PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

gw1.9.308.1

Common Name

CHLNCDRAFT_15057

Organism

Chlorella variabilis NC64A

Taxonomic ID

554065

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Chlorophyta; Trebouxiophyceae; Chlorellales; Chlorellaceae; Chlorella

Family

MYB_related

Protein Properties

Length: 89aa MW: 10683.4 Da PI: 11.4604

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
gw1.9.308.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	55.4	1.4e-17	14	58	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r rWT eE++++v+a +++G W++I ++ ++t+ q++s+ qk+ gw1.9.308.1 14 RERWTDEEHDRFVEALRLHGRQ-WRKIEGHVK-TKTAVQIRSHAQKF 58 78****************77.****9.**********98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	8.97E-18	8	64	IPR009057	Homeodomain-like
PROSITE profile	PS51294	21.931	9	63	IPR017930	Myb domain
Gene3D	G3DSA:1.10.10.60	3.1E-10	11	61	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	1.6E-16	12	61	IPR006447	Myb domain, plants
SMART	SM00717	1.0E-11	13	61	IPR001005	SANT/Myb domain
Pfam	PF00249	3.1E-14	14	57	IPR001005	SANT/Myb domain
CDD	cd00167	2.11E-8	16	59	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009409	Biological Process	response to cold
GO:0009651	Biological Process	response to salt stress
GO:0009723	Biological Process	response to ethylene
GO:0009733	Biological Process	response to auxin
GO:0009737	Biological Process	response to abscisic acid
GO:0009739	Biological Process	response to gibberellin
GO:0009751	Biological Process	response to salicylic acid
GO:0009753	Biological Process	response to jasmonic acid
GO:0010243	Biological Process	response to organonitrogen compound
GO:0042754	Biological Process	negative regulation of circadian rhythm
GO:0043496	Biological Process	regulation of protein homodimerization activity
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0046686	Biological Process	response to cadmium ion
GO:0048574	Biological Process	long-day photoperiodism, flowering
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 89 aa Download sequence Send to blast
TLQMRKPYTI TKQRERWTDE EHDRFVEALR LHGRQWRKIE GHVKTKTAVQ IRSHAQKFFS 60 KLEKQQMQLQ AGLQPTLDLA VPPPRPKRK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription 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
MP00103	PBM	Transfer from AT2G46830	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: 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
PlantRegMap	-	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_005847876.1	2e-59	hypothetical protein CHLNCDRAFT_15057, partial
Swissprot	P92973	1e-28	CCA1_ARATH; Protein CCA1
TrEMBL	E1ZDY2	5e-58	E1ZDY2_CHLVA; Uncharacterized protein (Fragment)
STRING	XP_005847876.1	8e-59	(Chlorella variabilis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Chlorophytae	OGCP454	14	27

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G46830.1	5e-31	circadian clock associated 1

Link Out ? help Back to Top
Entrez Gene	17355476

Publications ? help Back to Top
Blanc G, et al. The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. Plant Cell, 2010. 22(9): p. 2943-55 [PMID:20852019] 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] 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] 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] 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] 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] 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] McClung CR Wheels within wheels: new transcriptional feedback loops in the Arabidopsis circadian clock. F1000Prime Rep, 2014. 6: p. 2 [PMID:24592314] 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] 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] 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] 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] Hsiao AS, et al. Gene expression in plant lipid metabolism in Arabidopsis seedlings. PLoS ONE, 2014. 9(9): p. e107372 [PMID:25264899] Filichkin SA, et al. Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis. Mol Plant, 2015. [PMID:25366180] 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] 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] 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] 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] 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] 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] 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] 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] Lee HG,Mas P,Seo PJ MYB96 shapes the circadian gating of ABA signaling in Arabidopsis. Sci Rep, 2016. 6: p. 17754 [PMID:26725725] 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] 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] 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] 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] 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] 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] 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] 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] Wu JF, et al. LWD-TCP complex activates the morning gene CCA1 in Arabidopsis. Nat Commun, 2016. 7: p. 13181 [PMID:27734958] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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]