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 KFK37450.1
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Arabideae; Arabis
Family MYB_related
Protein Properties Length: 561aa    MW: 62349.6 Da    PI: 5.0654
Description MYB_related family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KFK37450.1genomeMPIPBRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47
                     r rWT+eE+ ++++a +++G   W +I +++  ++t+ q++s+ qk+
                     78******************88.*********.************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129421.271973IPR017930Myb domain
TIGRFAMsTIGR015571.1E-162271IPR006447Myb domain, plants
SMARTSM007171.0E-122371IPR001005SANT/Myb domain
PfamPF002491.2E-122467IPR001005SANT/Myb domain
CDDcd001671.89E-92669No 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: 561 aa     Download sequence    Send to blast
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
Cis-element ? help Back to Top
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
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankATU284221e-131U28422.1 Arabidopsis thaliana DNA-binding protein CCA1 (CCA1) mRNA, complete cds.
GenBankAY5195111e-131AY519511.1 Arabidopsis thaliana MYB transcription factor (At2g46830) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_850460.10.0circadian clock associated 1
RefseqXP_002880268.10.0protein CCA1
RefseqXP_020883297.10.0protein CCA1
SwissprotP929730.0CCA1_ARATH; Protein CCA1
TrEMBLA0A087H5P80.0A0A087H5P8_ARAAL; Protein late elongated hypocotyl
STRINGA0A087H5P80.0(Arabis alpina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G46830.10.0circadian 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
  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
  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
  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
  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
  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
  7. McClung CR
    Wheels within wheels: new transcriptional feedback loops in the Arabidopsis circadian clock.
    F1000Prime Rep, 2014. 6: p. 2
  8. Knowles SM,Lu SX,Tobin EM
    Pulsed induction of circadian clock genes in Arabidopsis seedlings.
    Methods Mol. Biol., 2014. 1158: p. 203-8
  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
  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
  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
  12. Hsiao AS, et al.
    Gene expression in plant lipid metabolism in Arabidopsis seedlings.
    PLoS ONE, 2014. 9(9): p. e107372
  13. Filichkin SA, et al.
    Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.
    Mol Plant, 2015.
  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
  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
  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
  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
  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
  19. Missra A, et al.
    The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading.
    Plant Cell, 2015. 27(9): p. 2582-99
  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.
  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
  22. Lee HG,Mas P,Seo PJ
    MYB96 shapes the circadian gating of ABA signaling in Arabidopsis.
    Sci Rep, 2016. 6: p. 17754
  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
  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
  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
  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
  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
  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
  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
  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
  31. Wu JF, et al.
    LWD-TCP complex activates the morning gene CCA1 in Arabidopsis.
    Nat Commun, 2016. 7: p. 13181
  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
  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
  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
  35. Staley C, et al.
    Diurnal cycling of rhizosphere bacterial communities is associated with shifts in carbon metabolism.
    Microbiome, 2017. 5(1): p. 65
  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
  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
  38. Hassidim M, et al.
    CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and the Circadian Control of Stomatal Aperture.
    Plant Physiol., 2017. 175(4): p. 1864-1877
  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
  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
  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
  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