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

114141

Common Name

PIF3, SELMODRAFT_114141

Organism

Selaginella moellendorffii

Taxonomic ID

88036

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Lycopodiidae; Selaginellales; Selaginellaceae; Selaginella

Family

bHLH

Protein Properties

Length: 86aa MW: 9548.92 Da PI: 10.7172

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
114141	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	55.8	8.4e-18	24	70	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn ErrRRdriN+++ L+el+P++ K +Ka++L +A+eY+k+Lq 114141 24 VHNLSERRRRDRINEKMKALQELIPNS-----NKTDKASMLDEAIEYLKMLQ 70 6***********************7.....5****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	1.3E-20	17	77	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	7.98E-22	17	78	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	18.495	20	69	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	3.14E-14	23	74	No hit	No description
Pfam	PF00010	2.9E-15	24	70	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	6.0E-18	26	75	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009704	Biological Process	de-etiolation
GO:0009740	Biological Process	gibberellic acid mediated signaling pathway
GO:0010017	Biological Process	red or far-red light signaling pathway
GO:0031539	Biological Process	positive regulation of anthocyanin metabolic process
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0042802	Molecular Function	identical protein binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 86 aa Download sequence Send to blast
GESVDVKKAP PARTSSKRSR AAEVHNLSER RRRDRINEKM KALQELIPNS NKTDKASMLD 60 EAIEYLKMLQ LQLQVLSPGS SKVSS*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	28	33	ERRRRD

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00081	ChIP-seq	Transfer from AT1G09530	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By UV treatment. {ECO:0000269\|PubMed:12679534}.

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_002982619.2	2e-43	transcription factor PIF3
Swissprot	O80536	4e-32	PIF3_ARATH; Transcription factor PIF3
TrEMBL	D8SCD3	2e-53	D8SCD3_SELML; Uncharacterized protein PIF3 (Fragment)
STRING	EFJ17839	3e-54	(Selaginella moellendorffii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP258	16	128

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G09530.2	2e-34	phytochrome interacting factor 3

Link Out ? help Back to Top
Phytozome	114141
Entrez Gene	9657644

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] Banks JA, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science, 2011. 332(6032): p. 960-3 [PMID:21551031] 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] 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] 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] 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] 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]