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

Cagra.1968s0051.1.p

Organism

Capsella grandiflora

Taxonomic ID

264402

Taxonomic Lineage

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

Family

MYB_related

Protein Properties

Length: 646aa MW: 70370.1 Da PI: 6.6149

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cagra.1968s0051.1.p	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	50.6	4.3e-16	24	68	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r rWT++E+e++++a +++G W +I +++g ++t+ q++s+ qk+ Cagra.1968s0051.1.p 24 RERWTEDEHERFLEALRLYGRA-WQRIEEHIG-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	19.977	19	73	IPR017930	Myb domain
Gene3D	G3DSA:1.10.10.60	4.3E-8	21	71	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	2.9E-17	22	71	IPR006447	Myb domain, plants
SMART	SM00717	2.4E-12	23	71	IPR001005	SANT/Myb domain
Pfam	PF00249	3.5E-13	24	67	IPR001005	SANT/Myb domain
CDD	cd00167	2.88E-9	26	69	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:0042754	Biological Process	negative regulation of circadian rhythm
GO:0043433	Biological Process	negative regulation of sequence-specific DNA binding transcription factor activity
GO:0046686	Biological Process	response to cadmium ion
GO:0048574	Biological Process	long-day photoperiodism, flowering
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 646 aa Download sequence Send to blast
MDTNTSGEEL LTKARKPYTI TKQRERWTED EHERFLEALR LYGRAWQRIE EHIGTKTAVQ 60 IRSHAQKFFT KLEKEAETKG IPVCQALDIE IPPPRPKRKP NTPYPRKPGN NGTSSSQVSS 120 AKDAKLVSSA SSSQCNHAFL DLEKMPVSEK TSTGKENQDD NCSGVSTMNK YPLPKKVTQR 180 KGNADIETSK TSTVDNAVQD VPKKNKDKDG NDGTVHSLQN YPWHFHADIV NGNITKCPQN 240 HPSGMVSQDF MFHPMREEIH GHGFRQATTA SATTTTSHQP FPACHSQDDY RSFLQMSSTF 300 SNLIMSTLLQ NPAAHAAATF AASVWPCASV GNSGDSSTPV SSSPPNVAAI AAATVAAATA 360 WWASHGLLPV CAPAPLTCVP LPTVVPTPEM TEMDTDENAQ LPLEKQNTAL QDPKLASKSP 420 ASSSDDSEET GVTNVNAASK ANGDKVEEVV VTAAAHDSNV TKKKNLVDRS SCGSNTPSGS 480 DVETDALDKM EKDNEDVKET DENQADVNEL NNRKTKLRDN NNPATDSWKE VSEEGRMAFQ 540 ALFARERLPQ SFSPPLVAEN VNGKQSGTSM PLALNFKVQD SRDADQERVV MIGVGPGKSL 600 KTRQTGFKPY KRCSMELKES QGGNTNNQSD EKVCKRLRLE GEAST*

Sequence ? help Back to Top

Protein Sequence Length: 646 aa Download sequence Send to blast

MDTNTSGEEL LTKARKPYTI TKQRERWTED EHERFLEALR LYGRAWQRIE EHIGTKTAVQ  60
IRSHAQKFFT KLEKEAETKG IPVCQALDIE IPPPRPKRKP NTPYPRKPGN NGTSSSQVSS  120
AKDAKLVSSA SSSQCNHAFL DLEKMPVSEK TSTGKENQDD NCSGVSTMNK YPLPKKVTQR  180
KGNADIETSK TSTVDNAVQD VPKKNKDKDG NDGTVHSLQN YPWHFHADIV NGNITKCPQN  240
HPSGMVSQDF MFHPMREEIH GHGFRQATTA SATTTTSHQP FPACHSQDDY RSFLQMSSTF  300
SNLIMSTLLQ NPAAHAAATF AASVWPCASV GNSGDSSTPV SSSPPNVAAI AAATVAAATA  360
WWASHGLLPV CAPAPLTCVP LPTVVPTPEM TEMDTDENAQ LPLEKQNTAL QDPKLASKSP  420
ASSSDDSEET GVTNVNAASK ANGDKVEEVV VTAAAHDSNV TKKKNLVDRS SCGSNTPSGS  480
DVETDALDKM EKDNEDVKET DENQADVNEL NNRKTKLRDN NNPATDSWKE VSEEGRMAFQ  540
ALFARERLPQ SFSPPLVAEN VNGKQSGTSM PLALNFKVQD SRDADQERVV MIGVGPGKSL  600
KTRQTGFKPY KRCSMELKES QGGNTNNQSD EKVCKRLRLE GEAST*

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription 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
MP00119	DAP	Transfer from AT1G01060	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Cagra.1968s0051.1.p

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. {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
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ006404	0.0	AJ006404.1 Arabidopsis thaliana mRNA for LATE ELONGATED HYPOCOTYL MYB transcription factor.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006306976.1	0.0	protein LHY isoform X1
Refseq	XP_023644400.1	0.0	protein LHY isoform X1
Swissprot	Q6R0H1	0.0	LHY_ARATH; Protein LHY
TrEMBL	R0IBL5	0.0	R0IBL5_9BRAS; Uncharacterized protein
STRING	Cagra.1968s0051.1.p	0.0	(Capsella grandiflora)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5576	26	45

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G01060.4	0.0	MYB_related family protein

Link Out ? help Back to Top
Phytozome	Cagra.1968s0051.1.p

Publications ? help Back to Top
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] 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] 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] 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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] 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] 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] Hsiao AS, et al. Gene expression in plant lipid metabolism in Arabidopsis seedlings. PLoS ONE, 2014. 9(9): p. e107372 [PMID:25264899] 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] 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] 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] 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] 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] 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] 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] 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] 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] Woloszynska M, et al. The Elongator complex regulates hypocotyl growth in darkness and during photomorphogenesis. J. Cell. Sci., 2019. [PMID:28720596] 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] 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] 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]