PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

MYB_related

Protein Properties

Length: 721aa MW: 79384.6 Da PI: 5.5644

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC3039_p4	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	47.6	3.8e-15	24	68	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r rWT+eE+ +++da +++G W +I +++ ++t+ q++s+ qk+ RrC3039_p4 24 RERWTEEEHNRFLDALRLYGRA-WQKIEEHVA-TKTAVQIRSHAQKF 68 78****************88.*****.**********98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	1.94E-16	18	74	IPR009057	Homeodomain-like
PROSITE profile	PS51294	20.665	19	73	IPR017930	Myb domain
TIGRFAMs	TIGR01557	9.8E-17	22	71	IPR006447	Myb domain, plants
SMART	SM00717	2.4E-12	23	71	IPR001005	SANT/Myb domain
Pfam	PF00249	3.5E-12	24	67	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	1.7E-8	24	64	IPR009057	Homeodomain-like
CDD	cd00167	5.22E-9	26	69	No hit	No description
SuperFamily	SSF50324	3.53E-41	571	716	IPR008162	Inorganic pyrophosphatase
Gene3D	G3DSA:3.90.80.10	5.9E-10	572	617	IPR008162	Inorganic pyrophosphatase
CDD	cd00412	1.99E-48	593	709	IPR008162	Inorganic pyrophosphatase
Pfam	PF00719	6.4E-23	617	711	IPR008162	Inorganic pyrophosphatase
Gene3D	G3DSA:3.90.80.10	7.9E-31	618	715	IPR008162	Inorganic pyrophosphatase

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006796	Biological Process	phosphate-containing compound metabolic process
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:0005737	Cellular Component	cytoplasm
GO:0000287	Molecular Function	magnesium ion binding
GO:0004427	Molecular Function	inorganic diphosphatase activity
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 721 aa Download sequence Send to blast
METNSSGEDL LVKTRKPYTI TKQRERWTEE EHNRFLDALR LYGRAWQKIE EHVATKTAVQ 60 IRSHAQKFFS KVEKEAEAKG VPVAQALDIA IPPPRPKHSP GSANVSLPQM ENEYPQEDNC 120 SDCLTHQHLS AASSIKTSKA STFREFLPSR EEEQGNNNKE SNSANYSENI EAGGPPQTYP 180 SHIPMLLPLG SSITTSLSHA PSEPDETSHH HHPHTVAGND HHQSFPDHIM SSLLQTPALY 240 TAATFASTFW PPSTGGGGGG GGTQGNLAAM AAATVAAASA WWAANGLLPL CAPPFSSGGL 300 TCHPPATTYG PSSGEVNVTK TMDQEHSEAS KARSSLESEE TKNGGSKPDC HENHHPCAAA 360 AATETDAKGS DGARDRKQVD RSSCGSNTPS SSDDVEADAL ERQENDGTTN DEVKEVNADT 420 TNNPQTSESN ARRGRVSSNL ADPWKSVSDE GRIAFRALFA REVLPQSFSY QRENREDGQQ 480 QRYPMELDLN STAELTPADD EEENRNIAFL GASKLSRGRT DLNVKFNGFG KSCSITYDHQ 540 QMSEETYEET MESNGSPRPA PKLNERILST LSKRSVAAHP WHDLEIGPEA PLVFNVVVEI 600 TKGSKVKYEL DKKTGLIKEP VLPGCFLRAR AIGLMPMIDQ GEMDDKIIAV CADDPEYRHF 660 TDIKQLAPHR LSEIRRFFED YKKNEHKEVA VNDFLPSEKA HEAIQYSMDL YAEYILHSLR 720 R

Sequence ? help Back to Top

Protein Sequence Length: 721 aa Download sequence Send to blast

METNSSGEDL LVKTRKPYTI TKQRERWTEE EHNRFLDALR LYGRAWQKIE EHVATKTAVQ  60
IRSHAQKFFS KVEKEAEAKG VPVAQALDIA IPPPRPKHSP GSANVSLPQM ENEYPQEDNC  120
SDCLTHQHLS AASSIKTSKA STFREFLPSR EEEQGNNNKE SNSANYSENI EAGGPPQTYP  180
SHIPMLLPLG SSITTSLSHA PSEPDETSHH HHPHTVAGND HHQSFPDHIM SSLLQTPALY  240
TAATFASTFW PPSTGGGGGG GGTQGNLAAM AAATVAAASA WWAANGLLPL CAPPFSSGGL  300
TCHPPATTYG PSSGEVNVTK TMDQEHSEAS KARSSLESEE TKNGGSKPDC HENHHPCAAA  360
AATETDAKGS DGARDRKQVD RSSCGSNTPS SSDDVEADAL ERQENDGTTN DEVKEVNADT  420
TNNPQTSESN ARRGRVSSNL ADPWKSVSDE GRIAFRALFA REVLPQSFSY QRENREDGQQ  480
QRYPMELDLN STAELTPADD EEENRNIAFL GASKLSRGRT DLNVKFNGFG KSCSITYDHQ  540
QMSEETYEET MESNGSPRPA PKLNERILST LSKRSVAAHP WHDLEIGPEA PLVFNVVVEI  600
TKGSKVKYEL DKKTGLIKEP VLPGCFLRAR AIGLMPMIDQ GEMDDKIIAV CADDPEYRHF  660
TDIKQLAPHR LSEIRRFFED YKKNEHKEVA VNDFLPSEKA HEAIQYSMDL YAEYILHSLR  720
R

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4lug_A	6e-83	578	721	1	180	Inorganic pyrophosphatase
4lug_B	6e-83	578	721	1	180	Inorganic pyrophosphatase
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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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HQ615939	1e-170	HQ615939.1 Brassica rapa CIRCADIAN AND CLOCK ASSOCIATED 1 (CCA1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018441165.1	0.0	PREDICTED: protein CCA1 isoform X1
Swissprot	P92973	0.0	CCA1_ARATH; Protein CCA1
TrEMBL	A0A3P5Z5J8	0.0	A0A3P5Z5J8_BRACM; Uncharacterized protein
STRING	Bra004503.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM15267	15	18

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G46830.1	0.0	circadian clock associated 1

Publications ? help Back to Top
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]