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

Seita.1G357300.1.p

Organism

Setaria italica

Taxonomic ID

4555

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Cenchrinae; Setaria

Family

bHLH

Protein Properties

Length: 109aa MW: 12336.1 Da PI: 10.1586

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Seita.1G357300.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	54.4	2.2e-17	50	96	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn E+rRR+riN+++ L++l+P++ K +Ka++L A+eY+k+Lq Seita.1G357300.1.p 50 VHNLSEKRRRSRINEKMKALQTLIPNS-----SKTDKASMLDDAIEYLKQLQ 96 6***********************8.....7****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	5.1E-20	43	104	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	17.981	46	95	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	3.99E-13	49	100	No hit	No description
Pfam	PF00010	5.7E-15	50	96	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.6E-19	50	104	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.0E-18	52	101	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 109 aa Download sequence Send to blast
MDAQQLDLIL RHHHQSMANV CESEDALGSS ESEPARPARP RGKRSRAAEV HNLSEKRRRS 60 RINEKMKALQ TLIPNSSKTD KASMLDDAIE YLKQLQLQVQ VSKQMLRC*

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor acting positively in the phytochrome signaling pathway. Activates transcription by binding to the G box (5'-CACGTG-3'). {ECO:0000269\|PubMed:10466729, ECO:0000269\|PubMed:10797009}.
UniProt	Transcription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them. {ECO:0000269\|PubMed:10225997, ECO:0000269\|Ref.8}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Seita.1G357300.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By UV treatment. {ECO:0000269\|PubMed:12679534}.
UniProt	INDUCTION: Down-regulated by the A class gene AP2 in the first whorl and by ARF3/ETT in gynoecium. {ECO:0000269\|PubMed:11245574}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT033382	1e-122	BT033382.1 Zea mays full-length cDNA clone ZM_BFb0041N16 mRNA, complete cds.
GenBank	BT064056	1e-122	BT064056.1 Zea mays full-length cDNA clone ZM_BFc0135E23 mRNA, complete cds.
GenBank	KJ726988	1e-122	KJ726988.1 Zea mays clone pUT3689 bHLH transcription factor (bHLH168) mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004954276.1	8e-65	transcription factor SPATULA isoform X1
Refseq	XP_022682068.1	2e-65	transcription factor SPATULA isoform X2
Swissprot	O80536	6e-27	PIF3_ARATH; Transcription factor PIF3
Swissprot	Q9FUA4	1e-27	SPT_ARATH; Transcription factor SPATULA
TrEMBL	A0A368PTP7	2e-72	A0A368PTP7_SETIT; Uncharacterized protein
STRING	Si017762m	3e-64	(Setaria italica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP3336	37	76

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G36930.1	2e-23	bHLH family protein

Link Out ? help Back to Top
Phytozome	Seita.1G357300.1.p

Publications ? help Back to Top
Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation, 2010. 80(1): p. 1-8 [PMID:20219281] Zhong S, et al. Ethylene-orchestrated circuitry coordinates a seedling's response to soil cover and etiolated growth. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(11): p. 3913-20 [PMID:24599595] Van Buskirk EK,Reddy AK,Nagatani A,Chen M Photobody Localization of Phytochrome B Is Tightly Correlated with Prolonged and Light-Dependent Inhibition of Hypocotyl Elongation in the Dark. Plant Physiol., 2014. 165(2): p. 595-607 [PMID:24769533] Zhao Y,Zhou J,Xing D Phytochrome B-mediated activation of lipoxygenase modulates an excess red light-induced defence response in Arabidopsis. J. Exp. Bot., 2014. 65(17): p. 4907-18 [PMID:24916071] Zhang D,Jing Y,Jiang Z,Lin R The Chromatin-Remodeling Factor PICKLE Integrates Brassinosteroid and Gibberellin Signaling during Skotomorphogenic Growth in Arabidopsis. Plant Cell, 2014. 26(6): p. 2472-2485 [PMID:24920333] Wang Y, et al. Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(28): p. 10359-64 [PMID:24982146] Pabón-Mora N,Wong GK,Ambrose BA Evolution of fruit development genes in flowering plants. Front Plant Sci, 2014. 5: p. 300 [PMID:25018763] Zhu L,Huq E Suicidal co-degradation of the phytochrome interacting factor 3 and phytochrome B in response to light. Mol Plant, 2014. 7(12): p. 1709-11 [PMID:25281666] Moubayidin L,Ostergaard L Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development. Curr. Biol., 2014. 24(22): p. 2743-8 [PMID:25455035] Adams E,Diaz C,Hong JP,Shin R 14-3-3 proteins participate in light signaling through association with PHYTOCHROME INTERACTING FACTORs. Int J Mol Sci, 2014. 15(12): p. 22801-14 [PMID:25501334] Horvath DP, et al. RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean. New Phytol., 2015. 207(1): p. 196-210 [PMID:25711503] Geilen K,Böhmer M Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana. Sci Rep, 2015. 5: p. 13369 [PMID:26293691] Galvão VC,Collani S,Horrer D,Schmid M Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana. Plant J., 2015. 84(5): p. 949-62 [PMID:26466761] Yue J, et al. TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis. Plant Physiol., 2016. 170(3): p. 1381-97 [PMID:26704640] Eprintsev AT,Fedorin DN,Sazonova OV,Igamberdiev AU Light inhibition of fumarase in Arabidopsis leaves is phytochrome A-dependent and mediated by calcium. Plant Physiol. Biochem., 2016. 102: p. 161-6 [PMID:26949024] Soy J, et al. Molecular convergence of clock and photosensory pathways through PIF3-TOC1 interaction and co-occupancy of target promoters. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(17): p. 4870-5 [PMID:27071129] Pacín M,Semmoloni M,Legris M,Finlayson SA,Casal JJ Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance. New Phytol., 2016. 211(3): p. 967-79 [PMID:27105120] Yoo J,Cho MH,Lee SW,Bhoo SH Phytochrome-interacting ankyrin repeat protein 2 modulates phytochrome A-mediated PIF3 phosphorylation in light signal transduction. J. Biochem., 2016. 160(4): p. 243-249 [PMID:27143545] Kumar I,Swaminathan K,Hudson K,Hudson ME Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling. J. Exp. Bot., 2016. 67(14): p. 4231-40 [PMID:27262126] Li K, et al. DELLA-mediated PIF degradation contributes to coordination of light and gibberellin signalling in Arabidopsis. Nat Commun, 2016. 7: p. 11868 [PMID:27282989] Jeong AR, et al. New Constitutively Active Phytochromes Exhibit Light-Independent Signaling Activity. Plant Physiol., 2016. 171(4): p. 2826-40 [PMID:27325667] Martin G,Soy J,Monte E Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes. Front Plant Sci, 2016. 7: p. 962 [PMID:27458465] Pfannebecker KC,Lange M,Rupp O,Becker A Seed Plant-Specific Gene Lineages Involved in Carpel Development. Mol. Biol. Evol., 2017. 34(4): p. 925-942 [PMID:28087776] Yu Y,Huang R Integration of Ethylene and Light Signaling Affects Hypocotyl Growth in Arabidopsis. Front Plant Sci, 2017. 8: p. 57 [PMID:28174592] Zentella R, et al. The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA. Nat. Chem. Biol., 2017. 13(5): p. 479-485 [PMID:28244988] Ling JJ,Li J,Zhu D,Deng XW Noncanonical role of Arabidopsis COP1/SPA complex in repressing BIN2-mediated PIF3 phosphorylation and degradation in darkness. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(13): p. 3539-3544 [PMID:28292892] Kasulin L, et al. A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina. Mol. Ecol., 2017. 26(13): p. 3389-3404 [PMID:28316114] Zumajo-Cardona C,Ambrose BA,Pabón-Mora N Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae). Evodevo, 2017. 8: p. 5 [PMID:28331573] Reyes-Olalde JI, et al. The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium. PLoS Genet., 2017. 13(4): p. e1006726 [PMID:28388635] Shor E,Paik I,Kangisser S,Green R,Huq E PHYTOCHROME INTERACTING FACTORS mediate metabolic control of the circadian system in Arabidopsis. New Phytol., 2017. 215(1): p. 217-228 [PMID:28440582] Ni W, et al. PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nat Commun, 2017. 8: p. 15236 [PMID:28492231] Zhang X, et al. A PIF1/PIF3-HY5-BBX23 Transcription Factor Cascade Affects Photomorphogenesis. Plant Physiol., 2017. 174(4): p. 2487-2500 [PMID:28687557] Paik I,Kathare PK,Kim JI,Huq E Expanding Roles of PIFs in Signal Integration from Multiple Processes. Mol Plant, 2017. 10(8): p. 1035-1046 [PMID:28711729] Dong J, et al. Light-Dependent Degradation of PIF3 by SCFEBF1/2 Promotes a Photomorphogenic Response in Arabidopsis. Curr. Biol., 2017. 27(16): p. 2420-2430.e6 [PMID:28736168] Jiang B, et al. PIF3 is a negative regulator of the CBF pathway and freezing tolerance in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(32): p. E6695-E6702 [PMID:28739888] Hochrein L,Machens F,Messerschmidt K,Mueller-Roeber B PhiReX: a programmable and red light-regulated protein expression switch for yeast. Nucleic Acids Res., 2017. 45(15): p. 9193-9205 [PMID:28911120] Liu X, et al. EIN3 and PIF3 Form an Interdependent Module That Represses Chloroplast Development in Buried Seedlings. Plant Cell, 2017. 29(12): p. 3051-3067 [PMID:29114016] Wang Y,Li J,Deng XW,Zhu D Arabidopsis noncoding RNA modulates seedling greening during deetiolation. Sci China Life Sci, 2018. 61(2): p. 199-203 [PMID:29143279] Ma Q,Wang X,Sun J,Mao T Coordinated Regulation of Hypocotyl Cell Elongation by Light and Ethylene through a Microtubule Destabilizing Protein. Plant Physiol., 2018. 176(1): p. 678-690 [PMID:29167353] Qiu Y, et al. Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun, 2017. 8(1): p. 1905 [PMID:29199270] Xin X, et al. Arabidopsis MKK10-MPK6 mediates red-light-regulated opening of seedling cotyledons through phosphorylation of PIF3. J. Exp. Bot., 2018. 69(3): p. 423-439 [PMID:29244171] Wu M, et al. SPATULA regulates floral transition and photomorphogenesis in a PHYTOCHROME B-dependent manner in Arabidopsis. Biochem. Biophys. Res. Commun., 2018. 503(4): p. 2380-2385 [PMID:29966653]