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

676747458

Organism

Sisymbrium irio

Taxonomic ID

3730

Taxonomic Lineage

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

Family

MYB_related

Protein Properties

Length: 1089aa MW: 119311 Da PI: 8.1805

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
676747458	genome	VEGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	48.3	2.4e-15	450	494	1	47
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 r rWT++E++++++a +++G W +I +++g ++t+ q++s+ qk+ 676747458 450 RERWTEDEHDRFLEALRLYGRA-WQRIEEHIG-TKTAVQIRSHAQKF 494 78****************88.*****.**********98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF00892	1.2E-11	12	153	IPR000620	EamA domain
SuperFamily	SSF103481	7.72E-7	46	157	No hit	No description
Pfam	PF00892	4.2E-8	186	324	IPR000620	EamA domain
SuperFamily	SSF103481	1.83E-6	244	328	No hit	No description
SuperFamily	SSF46689	5.68E-15	444	497	IPR009057	Homeodomain-like
PROSITE profile	PS51294	18.413	445	499	IPR017930	Myb domain
TIGRFAMs	TIGR01557	3.3E-17	448	497	IPR006447	Myb domain, plants
SMART	SM00717	4.7E-12	449	497	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	1.6E-7	450	490	IPR009057	Homeodomain-like
Pfam	PF00249	1.0E-12	450	493	IPR001005	SANT/Myb domain
CDD	cd00167	1.56E-8	452	495	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:0016021	Cellular Component	integral component of membrane
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: 1089 aa Download sequence Send to blast
MQGVRVIEEW SPVIVMVISN VAMGSVNALV KKALDGGVNH MVVGAYRMAI SAFILAPFAY 60 ILERKTRPDL TFRLLVDHFF SGLLGASLMQ FFFLLGLSYT SATVSCALVS MLPAITFALA 120 LIFRTENVKN LKTKAGILKM LGTLICISGA LFLTFYKGPQ ITNPHSHPKA LQHNDNDHDK 180 TKNWLLGCLY LTIGTTLLSL WMVFQGTLNI KYPCKYSSTC LMSVFAAFQC ALLSLYKERN 240 VKDWVIDDKF VITVIIYAGV VGQAMSTVAT TWGIKKLGAV FASTFSPVIL ISATLFDFLI 300 LHTPLYLGSV IGSVVAVMGL YVFLWGKKNE TKTSTTLPPQ MDNEDQIYTA DTYGFLDHPS 360 WNRTHHFSHL LPTTGKPPRK NDGPHSRFYL RDLHKERRLL AQREASWEIR KSARGFEAAE 420 SCKDPVMDTN TSGEELLTKA RKPYTITKQR ERWTEDEHDR FLEALRLYGR AWQRIEEHIG 480 TKTAVQIRSH AQKFFTKLWF TLQLEKEAEA KGIPVCQALD IEIPPPRPKR KPNTPYPRKP 540 GNNGSPSSQV SSAKDAKLVS SASSSQCNQA FLDLEKVPMS EKTSTGKENQ DDNCSGISTV 600 NKHPLPKKVT QISEPSLRKE SADNETSKAS NVDNMVQDVP EKNKGKDGDG LHSARNYPWH 660 FPAGFVNGNM AKFPQFHPPG MVSQDFMFCP MGDRFHGHAS SHVNLPATTA SSATTTTSQQ 720 AFPACPSQDD YRSFLQISST FSNLIMSTLL QNPAAHAAAA FAASVWSYTN AGNSGDSATQ 780 MSSSPPSIAA IAAATVAAAT AWWASHGILP VCAPTPVTCL PLPTVAVPTP AMDKMDTGEN 840 DQLPLEKQNT ALQDQNLVSK SPASSSDDSE ETGITKLNAD SKTNGDKEEV AVDAAALHDS 900 NVSPKKKLVD RSSCGSNTPS GSDAETDALD KVEKDKEDVK EADANQPGVM ELSNRRSKSR 960 DNNNNPATDS WKEVSQGGRI AFQALFARER LPQSFSPPLG AENVNGKQSD TSMPMAPDLN 1020 KIQDSCDADQ ESVVMIGGGP GKSLKTRQTG FKPYKRCSME MKESQVGNTN NQSDEKVCKR 1080 LRLEGEAST

Sequence ? help Back to Top

Protein Sequence Length: 1089 aa Download sequence Send to blast

MQGVRVIEEW SPVIVMVISN VAMGSVNALV KKALDGGVNH MVVGAYRMAI SAFILAPFAY  60
ILERKTRPDL TFRLLVDHFF SGLLGASLMQ FFFLLGLSYT SATVSCALVS MLPAITFALA  120
LIFRTENVKN LKTKAGILKM LGTLICISGA LFLTFYKGPQ ITNPHSHPKA LQHNDNDHDK  180
TKNWLLGCLY LTIGTTLLSL WMVFQGTLNI KYPCKYSSTC LMSVFAAFQC ALLSLYKERN  240
VKDWVIDDKF VITVIIYAGV VGQAMSTVAT TWGIKKLGAV FASTFSPVIL ISATLFDFLI  300
LHTPLYLGSV IGSVVAVMGL YVFLWGKKNE TKTSTTLPPQ MDNEDQIYTA DTYGFLDHPS  360
WNRTHHFSHL LPTTGKPPRK NDGPHSRFYL RDLHKERRLL AQREASWEIR KSARGFEAAE  420
SCKDPVMDTN TSGEELLTKA RKPYTITKQR ERWTEDEHDR FLEALRLYGR AWQRIEEHIG  480
TKTAVQIRSH AQKFFTKLWF TLQLEKEAEA KGIPVCQALD IEIPPPRPKR KPNTPYPRKP  540
GNNGSPSSQV SSAKDAKLVS SASSSQCNQA FLDLEKVPMS EKTSTGKENQ DDNCSGISTV  600
NKHPLPKKVT QISEPSLRKE SADNETSKAS NVDNMVQDVP EKNKGKDGDG LHSARNYPWH  660
FPAGFVNGNM AKFPQFHPPG MVSQDFMFCP MGDRFHGHAS SHVNLPATTA SSATTTTSQQ  720
AFPACPSQDD YRSFLQISST FSNLIMSTLL QNPAAHAAAA FAASVWSYTN AGNSGDSATQ  780
MSSSPPSIAA IAAATVAAAT AWWASHGILP VCAPTPVTCL PLPTVAVPTP AMDKMDTGEN  840
DQLPLEKQNT ALQDQNLVSK SPASSSDDSE ETGITKLNAD SKTNGDKEEV AVDAAALHDS  900
NVSPKKKLVD RSSCGSNTPS GSDAETDALD KVEKDKEDVK EADANQPGVM ELSNRRSKSR  960
DNNNNPATDS WKEVSQGGRI AFQALFARER LPQSFSPPLG AENVNGKQSD TSMPMAPDLN  1020
KIQDSCDADQ ESVVMIGGGP GKSLKTRQTG FKPYKRCSME MKESQVGNTN NQSDEKVCKR  1080
LRLEGEAST

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	676747458

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006418374.1	0.0	protein LHY
Refseq	XP_006418375.1	0.0	protein LHY
Refseq	XP_024007807.1	0.0	protein LHY
Swissprot	Q6R0H1	0.0	LHY_ARATH; Protein LHY
TrEMBL	E4MW67	0.0	E4MW67_EUTHA; mRNA, clone: RTFL01-03-N03
TrEMBL	V4L368	0.0	V4L368_EUTSA; Uncharacterized protein
STRING	XP_006418374.1	0.0	(Eutrema salsugineum)

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

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]