PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os01g68370.4
Common NameLOC4324314, Os01g0911700, P0470A12.15-1, P0470A12.15-2, VP1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family B3
Protein Properties Length: 705aa    MW: 73836.1 Da    PI: 6.3873
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g68370.4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3536e-17515610295
                       EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS.S CS
                B3   2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgr.s 88 
                       +kvl++sdv+++gr+vlpk+  e h  ++k++ ++ + +ed  ++++W++++++  ++ks++y+l+ ++ +Fv++n+L+egDf+v++  ++ +
  LOC_Os01g68370.4 515 QKVLKQSDVGSLGRIVLPKEA-EVHlpELKTRDGVSIPMEDiGTSQVWNMRYRFwpNNKSRMYLLE-NTGDFVRSNELQEGDFIVIY--SDiK 603
                       79****************996.6777*999***********7777*******99777777777777.********************..6668 PP

                       EE..EEE CS
                B3  89 efelvvk 95 
                       +++++++
  LOC_Os01g68370.4 604 SGKYLIR 610
                       8877776 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.3E-25505619IPR015300DNA-binding pseudobarrel domain
CDDcd100151.10E-29512612No hitNo description
SuperFamilySSF1019364.45E-19513606IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086310.08514615IPR003340B3 DNA binding domain
SMARTSM010191.2E-12514615IPR003340B3 DNA binding domain
PfamPF023623.6E-14515609IPR003340B3 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:0009738Biological Processabscisic acid-activated signaling pathway
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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009009anatomyplant embryo
PO:0001081developmental stagemature plant embryo stage
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 705 aa     Download sequence    Send to blast
MDASAGSSAP AAEIRGEAAR DDVFFADDTF PLLPDFPCLS SPSSSTFSSS SSSNSSSAFT  60
TAAGGGCGGE PSEPASAADG FGELADIDQL LDLASLSVPW EAEQPLFPDD VGMMIEDAMS  120
GQPHQADDCT GDGDTKAVME AAGGGDDAGD ACMEGSDAPD DLPAFFMEWL TSNREYISAD  180
DLRSIRLRRS TIEAAAARLG GGRQGTMQLL KLILTWVQNH HLQKKRPRTA IDDGAASSDP  240
QLPSPGANPG YEFPSGGQEM GSAAATSWMP YQAFTPPAAY GGDAMYPGAA GPFPFQQSCS  300
KSSVVVSSQP FSPPTAAAAG DMHASGGGNM AWPQQFAPFP VSSTSSYTMP SVVPPPFTAG  360
FPGQYSGGHA MCSPRLAGVE PSSTKEARKK RMARQRRLSC LQQQRSQQLN LSQIHISGHP  420
QEPSPRAAHS APVTPSSAGC RSWGIWPPAA QIIQNPLSNK PNPPPATSKQ PKPSPEKPKP  480
KPQAAATAGA ESLQRSTASE KRQAKTDKNL RFLLQKVLKQ SDVGSLGRIV LPKEAEVHLP  540
ELKTRDGVSI PMEDIGTSQV WNMRYRFWPN NKSRMYLLEN TGDFVRSNEL QEGDFIVIYS  600
DIKSGKYLIR GVKVRRAAQE QGNSSGAVGK HKHGSPEKPG VSSNTKAAGA EDGTGGDDSA  660
EAAAAAAAGK ADGGGCKGKS PHGVRRSRQE AAAAASMSQM AVSI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9b_A2e-365106211110B3 domain-containing transcription factor FUS3
6j9b_D2e-365106211110B3 domain-containing transcription factor FUS3
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.73600.0callus| flower| panicle| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329838280.0
Expression AtlasP37398-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the whole embryo from 2 to 4 days after pollination (DAP). At 6 DAP, expressed in the regions where the shoot and radicle are developing, and in the aleurone layers and the outermost cell layers of the endosperm. Later, in the embryo development, expressed in vascular tissue, coleoptile, leaf, shoot meristem, radicle, scutellum and epiblast. In mature embryo (20 DAP), expression levels decrease. {ECO:0000269|PubMed:11917085}.
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
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os01g68370.4
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g68370
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0738050.0AK073805.1 Oryza sativa Japonica Group cDNA clone:J033069I02, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015629318.10.0B3 domain-containing protein VP1 isoform X4
SwissprotP373980.0VIV_ORYSJ; B3 domain-containing protein VP1
TrEMBLA0A0E0FXG00.0A0A0E0FXG0_ORYNI; Uncharacterized protein
STRINGONIVA01G46510.10.0(Oryza nivara)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24650.13e-59B3 family protein
Publications ? help Back to Top
  1. Hobo T,Kowyama Y,Hattori T
    A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription.
    Proc. Natl. Acad. Sci. U.S.A., 1999. 96(26): p. 15348-53
    [PMID:10611387]
  2. 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]
  3. 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]
  4. 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]
  5. Miyoshi K,Kagaya Y,Ogawa Y,Nagato Y,Hattori T
    Temporal and spatial expression pattern of the OSVP1 and OSEM genes during seed development in rice.
    Plant Cell Physiol., 2002. 43(3): p. 307-13
    [PMID:11917085]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  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. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Mukhopadhyay P,Tyagi AK
    OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways.
    Sci Rep, 2015. 5: p. 9998
    [PMID:25925167]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. Chen L, et al.
    Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon.
    Sci Rep, 2016. 6: p. 21623
    [PMID:26869021]
  26. 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]
  27. 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]
  28. 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]
  29. Hattori T,Terada T,Hamasuna ST
    Sequence and functional analyses of the rice gene homologous to the maize Vp1.
    Plant Mol. Biol., 1994. 24(5): p. 805-10
    [PMID:8193305]
  30. Nakagawa H,Ohkura E,Ohmiya K,Hattori T
    The seed-specific transcription factor VP1 (OSVP1) is expressed in rice suspension-cultured cells.
    Plant Cell Physiol., 1996. 37(3): p. 355-62
    [PMID:8673344]
  31. Schultz TF,Quatrano RS
    Characterization and expression of a rice RAD23 gene.
    Plant Mol. Biol., 1997. 34(3): p. 557-62
    [PMID:9225866]
  32. 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]
  33. 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]