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 GSVIVT01027456001
Common NameLOC100250535, VIT_15s0048g02410
Organism
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 MYB_related
Protein Properties Length: 219aa    MW: 24569.8 Da    PI: 8.0666
Description MYB_related family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01027456001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding537.8e-172468147
                       TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
    Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47
                       r rWT+eE+ ++++a k++G   W +I +++g ++t+ q++s+ qk+
  GSVIVT01027456001 24 RERWTEEEHNRFLEALKLYGRA-WQRIEEHIG-TKTAVQIRSHAQKF 68
                       78******************88.*********.************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466898.97E-181874IPR009057Homeodomain-like
PROSITE profilePS5129421.0911973IPR017930Myb domain
Gene3DG3DSA:1.10.10.602.9E-92170IPR009057Homeodomain-like
TIGRFAMsTIGR015571.4E-172271IPR006447Myb domain, plants
SMARTSM007177.3E-132371IPR001005SANT/Myb domain
PfamPF002495.7E-142467IPR001005SANT/Myb domain
CDDcd001672.30E-102669No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009409Biological Processresponse to cold
GO:0009651Biological Processresponse to salt stress
GO:0009723Biological Processresponse to ethylene
GO:0009733Biological Processresponse to auxin
GO:0009737Biological Processresponse to abscisic acid
GO:0009739Biological Processresponse to gibberellin
GO:0009751Biological Processresponse to salicylic acid
GO:0009753Biological Processresponse to jasmonic acid
GO:0010243Biological Processresponse to organonitrogen compound
GO:0042754Biological Processnegative regulation of circadian rhythm
GO:0043496Biological Processregulation of protein homodimerization activity
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0046686Biological Processresponse to cadmium ion
GO:0048574Biological Processlong-day photoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 219 aa     Download sequence    Send to blast
MDIYSSGEDL IIKTRKPYTI TKQRERWTEE EHNRFLEALK LYGRAWQRIE EHIGTKTAVQ  60
IRSHAQKFFS KLEKEALVKG VPIGQAIDIE IPPPRPKRKP SNPYPRKTGV AAPTLQAGTK  120
DGKLLASVSS SHPGKQILDL EKDPLPERPS GDEKPGNENE NQDEDNCSEV FTLFQEAPCT  180
SMSSANKNSI PTPVPLRNSC TFREFVPLMK EGTQDTEK*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.28560.0flower| fruit| inflorescence| leaf
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaves, roots, stems, flowers and siliques. {ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in the circadian clock and in the phytochrome regulation. Binds to the promoter regions of APRR1/TOC1 and TCP21/CHE to repress their transcription. Binds to the promoter regions of CAB2A and CAB2B to promote their transcription. Represses both LHY and itself. {ECO:0000269|PubMed:11486091, ECO:0000269|PubMed:12007421, ECO:0000269|PubMed:12015970, ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:19339503, ECO:0000269|PubMed:9657153}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00103PBMTransfer from AT2G46830Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Circadian-regulation with peak levels occurring around 1 hour after dawn. Up-regulated by APRR1/TOC1 and transiently by light treatment. Down-regulated by APRR5, APRR7 and APRR9. The CCA1 mRNA is relatively stable in the dark and in far-red light but has a short half-life in red and blue light. {ECO:0000269|PubMed:17873091, ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:19286557, ECO:0000269|PubMed:20233950, ECO:0000269|PubMed:9144958, ECO:0000269|PubMed:9657153}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4670281e-123AM467028.2 Vitis vinifera contig VV78X185711.26, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010661511.11e-152PREDICTED: protein LHY isoform X3
RefseqXP_010661512.11e-152PREDICTED: protein LHY isoform X3
RefseqXP_019081159.11e-152PREDICTED: protein LHY isoform X3
RefseqXP_019081160.11e-152PREDICTED: protein LHY isoform X3
SwissprotP929732e-63CCA1_ARATH; Protein CCA1
TrEMBLF6I2Z41e-151F6I2Z4_VITVI; Uncharacterized protein
STRINGVIT_15s0048g02410.t011e-152(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP12551549
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G46830.15e-61circadian clock associated 1
Publications ? help Back to Top
  1. Kangisser S,Yakir E,Green RM
    Proteasomal regulation of CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) stability is part of the complex control of CCA1.
    Plant Signal Behav, 2013. 8(3): p. e23206
    [PMID:23299326]
  2. Pokhilko A,Mas P,Millar AJ
    Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs.
    BMC Syst Biol, 2013. 7: p. 23
    [PMID:23506153]
  3. Karayekov E,Sellaro R,Legris M,Yanovsky MJ,Casal JJ
    Heat shock-induced fluctuations in clock and light signaling enhance phytochrome B-mediated Arabidopsis deetiolation.
    Plant Cell, 2013. 25(8): p. 2892-906
    [PMID:23933882]
  4. Muranaka T,Kubota S,Oyama T
    A single-cell bioluminescence imaging system for monitoring cellular gene expression in a plant body.
    Plant Cell Physiol., 2013. 54(12): p. 2085-93
    [PMID:24058151]
  5. Higham CF,Husmeier D
    A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana.
    BMC Bioinformatics, 2013. 14 Suppl 10: p. S3
    [PMID:24267177]
  6. Qian H, et al.
    The circadian clock gene regulatory module enantioselectively mediates imazethapyr-induced early flowering in Arabidopsis thaliana.
    J. Plant Physiol., 2014. 171(5): p. 92-8
    [PMID:24484962]
  7. McClung CR
    Wheels within wheels: new transcriptional feedback loops in the Arabidopsis circadian clock.
    F1000Prime Rep, 2014. 6: p. 2
    [PMID:24592314]
  8. Knowles SM,Lu SX,Tobin EM
    Pulsed induction of circadian clock genes in Arabidopsis seedlings.
    Methods Mol. Biol., 2014. 1158: p. 203-8
    [PMID:24792053]
  9. Ng DW, et al.
    A Role for CHH Methylation in the Parent-of-Origin Effect on Altered Circadian Rhythms and Biomass Heterosis in Arabidopsis Intraspecific Hybrids.
    Plant Cell, 2014. 26(6): p. 2430-2440
    [PMID:24894042]
  10. Muranaka T,Okada M,Yomo J,Kubota S,Oyama T
    Characterisation of circadian rhythms of various duckweeds.
    Plant Biol (Stuttg), 2015. 17 Suppl 1: p. 66-74
    [PMID:24942699]
  11. Pruneda-Paz JL, et al.
    A genome-scale resource for the functional characterization of Arabidopsis transcription factors.
    Cell Rep, 2014. 8(2): p. 622-32
    [PMID:25043187]
  12. Hsiao AS, et al.
    Gene expression in plant lipid metabolism in Arabidopsis seedlings.
    PLoS ONE, 2014. 9(9): p. e107372
    [PMID:25264899]
  13. Filichkin SA, et al.
    Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.
    Mol Plant, 2015.
    [PMID:25366180]
  14. Wang G,Zhang C,Battle S,Lu H
    The phosphate transporter PHT4;1 is a salicylic acid regulator likely controlled by the circadian clock protein CCA1.
    Front Plant Sci, 2014. 5: p. 701
    [PMID:25566276]
  15. Thommen Q, et al.
    Probing entrainment of Ostreococcus tauri circadian clock by green and blue light through a mathematical modeling approach.
    Front Genet, 2015. 6: p. 65
    [PMID:25774167]
  16. Xing H, et al.
    LNK1 and LNK2 recruitment to the evening element require morning expressed circadian related MYB-like transcription factors.
    Plant Signal Behav, 2015. 10(3): p. e1010888
    [PMID:25848708]
  17. Zheng XY, et al.
    Spatial and temporal regulation of biosynthesis of the plant immune signal salicylic acid.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(30): p. 9166-73
    [PMID:26139525]
  18. Litthauer S,Battle MW,Lawson T,Jones MA
    Phototropins maintain robust circadian oscillation of PSII operating efficiency under blue light.
    Plant J., 2015. 83(6): p. 1034-45
    [PMID:26215041]
  19. Missra A, et al.
    The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading.
    Plant Cell, 2015. 27(9): p. 2582-99
    [PMID:26392078]
  20. Flis A, et al.
    Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
    Open Biol, 2016.
    [PMID:26468131]
  21. Delis C, et al.
    AtHESPERIN: a novel regulator of circadian rhythms with poly(A)-degrading activity in plants.
    RNA Biol, 2016. 13(1): p. 68-82
    [PMID:26619288]
  22. Lee HG,Mas P,Seo PJ
    MYB96 shapes the circadian gating of ABA signaling in Arabidopsis.
    Sci Rep, 2016. 6: p. 17754
    [PMID:26725725]
  23. Shi H,Wei Y,He C
    Melatonin-induced CBF/DREB1s are essential for diurnal change of disease resistance and CCA1 expression in Arabidopsis.
    Plant Physiol. Biochem., 2016. 100: p. 150-155
    [PMID:26828406]
  24. Shimizu H,Torii K,Araki T,Endo M
    Importance of epidermal clocks for regulation of hypocotyl elongation through PIF4 and IAA29.
    Plant Signal Behav, 2016. 11(2): p. e1143999
    [PMID:26829165]
  25. Kamioka M, et al.
    Direct Repression of Evening Genes by CIRCADIAN CLOCK-ASSOCIATED1 in the Arabidopsis Circadian Clock.
    Plant Cell, 2016. 28(3): p. 696-711
    [PMID:26941090]
  26. Park MJ,Kwon YJ,Gil KE,Park CM
    LATE ELONGATED HYPOCOTYL regulates photoperiodic flowering via the circadian clock in Arabidopsis.
    BMC Plant Biol., 2016. 16(1): p. 114
    [PMID:27207270]
  27. Yuan S, et al.
    Arabidopsis cryptochrome 1 functions in nitrogen regulation of flowering.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(27): p. 7661-6
    [PMID:27325772]
  28. Nitschke S, et al.
    Circadian Stress Regimes Affect the Circadian Clock and Cause Jasmonic Acid-Dependent Cell Death in Cytokinin-Deficient Arabidopsis Plants.
    Plant Cell, 2016. 28(7): p. 1616-39
    [PMID:27354555]
  29. Higashi T,Aoki K,Nagano AJ,Honjo MN,Fukuda H
    Circadian Oscillation of the Lettuce Transcriptome under Constant Light and Light-Dark Conditions.
    Front Plant Sci, 2016. 7: p. 1114
    [PMID:27512400]
  30. Marshall CM,Tartaglio V,Duarte M,Harmon FG
    The Arabidopsis sickle Mutant Exhibits Altered Circadian Clock Responses to Cool Temperatures and Temperature-Dependent Alternative Splicing.
    Plant Cell, 2016. 28(10): p. 2560-2575
    [PMID:27624757]
  31. Wu JF, et al.
    LWD-TCP complex activates the morning gene CCA1 in Arabidopsis.
    Nat Commun, 2016. 7: p. 13181
    [PMID:27734958]
  32. Li X, et al.
    Blue Light- and Low Temperature-Regulated COR27 and COR28 Play Roles in the Arabidopsis Circadian Clock.
    Plant Cell, 2016. 28(11): p. 2755-2769
    [PMID:27837007]
  33. Wang P, et al.
    COR27 and COR28 encode nighttime repressors integrating Arabidopsis circadian clock and cold response.
    J Integr Plant Biol, 2017. 59(2): p. 78-85
    [PMID:27990760]
  34. Ng DW,Chen HH,Chen ZJ
    Heterologous protein-DNA interactions lead to biased allelic expression of circadian clock genes in interspecific hybrids.
    Sci Rep, 2017. 7: p. 45087
    [PMID:28345627]
  35. Staley C, et al.
    Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.
    Microbiome, 2017. 5(1): p. 65
    [PMID:28646918]
  36. Zha P,Jing Y,Xu G,Lin R
    PICKLE chromatin-remodeling factor controls thermosensory hypocotyl growth of Arabidopsis.
    Plant Cell Environ., 2017. 40(10): p. 2426-2436
    [PMID:28771755]
  37. Su Y, et al.
    Phosphorylation of Histone H2A at Serine 95: A Plant-Specific Mark Involved in Flowering Time Regulation and H2A.Z Deposition.
    Plant Cell, 2017. 29(9): p. 2197-2213
    [PMID:28790150]
  38. Hassidim M, et al.
    CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and the Circadian Control of Stomatal Aperture.
    Plant Physiol., 2017. 175(4): p. 1864-1877
    [PMID:29084902]
  39. Hansen LL,Imrie L,Le Bihan T,van den Burg HA,van Ooijen G
    Sumoylation of the Plant Clock Transcription Factor CCA1 Suppresses DNA Binding.
    J. Biol. Rhythms, 2017. 32(6): p. 570-582
    [PMID:29172852]
  40. Zheng H, et al.
    MLK1 and MLK2 Coordinate RGA and CCA1 Activity to Regulate Hypocotyl Elongation in Arabidopsis thaliana.
    Plant Cell, 2018. 30(1): p. 67-82
    [PMID:29255112]
  41. Li Z,Bonaldi K,Uribe F,Pruneda-Paz JL
    A Localized Pseudomonas syringae Infection Triggers Systemic Clock Responses in Arabidopsis.
    Curr. Biol., 2018. 28(4): p. 630-639.e4
    [PMID:29398214]
  42. Zhao X, et al.
    COP1 SUPPRESSOR 4 promotes seedling photomorphogenesis by repressing CCA1 and PIF4 expression in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2018. 115(45): p. 11631-11636
    [PMID:30352855]