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

ONIVA08G03410.3

Organism

Oryza nivara

Taxonomic ID

4536

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza

Family

MYB_related

Protein Properties

Length: 776aa MW: 84368.3 Da PI: 6.4755

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
ONIVA08G03410.3	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	46.9	6.3e-15	81	125	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r rWT+ E+ ++++a k++G W +I +++g ++t+ q++s+ qk+ ONIVA08G03410.3 81 RERWTEAEHNRFLEALKLYGRA-WQRIEEHVG-TKTAVQIRSHAQKF 125 78****************88.*****.**********98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	3.14E-16	75	131	IPR009057	Homeodomain-like
PROSITE profile	PS51294	19.593	76	130	IPR017930	Myb domain
TIGRFAMs	TIGR01557	1.7E-16	79	128	IPR006447	Myb domain, plants
SMART	SM00717	6.6E-12	80	128	IPR001005	SANT/Myb domain
Pfam	PF00249	3.0E-12	81	124	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	7.4E-8	81	121	IPR009057	Homeodomain-like
CDD	cd00167	1.40E-8	83	126	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:0005634	Cellular Component	nucleus
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: 776 aa Download sequence Send to blast
MQLLSRRRRG RRSEAASLVG IALLALEGDG AVGHSFGGGG ARIKEVFGLR RLTAIGSIQI 60 NSSGEEAVVK VRKPYTITKQ RERWTEAEHN RFLEALKLYG RAWQRIEEHV GTKTAVQIRS 120 HAQKFFTKLE KEAINNGTSP GQAHDIDIPP PRPKRKPNSP YPRKSCLSSE TSTREVQNDK 180 ATISNMTNNS TAQMAGDAAL EKLQRKEISE KGSCSEVLNL FREVPSASFS SVNKSSSNYG 240 ASRGLEPTKT EVKDVVILER DSISNGAGKD AKDINDQEME RLNGIHISSK PDHSHENCLD 300 TSSQQFKPKS NSVETTYVDW SAAKASHYQM DRNGVTGFQA TGTEGSHPDQ TSDQMGGASG 360 TMNQCIHPTL PVDPKFDGNA AAQPFPHNYA AFAPMMQCHC NQDAYRSFAN MSSTFSSMLV 420 STLLSNPAIH AAARLAASYW PTVDGNTPDP NQENLSESAQ GSHAGSPPNM ASIVAATVAA 480 ASAWWATQGL LPLFPPPIAF PFVPAPSAPF STADVQRAQE KDIDCPMDNA QKELQETRKQ 540 DNSEAMKVIV SSETDESGKG EVSLHTELKI SPADKADTKP AAGAETSDVF GNKKKQDRSS 600 CGSNTPSSSD IEADNAPENQ EKANDKAKQA SCSNSSAGDN NHRRFRSSAS TSDSWKEVSE 660 EGRLAFDALF SRERLPQSFS PPQVEGSKEI SKEEEDEVTT VTVDLNKNAA IIDQELDTAD 720 EPRASFPNEL SNLKLKSRRT GFKPYKRCSV EAKENRVPAS DEVGTKRIRL ESEAST

Sequence ? help Back to Top

Protein Sequence Length: 776 aa Download sequence Send to blast

MQLLSRRRRG RRSEAASLVG IALLALEGDG AVGHSFGGGG ARIKEVFGLR RLTAIGSIQI  60
NSSGEEAVVK VRKPYTITKQ RERWTEAEHN RFLEALKLYG RAWQRIEEHV GTKTAVQIRS  120
HAQKFFTKLE KEAINNGTSP GQAHDIDIPP PRPKRKPNSP YPRKSCLSSE TSTREVQNDK  180
ATISNMTNNS TAQMAGDAAL EKLQRKEISE KGSCSEVLNL FREVPSASFS SVNKSSSNYG  240
ASRGLEPTKT EVKDVVILER DSISNGAGKD AKDINDQEME RLNGIHISSK PDHSHENCLD  300
TSSQQFKPKS NSVETTYVDW SAAKASHYQM DRNGVTGFQA TGTEGSHPDQ TSDQMGGASG  360
TMNQCIHPTL PVDPKFDGNA AAQPFPHNYA AFAPMMQCHC NQDAYRSFAN MSSTFSSMLV  420
STLLSNPAIH AAARLAASYW PTVDGNTPDP NQENLSESAQ GSHAGSPPNM ASIVAATVAA  480
ASAWWATQGL LPLFPPPIAF PFVPAPSAPF STADVQRAQE KDIDCPMDNA QKELQETRKQ  540
DNSEAMKVIV SSETDESGKG EVSLHTELKI SPADKADTKP AAGAETSDVF GNKKKQDRSS  600
CGSNTPSSSD IEADNAPENQ EKANDKAKQA SCSNSSAGDN NHRRFRSSAS TSDSWKEVSE  660
EGRLAFDALF SRERLPQSFS PPQVEGSKEI SKEEEDEVTT VTVDLNKNAA IIDQELDTAD  720
EPRASFPNEL SNLKLKSRRT GFKPYKRCSV EAKENRVPAS DEVGTKRIRL ESEAST

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
MP00654	PBM	Transfer from LOC_Os08g06110	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. {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	AK242771	0.0	AK242771.1 Oryza sativa Japonica Group cDNA, clone: J090053J23, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015649844.1	0.0	protein LHY isoform X2
Refseq	XP_015649845.1	0.0	protein LHY isoform X2
Swissprot	Q6R0H1	5e-44	LHY_ARATH; Protein LHY
TrEMBL	A0A0E0I7E8	0.0	A0A0E0I7E8_ORYNI; Uncharacterized protein
STRING	OMERI08G03470.2	0.0	(Oryza meridionalis)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G46830.1	3e-40	circadian clock associated 1

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]