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

XP_009788870.1

Organism

Nicotiana sylvestris

Taxonomic ID

4096

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana

Family

bHLH

Protein Properties

Length: 196aa MW: 21992.6 Da PI: 9.6015

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009788870.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	41.3	2.9e-13	2	42	10	55
HHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 10 rrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +rRRdriN+++ L+el+P + K +Ka++L +A+eY+ksLq XP_009788870.1 2 QRRRDRINEKMKALQELIPRC-----NKSDKASMLDEAIEYLKSLQ 42 8*****************8.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	15.237	1	41	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	7.9E-11	2	47	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.4E-10	2	42	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.25E-13	2	46	No hit	No description
Gene3D	G3DSA:4.10.280.10	3.7E-18	2	53	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	3.53E-17	2	70	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: 196 aa Download sequence Send to blast
MQRRRDRINE KMKALQELIP RCNKSDKASM LDEAIEYLKS LQMQVQMMSM GCSMVPMMYP 60 GVPQYMPMMG MGMRMGMGTG MGMNRPVVPY PSLMPGPAMQ NAAAVAQMTP RFPVPAYHLP 120 SVPVPDPSRI RAANQPDHPI MNSLVGHNTN QPRLPNLSDP YQQYYALHQA QVLPQNQRAE 180 QPSSRLEESP ANHQTG

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator. Regulates negatively chlorophyll biosynthesis and seed germination in the dark, and lightinduced degradation of PIF1 relieves this negative regulation to promote photomorphogenesis. Binds to the G-box motif (5'-CACGTG-3') found in many light-regulated promoters. Promotes the expression of SOM, and thus modulates responses to abscisic acid (ABA) and gibberellic acid (GA). {ECO:0000269\|PubMed:15448264, ECO:0000269\|PubMed:16359394, ECO:0000269\|PubMed:18487351, ECO:0000269\|PubMed:18539749, ECO:0000269\|PubMed:18591656}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by red (R) and far red (FR) light treatments in a phyB- and phyA-dependent manner. {ECO:0000269\|PubMed:15448264}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009788870.1	1e-140	PREDICTED: transcription factor PIF1-like
Swissprot	Q8GZM7	2e-38	PIF1_ARATH; Transcription factor PIF1
TrEMBL	A0A1U7XQX0	1e-139	A0A1U7XQX0_NICSY; transcription factor PIF1-like
STRING	XP_009788870.1	1e-140	(Nicotiana sylvestris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA4059	23	41

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G20180.1	6e-26	phytochrome interacting factor 3-like 5

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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] 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] Krzymuski M, et al. Phytochrome A antagonizes PHYTOCHROME INTERACTING FACTOR 1 to prevent over-activation of photomorphogenesis. Mol Plant, 2014. 7(9): p. 1415-1428 [PMID:25009301] 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] Zhu L, et al. CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1. Nat Commun, 2015. 6: p. 7245 [PMID:26037329] Bou-Torrent J, et al. Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors. Plant Physiol., 2015. 169(3): p. 1584-94 [PMID:26082398] 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] Zhu L, et al. A Negative Feedback Loop between PHYTOCHROME INTERACTING FACTORs and HECATE Proteins Fine-Tunes Photomorphogenesis in Arabidopsis. Plant Cell, 2016. 28(4): p. 855-74 [PMID:27073231] 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] Kim J, et al. PIF1-Interacting Transcription Factors and Their Binding Sequence Elements Determine the in Vivo Targeting Sites of PIF1. Plant Cell, 2016. 28(6): p. 1388-405 [PMID:27303023] 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] Zhu L,Xin R,Huq E A Protein-Based Genetic Screening Uncovers Mutants Involved in Phytochrome Signaling in Arabidopsis. Front Plant Sci, 2016. 7: p. 1086 [PMID:27499759] Gangl R,Tenhaken R Raffinose Family Oligosaccharides Act As Galactose Stores in Seeds and Are Required for Rapid Germination of Arabidopsis in the Dark. Front Plant Sci, 2016. 7: p. 1115 [PMID:27507985] Kim K, et al. PIF1 Regulates Plastid Development by Repressing Photosynthetic Genes in the Endodermis. Mol Plant, 2016. 9(10): p. 1415-1427 [PMID:27591813] Kim J, et al. Epidermal Phytochrome B Inhibits Hypocotyl Negative Gravitropism Non-Cell-Autonomously. Plant Cell, 2016. 28(11): p. 2770-2785 [PMID:27758895] Zhang D,Li Y,Zhang X,Zha P,Lin R The SWI2/SNF2 Chromatin-Remodeling ATPase BRAHMA Regulates Chlorophyll Biosynthesis in Arabidopsis. Mol Plant, 2017. 10(1): p. 155-167 [PMID:27865928] Xu X, et al. Reciprocal proteasome-mediated degradation of PIFs and HFR1 underlies photomorphogenic development in Arabidopsis. Development, 2017. 144(10): p. 1831-1840 [PMID:28420710] 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] Gu D, et al. Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark. Nucleic Acids Res., 2017. 45(12): p. 7137-7150 [PMID:28444370] 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] Li R, et al. Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1. Plant Physiol. Biochem., 2018. 123: p. 204-212 [PMID:29248678] Wu M, et al. PIL5 represses floral transition in Arabidopsis under long day conditions. Biochem. Biophys. Res. Commun., 2018. 499(3): p. 513-518 [PMID:29588173] Majee M, et al. KELCH F-BOX protein positively influences Arabidopsis seed germination by targeting PHYTOCHROME-INTERACTING FACTOR1. Proc. Natl. Acad. Sci. U.S.A., 2018. 115(17): p. E4120-E4129 [PMID:29632208]