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

Sopim07g043270.0.1

Organism

Solanum pimpinellifolium

Taxonomic ID

4084

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

FAR1

Protein Properties

Length: 850aa MW: 97472 Da PI: 6.7704

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sopim07g043270.0.1	genome	CSHL	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	85.3	9.8e-27	91	193	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk.............tekerrtraetrtgCkaklkvkkekdgkwevt 79 fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+ e++ +ra +t+Cka+++vk++ dgkw ++ Sopim07g043270.0.1 91 FYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYEKSanrprsrqgnkqdPENATGRRACAKTDCKASMHVKRRPDGKWIIH 181 9*************************************999999899999888776555556699******************** PP FAR1 80 kleleHnHelap 91 ++e+eHnHel p Sopim07g043270.0.1 182 RFEKEHNHELLP 193 *******975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	1.2E-24	91	193	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	2.4E-27	291	383	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.569	571	607	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	2.4E-4	579	604	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	5.4E-6	582	609	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: 850 aa Download sequence Send to blast
MDIDLRLPSQ DHDKEEEEEE QNGIINMLDN EEKIHGDDGM HGMLVIEEKM HAEDRGDMNT 60 PVGTMIDFKE DVNLEPLAGM EFESHGEAYA FYQEYARSMG FNTAIQNSRR SKTSREFIDA 120 KFACSRYGTK REYEKSANRP RSRQGNKQDP ENATGRRACA KTDCKASMHV KRRPDGKWII 180 HRFEKEHNHE LLPAQAVSEQ TRRMYAAMAR QFAEYKNVVG LKSDTKVLFD KGRNSAIEGG 240 DISVLLEFFI QMQNLNSNFF YAVDVGEDQR VKNLFWVDAK ARHDYVNFSD VVSFDTTYVR 300 NKYKMPLALF VGVNQHFQFI LLGCALVSEE SASTFSWVMR TWLKAMGGQA PKTVITDHDL 360 VLKSVISEAL PLSLHYFCLW HVLGKVSDTL NHVIKQNEKF MPKFEKCLNR SWTDEEFEKR 420 WRKLVDKFDL REVELVHSLY EDRVKWAPTF IRDVVLAGMS TVQRSESVNS FFDKYVHKKT 480 TIQEFVKQYE SILQDRYEEE AKADSDTWNK QPALRSPSPF EKHLAGLYTH AVFKKFQSEV 540 VGATACGPKR EKQDEIVLTY RVQDFEKTQE FIVTLDEMKS EISCICHLFE YKGYLCRHAL 600 IVLQICAVSS IPPQYILKRW TKDAKSKYSM TDGSEDVQSR FQRYNELCHR AMKLSEEGSL 660 SQESYSFALR ALDDAFGSCV TFNNSNKNML EAGTSSASGL LCIEDDNQSR SMSKTNKKKN 720 NFTKKRKVNS EPDVMAVGAA DSLQQMDKLN SRPVTLDGYF GPQQSVQGMV QLNLMAPTRD 780 NYYANQQTIQ GLGQLNSIAP THDGYYGAQP TMHGLGQMDF FRSPSFSYGI RDEPTVRSSQ 840 LHDDASRHP*

Sequence ? help Back to Top

Protein Sequence Length: 850 aa Download sequence Send to blast

MDIDLRLPSQ DHDKEEEEEE QNGIINMLDN EEKIHGDDGM HGMLVIEEKM HAEDRGDMNT  60
PVGTMIDFKE DVNLEPLAGM EFESHGEAYA FYQEYARSMG FNTAIQNSRR SKTSREFIDA  120
KFACSRYGTK REYEKSANRP RSRQGNKQDP ENATGRRACA KTDCKASMHV KRRPDGKWII  180
HRFEKEHNHE LLPAQAVSEQ TRRMYAAMAR QFAEYKNVVG LKSDTKVLFD KGRNSAIEGG  240
DISVLLEFFI QMQNLNSNFF YAVDVGEDQR VKNLFWVDAK ARHDYVNFSD VVSFDTTYVR  300
NKYKMPLALF VGVNQHFQFI LLGCALVSEE SASTFSWVMR TWLKAMGGQA PKTVITDHDL  360
VLKSVISEAL PLSLHYFCLW HVLGKVSDTL NHVIKQNEKF MPKFEKCLNR SWTDEEFEKR  420
WRKLVDKFDL REVELVHSLY EDRVKWAPTF IRDVVLAGMS TVQRSESVNS FFDKYVHKKT  480
TIQEFVKQYE SILQDRYEEE AKADSDTWNK QPALRSPSPF EKHLAGLYTH AVFKKFQSEV  540
VGATACGPKR EKQDEIVLTY RVQDFEKTQE FIVTLDEMKS EISCICHLFE YKGYLCRHAL  600
IVLQICAVSS IPPQYILKRW TKDAKSKYSM TDGSEDVQSR FQRYNELCHR AMKLSEEGSL  660
SQESYSFALR ALDDAFGSCV TFNNSNKNML EAGTSSASGL LCIEDDNQSR SMSKTNKKKN  720
NFTKKRKVNS EPDVMAVGAA DSLQQMDKLN SRPVTLDGYF GPQQSVQGMV QLNLMAPTRD  780
NYYANQQTIQ GLGQLNSIAP THDGYYGAQP TMHGLGQMDF FRSPSFSYGI RDEPTVRSSQ  840
LHDDASRHP*

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT013715	0.0	BT013715.1 Lycopersicon esculentum clone 132560F, mRNA sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004243646.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_019070365.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_019070366.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Swissprot	Q9LIE5	0.0	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	A0A3Q7H991	0.0	A0A3Q7H991_SOLLC; Uncharacterized protein
STRING	Solyc07g043270.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA496	21	103

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G22170.2	0.0	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]