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

Neem_3898_f_3

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

FAR1

Protein Properties

Length: 620aa MW: 70316.6 Da PI: 6.5801

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_3898_f_3	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	86.2	5.1e-27	90	192	1	91
FAR1 1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwevtklele 84 +fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+ +e++ +r+ +t+Cka+++vk++ dgkw+++++++e Neem_3898_f_3 90 SFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSynrprarqskqdQENATGRRSCAKTDCKASMHVKRRPDGKWVIHSFVKE 185 5****************************************9999999887655555669999*********************** PP FAR1 85 HnHelap 91 HnHel p Neem_3898_f_3 186 HNHELLP 192 **975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	7.1E-25	90	192	IPR004330	FAR1 DNA binding domain
PROSITE profile	PS50966	9.26	341	377	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	1.7E-5	351	374	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	3.2E-7	352	379	IPR006564	Zinc finger, PMZ-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009585	Biological Process	red, far-red light phototransduction
GO:0010218	Biological Process	response to far red light
GO:0042753	Biological Process	positive regulation of circadian rhythm
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 620 aa Download sequence Send to blast
MDIDLRLPSG EQAKEEEEQN GIDNMLDGEE KLALHNGDVE TGNIAVVDEV RAEDGGGVNS 60 PAEDMVVFKE DTNLEPLSGM EFESHGEAYS FYQEYARSMG FNTAIQNSRR SKTSREFIDA 120 KFACSRYGTK REYDKSYNRP RARQSKQDQE NATGRRSCAK TDCKASMHVK RRPDGKWVIH 180 SFVKEHNHEL LPAQAVSEQT RKMYAAMARQ FAEYKSVVGL KNDPKNPFDK GRNLALELGD 240 AKILLDFFTQ MQNMNANFFY AVDLDRYEEE AKADSDTWNK QPALKSPSPF EKSVSAIYTH 300 AVFKKFQVEV LGAVACHPKQ ESQNEANVMF RVQDFEKNQD FIVMWNQMKS EVFCVCRLFE 360 YKGYLCRHAL IVLQIRGLSA IPSQYILKRW TRDAKSRQLL GEESDQIQSR VQRYNDLCQR 420 AMKLSEEGSL SQESYGVALR ALDEALANCS SVNTSNKSLV EAVTSPTHGL ICIEEDNQSR 480 SMSKTNKRKN PTKKRKVNSE QEVMTVGAQD SLQQMEKLNS RAVTSLDGYY GTQQSVQGMV 540 QLNLMAPTRD NYYSNQQTIQ GLGQLNSIAP SHDGYYSAQQ GMHGLGQMDF FRTPTSFTYG 600 IRDDPNVRTA QLQDDASRHA

Sequence ? help Back to Top

Protein Sequence Length: 620 aa Download sequence Send to blast

MDIDLRLPSG EQAKEEEEQN GIDNMLDGEE KLALHNGDVE TGNIAVVDEV RAEDGGGVNS  60
PAEDMVVFKE DTNLEPLSGM EFESHGEAYS FYQEYARSMG FNTAIQNSRR SKTSREFIDA  120
KFACSRYGTK REYDKSYNRP RARQSKQDQE NATGRRSCAK TDCKASMHVK RRPDGKWVIH  180
SFVKEHNHEL LPAQAVSEQT RKMYAAMARQ FAEYKSVVGL KNDPKNPFDK GRNLALELGD  240
AKILLDFFTQ MQNMNANFFY AVDLDRYEEE AKADSDTWNK QPALKSPSPF EKSVSAIYTH  300
AVFKKFQVEV LGAVACHPKQ ESQNEANVMF RVQDFEKNQD FIVMWNQMKS EVFCVCRLFE  360
YKGYLCRHAL IVLQIRGLSA IPSQYILKRW TRDAKSRQLL GEESDQIQSR VQRYNDLCQR  420
AMKLSEEGSL SQESYGVALR ALDEALANCS SVNTSNKSLV EAVTSPTHGL ICIEEDNQSR  480
SMSKTNKRKN PTKKRKVNSE QEVMTVGAQD SLQQMEKLNS RAVTSLDGYY GTQQSVQGMV  540
QLNLMAPTRD NYYSNQQTIQ GLGQLNSIAP SHDGYYSAQQ GMHGLGQMDF FRTPTSFTYG  600
IRDDPNVRTA QLQDDASRHA

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'. Activates the expression of FHY1 and FHL involved in light responses. When associated with PHYA, protects it from being recognized and degraded by the COP1/SPA complex. Positive regulator of chlorophyll biosynthesis via the activation of HEMB1 gene expression. {ECO:0000269\|PubMed:11889039, ECO:0000269\|PubMed:12753585, ECO:0000269\|PubMed:17012604, ECO:0000269\|PubMed:18033885, ECO:0000269\|PubMed:18715961, ECO:0000269\|PubMed:22634759}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00078	ChIP-seq	Transfer from AT3G22170	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated after exposure to far-red light. Subject to a negative feedback regulation by PHYA signaling. Up-regulated by white light. {ECO:0000269\|PubMed:11889039, ECO:0000269\|PubMed:18033885, ECO:0000269\|PubMed:22634759}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006481370.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_024037340.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3
Refseq	XP_024037341.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3
Refseq	XP_024037342.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3
Refseq	XP_024037343.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3
Refseq	XP_024955384.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_024955385.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_024955386.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_024955387.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Swissprot	Q9LIE5	1e-165	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	A0A3N6QE62	0.0	A0A3N6QE62_BRACR; Uncharacterized protein
STRING	XP_006481370.1	0.0	(Citrus sinensis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM118	26	253

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G22170.2	1e-165	far-red elongated hypocotyls 3

Publications ? help Back to Top
Chang N,Gao Y,Zhao L,Liu X,Gao H Arabidopsis FHY3/CPD45 regulates far-red light signaling and chloroplast division in parallel. Sci Rep, 2015. 5: p. 9612 [PMID:25872642] Wang C, et al. SCAB3 Is Required for Reorganization of Actin Filaments during Light Quality Changes. J Genet Genomics, 2015. 42(4): p. 161-8 [PMID:25953354] Wang W, et al. A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis. J Integr Plant Biol, 2016. 58(1): p. 91-103 [PMID:25989254] Ma L, et al. Arabidopsis FHY3 and FAR1 Regulate Light-Induced myo-Inositol Biosynthesis and Oxidative Stress Responses by Transcriptional Activation of MIPS1. Mol Plant, 2016. 9(4): p. 541-57 [PMID:26714049] Siddiqui H,Khan S,Rhodes BM,Devlin PF FHY3 and FAR1 Act Downstream of Light Stable Phytochromes. Front Plant Sci, 2016. 7: p. 175 [PMID:26941752] Li D, et al. FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(33): p. 9375-80 [PMID:27469166] Liu L,Li B,Liu X FAR-RED ELONGATED HYPOCOTYL3 promotes floral meristem determinacy in Arabidopsis. Plant Signal Behav, 2016. 11(10): p. e1238545 [PMID:27660915] Ma L,Xue N,Fu X,Zhang H,Li G Arabidopsis thaliana FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1) modulate starch synthesis in response to light and sugar. New Phytol., 2017. 213(4): p. 1682-1696 [PMID:27859295] Liu Y, et al. Light and Ethylene Coordinately Regulate the Phosphate Starvation Response through Transcriptional Regulation of PHOSPHATE STARVATION RESPONSE1. Plant Cell, 2017. 29(9): p. 2269-2284 [PMID:28842534] Joly-Lopez Z, et al. Abiotic Stress Phenotypes Are Associated with Conserved Genes Derived from Transposable Elements. Front Plant Sci, 2017. 8: p. 2027 [PMID:29250089]