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

XP_010559156.1

Organism

Tarenaya hassleriana

Taxonomic ID

28532

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Cleomaceae; Tarenaya

Family

MYB_related

Protein Properties

Length: 696aa MW: 75739.7 Da PI: 6.7922

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_010559156.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	51.9	1.8e-16	24	68	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r rWT+eE++++++a k++G W +I ++g ++t+ q++s+ qk+ XP_010559156.1 24 RERWTEEEHDRFLEALKLYGRA-WQKIEDHVG-TKTAVQIRSHAQKF 68 78****************88.*****.**********98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	4.86E-17	18	74	IPR009057	Homeodomain-like
PROSITE profile	PS51294	21.362	19	73	IPR017930	Myb domain
TIGRFAMs	TIGR01557	2.1E-17	22	71	IPR006447	Myb domain, plants
SMART	SM00717	2.3E-13	23	71	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	6.0E-9	24	64	IPR009057	Homeodomain-like
Pfam	PF00249	1.2E-13	24	67	IPR001005	SANT/Myb domain
CDD	cd00167	1.07E-9	26	69	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 696 aa Download sequence Send to blast
METNSSGEEL VIKMRKPYTI TKQRERWTEE EHDRFLEALK LYGRAWQKIE DHVGTKTAVQ 60 IRSHAQKFFS KVEKEAKAKG VPVGIALNID IPPPRPKKKP SNPYPRKTGN RTPTSQAAAQ 120 VGKQATSAST VLNCKEALLL QKGSLSEYPS EELLPSNLED DHSASSMNKS SVETMAFANG 180 CSFTEFLPPR KEANQDNGTR KASNSEKDCC DLHAKSVQGS AKKYVSGISH VDEEQGPQTY 240 TRHVPVHTID GSSVASPISP FPTVSEGIHV CLNKFTDMSA CANRSKHDND GPRYKSRALP 300 AVHLASAPIP HTLDDYWSFA NLFVSNPLQN PAAHAASTFA ASVWPGGTST CAEIGVPPSQ 360 VSSPSSLAAI AAATVSAATA WWAAHGLLPL CAPIHSAFPC HPPPTTLAPI SDDNGHAPYA 420 NVDTKESTLQ NPSVQSQDAD PEHSEASKAQ SSPLKTTLSP SYSEQSGSTK TETGGKPASH 480 EQTEAETDQN RAKNRKQVDR SSCGSNTPSS SDAEVDASEK LEKDKDEEKE VEVDVNPPAE 540 ESNIRRSRSS SNLSDPWKSV SDEVLGQGRL AFQALFSREV LPQSFPPRRD SKDKKDLRGN 600 EDGEKKKSAE TEHGEGQELD LNRTAQATDS DHQEEKGDQD GYLAIGLGAS KLKERTGFKP 660 YKRCSVDAKE NRITNSSTLN RVEQKDPKRI CLERRA

Sequence ? help Back to Top

Protein Sequence Length: 696 aa Download sequence Send to blast

METNSSGEEL VIKMRKPYTI TKQRERWTEE EHDRFLEALK LYGRAWQKIE DHVGTKTAVQ  60
IRSHAQKFFS KVEKEAKAKG VPVGIALNID IPPPRPKKKP SNPYPRKTGN RTPTSQAAAQ  120
VGKQATSAST VLNCKEALLL QKGSLSEYPS EELLPSNLED DHSASSMNKS SVETMAFANG  180
CSFTEFLPPR KEANQDNGTR KASNSEKDCC DLHAKSVQGS AKKYVSGISH VDEEQGPQTY  240
TRHVPVHTID GSSVASPISP FPTVSEGIHV CLNKFTDMSA CANRSKHDND GPRYKSRALP  300
AVHLASAPIP HTLDDYWSFA NLFVSNPLQN PAAHAASTFA ASVWPGGTST CAEIGVPPSQ  360
VSSPSSLAAI AAATVSAATA WWAAHGLLPL CAPIHSAFPC HPPPTTLAPI SDDNGHAPYA  420
NVDTKESTLQ NPSVQSQDAD PEHSEASKAQ SSPLKTTLSP SYSEQSGSTK TETGGKPASH  480
EQTEAETDQN RAKNRKQVDR SSCGSNTPSS SDAEVDASEK LEKDKDEEKE VEVDVNPPAE  540
ESNIRRSRSS SNLSDPWKSV SDEVLGQGRL AFQALFSREV LPQSFPPRRD SKDKKDLRGN  600
EDGEKKKSAE TEHGEGQELD LNRTAQATDS DHQEEKGDQD GYLAIGLGAS KLKERTGFKP  660
YKRCSVDAKE NRITNSSTLN RVEQKDPKRI CLERRA

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_010559156.1

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_019059784.1	0.0	PREDICTED: protein CCA1-like isoform X1
Refseq	XP_019059785.1	0.0	PREDICTED: protein CCA1-like isoform X1
Refseq	XP_019059786.1	0.0	PREDICTED: protein CCA1-like isoform X1
Refseq	XP_019059787.1	0.0	PREDICTED: protein CCA1-like isoform X1
Refseq	XP_019059788.1	0.0	PREDICTED: protein CCA1-like isoform X1
Refseq	XP_019059789.1	0.0	PREDICTED: protein CCA1-like isoform X1
Refseq	XP_019059790.1	0.0	PREDICTED: protein CCA1-like isoform X1
Swissprot	P92973	1e-156	CCA1_ARATH; Protein CCA1
TrEMBL	A0A076L4N2	1e-168	A0A076L4N2_9ROSI; Late elongated hypocotyl a
STRING	XP_010559151.1	0.0	(Tarenaya hassleriana)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G46830.1	1e-133	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]