GSVIVT01024559001
Common NameVIT_06s0004g08100
Organism
Vitis vinifera
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
Family B3
Protein Properties Length: 709aa    MW: 78812.4 Da    PI: 8.0291
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01024559001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B358.61.1e-18297396198
                        EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
                 B3   1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                        f+kvl+ sd+++ grlvlpk +ae++   +++ e+  l+++d +g +W++++++  +++s++yvl+ G     ++ +L++gD+v+F++++  
  GSVIVT01024559001 297 FEKVLSASDAGRIGRLVLPKACAEAYfpPISQSEGLPLRVQDAKGTEWTFQFRFwpNNNSRMYVLE-GVTPCIQSMQLRAGDTVIFSRID-P 386
                        99**************************555556677***************9989999999***9.********************887.6 PP

                        EE..EEEEE- CS
                 B3  89 efelvvkvfr 98 
                        + +lv++ ++
  GSVIVT01024559001 387 GNKLVIGCRK 396
                        7777877766 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.2E-29293397IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.07E-19294393IPR015300DNA-binding pseudobarrel domain
CDDcd100171.75E-22295396No hitNo description
PfamPF023622.0E-15297396IPR003340B3 DNA binding domain
SMARTSM010191.9E-21297397IPR003340B3 DNA binding domain
PROSITE profilePS5086310.588297398IPR003340B3 DNA binding domain
PROSITE profilePS5105013.014522572IPR011124Zinc finger, CW-type
PfamPF074966.3E-8527569IPR011124Zinc 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: 709 aa     Download sequence    Send to blast
MGSRICKNKW CGTTASFEWK KGWTIKSGAV VDLCYKCGSA YENLVFCETF HQEEDGWRQC  60
SLCHKRIHCG CIVSNYQFEA LDYGGVRCSS CLKSPQCHPV RSDNFMQLGK TMEADELNHL  120
LQSQKGDANV SLGQIKQDDS MHAVREVNTI FPTTSLPSIG PSEFAKSDNS IPMLMGKDVY  180
ESLVQPSLNI SLSSSSGPPN FLLPFPGNAV EGMEHSKSAF TFQQGQRTRH ILPKPPNSSL  240
SIGSEANKSM VPEIRIARPP AEGRGRNQLL PRYWPRITDQ ELQQLSGDLN STIVPLFEKV  300
LSASDAGRIG RLVLPKACAE AYFPPISQSE GLPLRVQDAK GTEWTFQFRF WPNNNSRMYV  360
LEGVTPCIQS MQLRAGDTVI FSRIDPGNKL VIGCRKASNC VDVQDAQTSA LSNGTIYGGS  420
SFSSVTENLS TCAGKMNEDS PQQSLLIPEK KRTRNIGSKN KRLLMHSEDA LELKITWQET  480
QDILRPPPSV EPNIVTIEGY EIEEYTEPPV FGKRSIFTAR PSGGQDQWGQ CDNCSKWRKL  540
PIDVFLPLKW TCADNIWDLS RCSCSAPDEW NPKESESLSR LGKDYKRQKS MESHKLAQEG  600
EPTGLDALAN AAVLEENGGD SGEPSAEATT RHPRHRPGCS CIVCIQPPSG KGKHKSTCIC  660
NVCMTVKRRF RTLMLRKKKR QSEHEAESSQ IKHQIHPINE SEISGMKR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A2e-702754042131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1666677KRRFRTLMLRKK
2666679KRRFRTLMLRKKKR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.61170.0fruit
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4415340.0AM441534.1 Vitis vinifera contig VV78X035471.3, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019076084.10.0PREDICTED: B3 domain-containing transcription repressor VAL1 isoform X2
SwissprotQ8W4L50.0VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBLF6GUB30.0F6GUB3_VITVI; Uncharacterized protein
STRINGVIT_06s0004g08100.t010.0(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP12361446
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G32010.10.0HSI2-like 1
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. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]
  8. 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]
  9. 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]
  10. 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]