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

AT2G46970.1

Common Name

BHLH124, EN110, F14M4.20, PIL1

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 416aa MW: 46579.7 Da PI: 9.4395

Description

phytochrome interacting factor 3-like 1

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT2G46970.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.1	2.8e-12	233	279	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 h+ Er+RRd+ N+++ L++llP++ K +Ka+ L +A++Y++ Lq AT2G46970.1 233 VHKLYERKRRDEFNKKMRALQDLLPNC-----YKDDKASLLDEAIKYMRTLQ 279 59999*******************8.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	9.5E-17	226	289	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.83E-17	227	304	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	9.57E-12	227	283	No hit	No description
PROSITE profile	PS50888	15.332	229	278	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	7.6E-10	233	279	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	6.5E-11	235	284	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009641	Biological Process	shade avoidance
GO:0010017	Biological Process	red or far-red light signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 416 aa Download sequence Send to blast
MEAKPLASSS SEPNMISPSS NIKPKLKDED YMELVCENGQ ILAKIRRPKN NGSFQKQRRQ 60 SLLDLYETEY SEGFKKNIKI LGDTQVVPVS QSKPQQDKET NEQMNNNKKK LKSSKIEFER 120 NVSKSNKCVE SSTLIDVSAK GPKNVEVTTA PPDEQSAAVG RSTELYFASS SKFSRGTSRD 180 LSCCSLKRKY GDIEEEESTY LSNNSDDESD DAKTQVHART RKPVTKRKRS TEVHKLYERK 240 RRDEFNKKMR ALQDLLPNCY KDDKASLLDE AIKYMRTLQL QVQMMSMGNG LIRPPTMLPM 300 GHYSPMGLGM HMGAAATPTS IPQFLPMNVQ ATGFPGMNNA PPQMLSFLNH PSGLIPNTPI 360 FSPLENCSQP FVVPSCVSQT QATSFTQFPK SASASNLEDA MQYRGSNGFS YYRSPN

Sequence ? help Back to Top

Protein Sequence Length: 416 aa Download sequence Send to blast

MEAKPLASSS SEPNMISPSS NIKPKLKDED YMELVCENGQ ILAKIRRPKN NGSFQKQRRQ  60
SLLDLYETEY SEGFKKNIKI LGDTQVVPVS QSKPQQDKET NEQMNNNKKK LKSSKIEFER  120
NVSKSNKCVE SSTLIDVSAK GPKNVEVTTA PPDEQSAAVG RSTELYFASS SKFSRGTSRD  180
LSCCSLKRKY GDIEEEESTY LSNNSDDESD DAKTQVHART RKPVTKRKRS TEVHKLYERK  240
RRDEFNKKMR ALQDLLPNCY KDDKASLLDE AIKYMRTLQL QVQMMSMGNG LIRPPTMLPM  300
GHYSPMGLGM HMGAAATPTS IPQFLPMNVQ ATGFPGMNNA PPQMLSFLNH PSGLIPNTPI  360
FSPLENCSQP FVVPSCVSQT QATSFTQFPK SASASNLEDA MQYRGSNGFS YYRSPN

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	226	241	RKRSTEVHKLYERKRR
2	237	242	ERKRRD

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.36425	0.0	flower\| vegetative tissue

Expression -- Microarray ? help Back to Top
Source	ID
Expression Atlas	AT2G46970
AtGenExpress	AT2G46970

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Etiolated seedlings. {ECO:0000269\|PubMed:12826627}.

Functional Description ? help Back to Top
Source	Description
TAIR	encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family.
UniProt	Transcription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. {ECO:0000269\|PubMed:14668869, ECO:0000269\|PubMed:16565297, ECO:0000269\|PubMed:16891401}.

Function -- GeneRIF ? help Back to Top
PIL1 is a direct target of phytochrome signaling and plays a key role in response to long-term shade in Arabidopsis. [PMID: 16565297] PIL1 is necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network. [PMID: 16891401] These data suggest that the second-phase decline in robustness of PIL1 derepression is an indirect consequence of the global developmental transition from the etiolated to the de-etiolated state. [PMID: 18296722] PIL1 plays a role as a decelerator of growth during early shade avoidance. [PMID: 24895419]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT2G46970.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Expressed with a circadian rhythm showing peaks during the light period. Up-regulated by simulated shade in light-grown plants, in a phytochrome-dependent manner; low red/far-red ratio (R/FR) light, but repressed by a high R/FR light. Rapidly down-regulated after seedling deetiolation. {ECO:0000269\|PubMed:14668869, ECO:0000269\|PubMed:16565297, ECO:0000269\|PubMed:16891401}.

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G02340(A), AT2G46790(A)

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q8L5W8

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT2G46970

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY954840	0.0	AY954840.1 Arabidopsis thaliana hypothetical protein (At2g46970) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_182220.2	0.0	phytochrome interacting factor 3-like 1
Swissprot	Q8L5W8	0.0	PIL1_ARATH; Transcription factor PIL1
TrEMBL	A0A178VNL3	0.0	A0A178VNL3_ARATH; PIL1
STRING	AT2G46970.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM13937	17	25
Representative plant	OGRP258	16	128

Link Out ? help Back to Top
Phytozome	AT2G46970.1
Entrez Gene	819311
iHOP	AT2G46970
wikigenes	AT2G46970

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Makino S,Matsushika A,Kojima M,Yamashino T,Mizuno T The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants. Plant Cell Physiol., 2002. 43(1): p. 58-69 [PMID:11828023] Matsushika A,Makino S,Kojima M,Yamashino T,Mizuno T The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: II. Characterization with CCA1-overexpressing plants. Plant Cell Physiol., 2002. 43(1): p. 118-22 [PMID:11828029] Fowler S,Thomashow MF Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. Plant Cell, 2002. 14(8): p. 1675-90 [PMID:12172015] Xiao YL,Malik M,Whitelaw CA,Town CD Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis. Plant Physiol., 2002. 130(4): p. 2118-28 [PMID:12481096] Heim MA, et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol., 2003. 20(5): p. 735-47 [PMID:12679534] Yamashino T, et al. A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant Cell Physiol., 2003. 44(6): p. 619-29 [PMID:12826627] Toledo-Ortiz G,Huq E,Quail PH The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 2003. 15(8): p. 1749-70 [PMID:12897250] Bailey PC, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell, 2003. 15(11): p. 2497-502 [PMID:14600211] Ito S, et al. Characterization of the APRR9 pseudo-response regulator belonging to the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant Cell Physiol., 2003. 44(11): p. 1237-45 [PMID:14634162] Devlin PF,Yanovsky MJ,Kay SA A genomic analysis of the shade avoidance response in Arabidopsis. Plant Physiol., 2003. 133(4): p. 1617-29 [PMID:14645734] Salter MG,Franklin KA,Whitelam GC Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature, 2003. 426(6967): p. 680-3 [PMID:14668869] Tepperman JM, et al. Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J., 2004. 38(5): p. 725-39 [PMID:15144375] Sessa G, et al. A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis. Genes Dev., 2005. 19(23): p. 2811-5 [PMID:16322556] Roig-Villanova I,Bou J,Sorin C,Devlin PF,Martínez-García JF Identification of primary target genes of phytochrome signaling. Early transcriptional control during shade avoidance responses in Arabidopsis. Plant Physiol., 2006. 141(1): p. 85-96 [PMID:16565297] Khanna R, et al. Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation. Plant Cell, 2006. 18(9): p. 2157-71 [PMID:16891401] Franklin KA,Whitelam GC Light-quality regulation of freezing tolerance in Arabidopsis thaliana. Nat. Genet., 2007. 39(11): p. 1410-3 [PMID:17965713] Hwang YS,Quail PH Phytochrome-regulated PIL1 derepression is developmentally modulated. Plant Cell Physiol., 2008. 49(4): p. 501-11 [PMID:18296722] Davi Transcriptional factor interaction: a central step in DELLA function. Curr. Opin. Genet. Dev., 2008. 18(4): p. 295-303 [PMID:18590820] Rehrauer H, et al. AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol., 2010. 152(2): p. 487-99 [PMID:20032078] 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] Yang R, et al. Assembly of synthetic locked phycocyanobilin derivatives with phytochrome in vitro and in vivo in Ceratodon purpureus and Arabidopsis. Plant Cell, 2012. 24(5): p. 1936-51 [PMID:22582099] Wang H, et al. CONSTANS-LIKE 7 regulates branching and shade avoidance response in Arabidopsis. J. Exp. Bot., 2013. 64(4): p. 1017-24 [PMID:23314820] Choi H, et al. The homeodomain-leucine zipper ATHB23, a phytochrome B-interacting protein, is important for phytochrome B-mediated red light signaling. Physiol Plant, 2014. 150(2): p. 308-20 [PMID:23964902] Li L, et al. PIL1 participates in a negative feedback loop that regulates its own gene expression in response to shade. Mol Plant, 2014. 7(10): p. 1582-5 [PMID:24895419] Luo Q, et al. COP1 and phyB Physically Interact with PIL1 to Regulate Its Stability and Photomorphogenic Development in Arabidopsis. Plant Cell, 2014. 26(6): p. 2441-2456 [PMID:24951480] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Qiu Y, et al. HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis. Plant Cell, 2015. 27(5): p. 1409-27 [PMID:25944101] 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]