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 Seita.6G055700.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria
Family MYB_related
Protein Properties Length: 748aa    MW: 82050.1 Da    PI: 5.9876
Description MYB_related family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Seita.6G055700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding47.83.4e-155195147
                        TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
     Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47
                        r rWT+ E++++++a k++G   W +I +++g ++t+ q++s+ qk+
  Seita.6G055700.1.p 51 RERWTEAEHKRFLEALKLYGRA-WQRIEEHVG-TKTAVQIRSHAQKF 95
                        78******************88.*********.************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466892.99E-1645101IPR009057Homeodomain-like
PROSITE profilePS5129419.14746100IPR017930Myb domain
TIGRFAMsTIGR015571.7E-164998IPR006447Myb domain, plants
SMARTSM007176.5E-125098IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.609.4E-85191IPR009057Homeodomain-like
PfamPF002491.5E-125194IPR001005SANT/Myb domain
CDDcd001671.09E-85396No 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:0042754Biological Processnegative regulation of circadian rhythm
GO:0043433Biological Processnegative regulation of sequence-specific DNA binding transcription factor activity
GO:0046686Biological Processresponse to cadmium ion
GO:0048574Biological Processlong-day photoperiodism, flowering
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 748 aa     Download sequence    Send to blast
MTSTPSDQAS SCWTIPFYFC FFFLDLEMEV NSSGEETVVK VRKPYTITKQ RERWTEAEHK  60
RFLEALKLYG RAWQRIEEHV GTKTAVQIRS HAQKFFTKLE KEAMNNGTSP GQAHDIDIPP  120
PRPKRKPNSP YPRKNGLSSE TPTKELPNDK SSKSNITLSS GNVQMVGDMS LQKFQRKEVS  180
EKGSCSEVLN LFRDAPSASF SSVNKSSSNN GVPRGVEPTK TEIRDMTTTE KNSINPTMEE  240
DVKEIDVPEI GRVNGIHVSS KCDYSNEEYL DFSMQQMKLK PKSSETTYVD KQTARTSHSL  300
AERNGATSIP VTGTDGTRPD QTGDQVGVNG SMNPCIHPML STDPKFDSSA TPQPFPHNYA  360
AFAPMMQCNC NQDTYRSFVN MSSTFSSMLV STLLSNPAIH AAARLAASYW PAAEGNTPVD  420
PTQENPAEGV QGRNLGSPPS MASIVAATVA AASAWWATQG LLPFFTPPMA FPFVPAPSAA  480
FTTADVPRPL DKDRDSPVEN AQKGCQEAQK QGQSEALRVA VSSESDGTRK GDMSLHTELK  540
ISPVQNTDAA PTTGADISDA FRNKKKQDRS SCGSNTPSSS DVEAGNVPEK EDKANDKAKQ  600
ASCSNSSAGD TNHRKFRSSG STSDSWKEVS EEGRMAFDAL FSREKLPQSF SPPQAEESKE  660
VAKEEEDEVT TVTVDLNKNA TTIDHDLDMM DEPRTSFPNE LSHLKLKSRK TGFKPYKRCS  720
VEAKENRVPA SDEVGTKRIR LESEEST*
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in the circadian clock. Binds to the promoter region of APRR1/TOC1 and TCP21/CHE to repress their transcription. Represses both CCA1 and itself. {ECO:0000269|PubMed:12015970, ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:9657154}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00654PBMTransfer from LOC_Os08g06110Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSeita.6G055700.1.p
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. {ECO:0000269|PubMed:12574129, ECO:0000269|PubMed:19095940, ECO:0000269|PubMed:19218364, ECO:0000269|PubMed:19286557, ECO:0000269|PubMed:20233950, ECO:0000269|PubMed:9657154}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004972798.10.0protein LHY
RefseqXP_004972799.10.0protein LHY
RefseqXP_012702448.10.0protein LHY
RefseqXP_012702451.10.0protein LHY
RefseqXP_012702452.10.0protein LHY
RefseqXP_022683283.10.0protein LHY
RefseqXP_022683284.10.0protein LHY
SwissprotQ6R0H12e-42LHY_ARATH; Protein LHY
TrEMBLA0A368RIS30.0A0A368RIS3_SETIT; Uncharacterized protein
STRINGSi013398m0.0(Setaria italica)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP60313447
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G46830.11e-40circadian clock associated 1
Publications ? help Back to Top
  1. 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]
  2. Kim Y, et al.
    Balanced nucleocytosolic partitioning defines a spatial network to coordinate circadian physiology in plants.
    Dev. Cell, 2013. 26(1): p. 73-85
    [PMID:23830866]
  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. 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]
  5. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  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. Gulledge AA,Vora H,Patel K,Loraine AE
    A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser.
    Methods Mol. Biol., 2014. 1158: p. 123-37
    [PMID:24792048]
  9. Hsiao AS, et al.
    Gene expression in plant lipid metabolism in Arabidopsis seedlings.
    PLoS ONE, 2014. 9(9): p. e107372
    [PMID:25264899]
  10. 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]
  11. 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]
  12. 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]
  13. Adams S,Manfield I,Stockley P,Carré IA
    Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions.
    PLoS ONE, 2015. 10(12): p. e0143943
    [PMID:26625126]
  14. 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]
  15. Baduel P,Arnold B,Weisman CM,Hunter B,Bomblies K
    Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis arenosa.
    Plant Physiol., 2016. 171(1): p. 437-51
    [PMID:26941193]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. Wu JF, et al.
    LWD-TCP complex activates the morning gene CCA1 in Arabidopsis.
    Nat Commun, 2016. 7: p. 13181
    [PMID:27734958]
  21. Wendell M, et al.
    Thermoperiodic Control of Floral Induction Involves Modulation of the Diurnal FLOWERING LOCUS T Expression Pattern.
    Plant Cell Physiol., 2017. 58(3): p. 466-477
    [PMID:28028164]
  22. Woloszynska M, et al.
    The Elongator complex regulates hypocotyl growth in darkness and during photomorphogenesis.
    J. Cell. Sci., 2019.
    [PMID:28720596]
  23. 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]
  24. James AB,Sullivan S,Nimmo HG
    Global spatial analysis of Arabidopsis natural variants implicates 5'UTR splicing of LATE ELONGATED HYPOCOTYL in responses to temperature.
    Plant Cell Environ., 2018. 41(7): p. 1524-1538
    [PMID:29520807]
  25. James AB, et al.
    How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY).
    Plant Cell Environ., 2018. 41(7): p. 1539-1550
    [PMID:29532482]