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

Gh_A11G0926

Organism

Gossypium hirsutum

Taxonomic ID

3635

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

MYB_related

Protein Properties

Length: 812aa MW: 89390.6 Da PI: 7.5602

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_A11G0926	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	50.4	5e-16	104	148	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+ Gh_A11G0926 104 RERWTEEEHNRFLEALKLYGRA-WQRIEEHIG-TKTAVQIRSHAQKF 148 78****************88.*****.**********98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF46689	6.73E-17	98	154	IPR009057	Homeodomain-like
PROSITE profile	PS51294	21.091	99	153	IPR017930	Myb domain
TIGRFAMs	TIGR01557	9.0E-17	102	151	IPR006447	Myb domain, plants
SMART	SM00717	7.3E-13	103	151	IPR001005	SANT/Myb domain
Pfam	PF00249	3.4E-13	104	147	IPR001005	SANT/Myb domain
Gene3D	G3DSA:1.10.10.60	2.3E-8	104	144	IPR009057	Homeodomain-like
CDD	cd00167	1.61E-9	106	149	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: 812 aa Download sequence Send to blast
MTSYLTQKGH VPVAHATLAQ CHPLFHTWWY GYNRGNLAGG EVTRRKRVPR GKCGGAFTDL 60 TSQNGNLWLR FEMNELSSSM AICQGFGVYG FVLTRKPYTI TKQRERWTEE EHNRFLEALK 120 LYGRAWQRIE EHIGTKTAVQ IRSHAQKFFS KLEKEALTKG IPTGQALDIE IPPPRPKRKP 180 RNPYPRKMSA ATSVQMGAKD GKSETPVSSL HCKQAFNLEK EPLPERPSRD EKSSNLKEIL 240 DDNCSEVFTL LHEANCSSMS SVNKNFIPTS TVLRNSCPLR EFVPSLKETI NKDTSKPSNL 300 ENSCTSYEKP AQVQRKDDMD GATCTDEMQA THNNPQHVAV HVLDGSPGTC APNPSMDITF 360 QDSIFHPMGD IHGQVNLFAN PAASATTAHQ NNAPRSTHQA FPTFHTPFMH LQPNQEDYRS 420 FLHVSSTFSS LVVSTLLQNP AAHAAASFAA TFWPYANVQN SDDSPACDQK GFPSRQMNSA 480 TSMAAIAAAT VAAATAWWAA HGLLSVCAPL QTGCTCAPAS TAAVTPMENG EAPAANMERK 540 MYAGQDPSMQ DQRLDPQYAE AMQCQPSASK SPTSSSSDRE ESGEAKANTE VKATAATEPQ 600 DPNKTKNGKQ VDRSSCGSNT PSSSDVEIDV LEKNKEDKED PKPADANHPQ VECSNRRGRS 660 STNLSDSWKE VSEGGRLAFQ ALFSREVLPQ SFSPPHDRKN KEQQKESVGE DEQNSDQNNG 720 ETSILHFSSE AFRSCSDHQG VEKKALSKAK NIVDKSLLTI GLGHEKLKAR QTGFKPYKRC 780 SVEAKESRVM NTGSQGEEKD PKRIRLEGEA PT

Sequence ? help Back to Top

Protein Sequence Length: 812 aa Download sequence Send to blast

MTSYLTQKGH VPVAHATLAQ CHPLFHTWWY GYNRGNLAGG EVTRRKRVPR GKCGGAFTDL  60
TSQNGNLWLR FEMNELSSSM AICQGFGVYG FVLTRKPYTI TKQRERWTEE EHNRFLEALK  120
LYGRAWQRIE EHIGTKTAVQ IRSHAQKFFS KLEKEALTKG IPTGQALDIE IPPPRPKRKP  180
RNPYPRKMSA ATSVQMGAKD GKSETPVSSL HCKQAFNLEK EPLPERPSRD EKSSNLKEIL  240
DDNCSEVFTL LHEANCSSMS SVNKNFIPTS TVLRNSCPLR EFVPSLKETI NKDTSKPSNL  300
ENSCTSYEKP AQVQRKDDMD GATCTDEMQA THNNPQHVAV HVLDGSPGTC APNPSMDITF  360
QDSIFHPMGD IHGQVNLFAN PAASATTAHQ NNAPRSTHQA FPTFHTPFMH LQPNQEDYRS  420
FLHVSSTFSS LVVSTLLQNP AAHAAASFAA TFWPYANVQN SDDSPACDQK GFPSRQMNSA  480
TSMAAIAAAT VAAATAWWAA HGLLSVCAPL QTGCTCAPAS TAAVTPMENG EAPAANMERK  540
MYAGQDPSMQ DQRLDPQYAE AMQCQPSASK SPTSSSSDRE ESGEAKANTE VKATAATEPQ  600
DPNKTKNGKQ VDRSSCGSNT PSSSDVEIDV LEKNKEDKED PKPADANHPQ VECSNRRGRS  660
STNLSDSWKE VSEGGRLAFQ ALFSREVLPQ SFSPPHDRKN KEQQKESVGE DEQNSDQNNG  720
ETSILHFSSE AFRSCSDHQG VEKKALSKAK NIVDKSLLTI GLGHEKLKAR QTGFKPYKRC  780
SVEAKESRVM NTGSQGEEKD PKRIRLEGEA PT

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	174	180	RPKRKPR

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in leaves, roots, stems, flowers and siliques. {ECO:0000269\|PubMed:19095940, ECO:0000269\|PubMed:19218364}.

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}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HQ526180	8e-46	HQ526180.1 Gossypium herbaceum clone NBRI_E_1400 simple sequence repeat marker, mRNA sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016709652.1	0.0	PREDICTED: protein LHY-like isoform X1
Swissprot	Q6R0H1	1e-137	LHY_ARATH; Protein LHY
TrEMBL	A0A1U8L4V6	0.0	A0A1U8L4V6_GOSHI; protein LHY-like isoform X1
STRING	Gorai.007G113900.1	0.0	(Gossypium raimondii)

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
AT1G01060.3	1e-112	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]