PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID TRAES3BF066400010CFD_t1
Common NameTRAES_3BF066400010CFD_c1, Vp-1B, Vp-1Bb
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Triticinae; Triticum
Family B3
Protein Properties Length: 688aa    MW: 72802.1 Da    PI: 8.4572
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
TRAES3BF066400010CFD_t1genomeIWGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B358.99.2e-19532628295
                              EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS
                       B3   2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvF 82 
                              +kvl++sdv+++gr+vlpkk ae+h  ++k+  ++ + +ed  ++++W++++++  ++ks++y+l+ ++ +Fv++n+L+egDf+v+
  TRAES3BF066400010CFD_t1 532 QKVLKQSDVGTLGRIVLPKKEAETHlpELKTGDGISIPIEDiGTSQVWSMRYRFwpNNKSRMYLLE-NTGDFVRSNELQEGDFIVL 616
                              79*************************99999*********7777*******99777777777777.******************* PP

                              EE-SS.SEE..EEE CS
                       B3  83 kldgr.sefelvvk 95 
                              +  ++ ++++++++
  TRAES3BF066400010CFD_t1 617 Y--SDvKSGKYLIR 628
                              *..55588877776 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.6E-27524637IPR015300DNA-binding pseudobarrel domain
CDDcd100154.35E-30529630No hitNo description
SuperFamilySSF1019368.5E-22530626IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086310.137531633IPR003340B3 DNA binding domain
SMARTSM010194.1E-18531633IPR003340B3 DNA binding domain
PfamPF023622.7E-15532627IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009657Biological Processplastid organization
GO:0009733Biological Processresponse to auxin
GO:0009737Biological Processresponse to abscisic acid
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0031930Biological Processmitochondria-nucleus signaling pathway
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0001076Molecular Functiontranscription factor activity, RNA polymerase II transcription factor binding
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 688 aa     Download sequence    Send to blast
MDASAGSSPP RHSQGDAPRR GGPHRGKGPA VEIRQGEDDF MFAQDTFPAL PDFPCLSSPS  60
SSTFSSSSSS NSSSAFAAPA GAGGRGAEGA RGEPSEPAAA GDGMDDLSDI DHLLDFASIN  120
DDVPWDDEPL FPDVGMMLED VISEQQLQQP PAGHGTAGRT ASHAASGGGE DAFMGGGGTG  180
SAADDLPLFF MEWLKNNRDC ISAEDLRSIR LRRSTIEAAA ARLGGGRQGT MQLLKLILTW  240
VQNHHLQKKR PRVGAMDQEA PPAGGQLPSP GANPGYEFPA ETGAAAATSW MPYQAFSPTG  300
SYGGEAIYPF QQGCSTSSVA VSSQPFSPPA APDMHAGAWP LQYAAFVPAG ATSAGTQTYP  360
MPPPGAVPQP FAAPGFAGQF PQRMEPAATR EARKKRMARQ RRLSCLQQQR SQQLNLSQIQ  420
TGGFPQEQSP RAAHSAPVTP PSSGWGGLWT QQAVQGQLMV QVPNPLSTKS NSSRQKQQKP  480
SPDAAARPPS GGAATPHRPG QASASNKQRQ QGARTPAAAP AAGDKNLRFL LQKVLKQSDV  540
GTLGRIVLPK KEAETHLPEL KTGDGISIPI EDIGTSQVWS MRYRFWPNNK SRMYLLENTG  600
DFVRSNELQE GDFIVLYSDV KSGKYLIRGV KVRAQQDLAK HKNASPEKGG ASDVKAGGED  660
GGCKEKSPHG VRRSRQEASS MNQMAVSI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9b_A1e-365276381112B3 domain-containing transcription factor FUS3
6j9b_D1e-365276381112B3 domain-containing transcription factor FUS3
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that may participate in abscisic acid-regulated gene expression during seed development. May be required for seed maturation and dormancy induction.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00083PBMTransfer from AT3G24650Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankFJ6405590.0FJ640559.1 Triticum aestivum cultivar Zhongyou 9507 VIVIPAROUS1 protein (Vp-1B) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020155421.10.0B3 domain-containing protein VP1 isoform X1
SwissprotP373980.0VIV_ORYSJ; B3 domain-containing protein VP1
TrEMBLA1XPK80.0A1XPK8_WHEAT; VIVIPAROUS1 protein
STRINGMLOC_69727.20.0(Hordeum vulgare)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP75293443
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24650.15e-59B3 family protein
Publications ? help Back to Top
  1. Espelund M,Bekele E,Holst-Jensen A,Jakobsen KS,Nordal I
    A molecular genetic analysis of Eragrostis tef (Zucc.) Trotter: non-coding regions of chloroplast DNA, 18S rDNA and the transcription factor VP1.
    Hereditas, 2000. 132(3): p. 193-202
    [PMID:11075514]
  2. Gampala SS,Hagenbeek D,Rock CD
    Functional interactions of lanthanum and phospholipase D with the abscisic acid signaling effectors VP1 and ABI1-1 in rice protoplasts.
    J. Biol. Chem., 2001. 276(13): p. 9855-60
    [PMID:11139577]
  3. Carrari F, et al.
    Cloning and expression of a sorghum gene with homology to maize vp1. Its potential involvement in pre-harvest sprouting resistance.
    Plant Mol. Biol., 2001. 45(6): p. 631-40
    [PMID:11430426]
  4. Hagiwara K,Rao S,Scott SW,Carner GR
    Nucleotide sequences of segments 1, 3 and 4 of the genome of Bombyx mori cypovirus 1 encoding putative capsid proteins VP1, VP3 and VP4, respectively.
    J. Gen. Virol., 2002. 83(Pt 6): p. 1477-82
    [PMID:12029163]
  5. Zhao SL,Liang CY,Hong JJ,Peng HY
    Genomic sequence analyses of segments 1 to 6 of Dendrolimus punctatus cytoplasmic polyhedrosis virus.
    Arch. Virol., 2003. 148(7): p. 1357-68
    [PMID:12827465]
  6. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  7. Suzuki N, et al.
    Molecular analysis of rice dwarf phytoreovirus segment S1: interviral homology of the putative RNA-dependent RNA polymerase between plant- and animal-infecting reoviruses.
    Virology, 1992. 190(1): p. 240-7
    [PMID:1529532]
  8. Yang Y, et al.
    Isolation and characterization of Viviparous-1 genes in wheat cultivars with distinct ABA sensitivity and pre-harvest sprouting tolerance.
    J. Exp. Bot., 2007. 58(11): p. 2863-71
    [PMID:17630295]
  9. Yang Y, et al.
    Development and validation of a Viviparous-1 STS marker for pre-harvest sprouting tolerance in Chinese wheats.
    Theor. Appl. Genet., 2007. 115(7): p. 971-80
    [PMID:17712543]
  10. Fan J, et al.
    Short, direct repeats (SDRs)-mediated post-transcriptional processing of a transcription factor gene OsVP1 in rice (Oryza sativa).
    J. Exp. Bot., 2007. 58(13): p. 3811-7
    [PMID:18057047]
  11. Sugimoto K, et al.
    Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice.
    Proc. Natl. Acad. Sci. U.S.A., 2010. 107(13): p. 5792-7
    [PMID:20220098]
  12. Sharoni AM, et al.
    Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice.
    Plant Cell Physiol., 2011. 52(2): p. 344-60
    [PMID:21169347]
  13. Kumar S,Jiang S,Jami SK,Hill RD
    Cloning and characterization of barley caryopsis FCA.
    Physiol Plant, 2011. 143(1): p. 93-106
    [PMID:21645000]
  14. Cao G, et al.
    Characterization of the complete genome segments from BmCPV-SZ, a novel Bombyx mori cypovirus 1 isolate.
    Can. J. Microbiol., 2012. 58(7): p. 872-83
    [PMID:22712678]
  15. Brenchley R, et al.
    Analysis of the bread wheat genome using whole-genome shotgun sequencing.
    Nature, 2012. 491(7426): p. 705-10
    [PMID:23192148]
  16. Ye H,Beighley DH,Feng J,Gu XY
    Genetic and physiological characterization of two clusters of quantitative trait Loci associated with seed dormancy and plant height in rice.
    G3 (Bethesda), 2013. 3(2): p. 323-31
    [PMID:23390608]
  17. Guo X, et al.
    The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism.
    Plant J., 2013. 75(3): p. 403-16
    [PMID:23581288]
  18. Lata C, et al.
    Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.).
    PLoS ONE, 2014. 9(11): p. e113092
    [PMID:25409524]
  19. Matsuno K,Fujimura T
    Do rice suspension-cultured cells treated with abscisic acid mimic developing seeds?
    Mol. Genet. Genomics, 2015. 290(4): p. 1551-62
    [PMID:25732383]
  20. Li S, et al.
    Facilitation of rice stripe virus accumulation in the insect vector by Himetobi P virus VP1.
    Viruses, 2015. 7(3): p. 1492-504
    [PMID:25807055]
  21. Mukhopadhyay P,Tyagi AK
    OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways.
    Sci Rep, 2015. 5: p. 9998
    [PMID:25925167]
  22. Du W, et al.
    Physiological characteristics and related gene expression of after-ripening on seed dormancy release in rice.
    Plant Biol (Stuttg), 2015. 17(6): p. 1156-64
    [PMID:26205956]
  23. Zhang X,Sun J,Cao X,Song X
    Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice.
    Plant Physiol., 2015. 169(3): p. 2118-28
    [PMID:26351308]
  24. Duan YB, et al.
    Identification of a regulatory element responsible for salt induction of rice OsRAV2 through ex situ and in situ promoter analysis.
    Plant Mol. Biol., 2016. 90(1-2): p. 49-62
    [PMID:26482477]
  25. Zhao Y, et al.
    ABA receptor PYL9 promotes drought resistance and leaf senescence.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(7): p. 1949-54
    [PMID:26831097]
  26. Chen L, et al.
    Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon.
    Sci Rep, 2016. 6: p. 21623
    [PMID:26869021]
  27. Li Z, et al.
    Serine carboxypeptidase 46 Regulates Grain Filling and Seed Germination in Rice (Oryza sativa L.).
    PLoS ONE, 2016. 11(7): p. e0159737
    [PMID:27448032]
  28. Zhu Z, et al.
    Overexpression of AtEDT1/HDG11 in Chinese Kale (Brassica oleracea var. alboglabra) Enhances Drought and Osmotic Stress Tolerance.
    Front Plant Sci, 2016. 7: p. 1285
    [PMID:27625663]
  29. Hattori T,Terada T,Hamasuna S
    Regulation of the Osem gene by abscisic acid and the transcriptional activator VP1: analysis of cis-acting promoter elements required for regulation by abscisic acid and VP1.
    Plant J., 1995. 7(6): p. 913-25
    [PMID:7599651]
  30. Hollung K,Espelund M,Schou K,Jakobsen KS
    Developmental, stress and ABA modulation of mRNA levels for bZip transcription factors and Vp1 in barley embryos and embryo-derived suspension cultures.
    Plant Mol. Biol., 1997. 35(5): p. 561-71
    [PMID:9349278]
  31. Schultz TF,Medina J,Hill A,Quatrano RS
    14-3-3 proteins are part of an abscisic acid-VIVIPAROUS1 (VP1) response complex in the Em promoter and interact with VP1 and EmBP1.
    Plant Cell, 1998. 10(5): p. 837-47
    [PMID:9596641]