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

Tp3g33420

Organism

Thellungiella parvula

Taxonomic ID

98039

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 484aa MW: 53270.9 Da PI: 6.5219

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp3g33420	genome	thellungiella	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	49.5	7.5e-16	293	339	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn Er+RRdriN+++ L+el+P + K +Ka++L +A+eY+ksLq Tp3g33420 293 VHNLSERKRRDRINERMKALQELIPRC-----NKSDKASMLDEAIEYMKSLQ 339 6***********************8.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	18.146	289	338	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.65E-16	292	343	No hit	No description
SuperFamily	SSF47459	9.16E-21	292	367	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.5E-13	293	339	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.5E-20	293	350	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	2.2E-17	295	344	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:0006783	Biological Process	heme biosynthetic process
GO:0009740	Biological Process	gibberellic acid mediated signaling pathway
GO:0009959	Biological Process	negative gravitropism
GO:0010100	Biological Process	negative regulation of photomorphogenesis
GO:0010161	Biological Process	red light signaling pathway
GO:0010187	Biological Process	negative regulation of seed germination
GO:0015995	Biological Process	chlorophyll biosynthetic process
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0010313	Molecular Function	phytochrome binding
GO:0042802	Molecular Function	identical protein binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 484 aa Download sequence Send to blast
MSHFVPDFDT DDDYVNVNTN SSSSNLPRKP IIGEDDDLME LLWHNGQVVL QNQRLNAKKQ 60 PSSSSVVKLH GEAALAPSLP QPLDHNLFIQ EDEMTSWLQC PLRDDDFCSD LLFSAAPTSE 120 RQTSYPVTVA RPPVPPSAGP PVPSSVRPPV PSSVRPPVPS SVRPPVPSSV RPPVPSSVRP 180 PVSSSVRPPE RNFMGTVVFG SNSAVAGGGA YSFGLNQKGK SVATASENPG ASSSVASRSE 240 IEPVNEQPET EKTIVDERKR KEREAIDETE CRSEEAKQGR GSTSTKRSRA AEVHNLSERK 300 RRDRINERMK ALQELIPRCN KSDKASMLDE AIEYMKSLQL QIQMMSMGCG MMPMMYSGMQ 360 QYMPHMAMGM GMGMEMGMNR PPPPPPFMPF PNMLASQRPL PAQTPMGGYP VHASDPPRVY 420 VPNQQFDPNS IQAQYPGYMD PYQQFRSLHS SQPPQFQNQA TSYPSSSRVS SSKEPEDQGN 480 QTTG

Sequence ? help Back to Top

Protein Sequence Length: 484 aa Download sequence Send to blast

MSHFVPDFDT DDDYVNVNTN SSSSNLPRKP IIGEDDDLME LLWHNGQVVL QNQRLNAKKQ  60
PSSSSVVKLH GEAALAPSLP QPLDHNLFIQ EDEMTSWLQC PLRDDDFCSD LLFSAAPTSE  120
RQTSYPVTVA RPPVPPSAGP PVPSSVRPPV PSSVRPPVPS SVRPPVPSSV RPPVPSSVRP  180
PVSSSVRPPE RNFMGTVVFG SNSAVAGGGA YSFGLNQKGK SVATASENPG ASSSVASRSE  240
IEPVNEQPET EKTIVDERKR KEREAIDETE CRSEEAKQGR GSTSTKRSRA AEVHNLSERK  300
RRDRINERMK ALQELIPRCN KSDKASMLDE AIEYMKSLQL QIQMMSMGCG MMPMMYSGMQ  360
QYMPHMAMGM GMGMEMGMNR PPPPPPFMPF PNMLASQRPL PAQTPMGGYP VHASDPPRVY  420
VPNQQFDPNS IQAQYPGYMD PYQQFRSLHS SQPPQFQNQA TSYPSSSRVS SSKEPEDQGN  480
QTTG

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	297	302	ERKRRD

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00074	ChIP-chip	Transfer from AT2G20180	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp3g33420

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	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF488560	3e-90	AF488560.2 Arabidopsis thaliana clone bHLH015 putative bHLH transcription factor mRNA, complete cds.
GenBank	AK228820	3e-90	AK228820.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL16-14-G11.
GenBank	BT029775	3e-90	BT029775.1 Arabidopsis thaliana At2g20180 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_022570928.1	0.0	LOW QUALITY PROTEIN: transcription factor PIF1-like
Swissprot	Q8GZM7	1e-177	PIF1_ARATH; Transcription factor PIF1
TrEMBL	A0A397YGV1	0.0	A0A397YGV1_BRACM; Uncharacterized protein
STRING	Bo7g003890.1	1e-179	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM7108	26	43

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G20180.1	1e-86	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]