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

Tp3g19980

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

FAR1

Protein Properties

Length: 847aa MW: 97023.1 Da PI: 6.6254

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp3g19980	genome	thellungiella	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	81	2.1e-25	92	194	1	91
FAR1 1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwevtkleleHnHe 88 +fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e +k+ e+ +r+ +t+Cka+++vk++ dgkw++++++ eHnHe Tp3g19980 92 SFYQEYSRAIGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKSfnrprarqskqdPENMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVREHNHE 191 5*****************************************99999999877654444444499999**************************** PP FAR1 89 lap 91 l p Tp3g19980 192 LLP 194 975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	2.9E-23	92	194	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	1.8E-25	292	383	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.137	572	608	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	6.7E-7	583	610	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: 847 aa Download sequence Send to blast
MDIDLRLHSG DLCKEGDEDR GLDNVLQNEH KLHDDADEDI DIGKIEDVTV EVQTDDSAGM 60 GVTTGELVEY TEGVNLEPLN GMEFESHGEA YSFYQEYSRA IGFNTAIQNS RRSKTTREFI 120 DAKFACSRYG TKREYDKSFN RPRARQSKQD PENMAGRRTC AKTDCKASMH VKRRPDGKWV 180 IHSFVREHNH ELLPAQAVSE QTRKIYAAMA KQFAEYKTVI SLKSDSKSSY EKGRNLSVET 240 GDFKTLLDFL SRMQILNSNF FYAVDLGDDQ RVKNVFWVDA KSRHNYGIFC DVVSLDTTYV 300 RNKYKMPLAV FVGVNQHYQY MVLGCALLSD ESAATFSWLM ETWLKAMGGQ APKVLITEHD 360 VVMNSIVPEI FPNTQHCLFL WHILITVSEN LGQVAKQHEN FTAKFEKCIY KSWKEEDFAR 420 RWWKILARFG LKEDQWMQSL YEDRRKWAPT YMTDVLLAGM STAQRADSIN AFFDKYLHKK 480 TSVQEFVKLY DTILQDRCEE EAKADSETWN KQPAMKSPSP FEKSVSEVYT PAVFKKFQIE 540 VLGAIACSPR EENRDATCST FRVQDFENNE DFVVTWNQAK AEVSCICRLF EYKGYLCRHT 600 LNVLQCCHLS SIPSQYILKR WTKDAKSRHF SGDPPQLQTR LQRYNDLCQR ALKLNEDASC 660 SQESYSIAFL AIEEALGNCA GVNTSGRSLP DVVSSPTQGL ISVEEDNQSR SAGKTSKKKN 720 PTKKRKVNSE QEVMPVAAPE SLQQMDKLSP RTVGIESYYG TQQSVQNMVQ LNLMAPNRDN 780 FYGNQQTIQG LRQLNSIAPS YDSYYTAQQG IHGQGVDFFR PPNFPYDIRD DPNVRTTQLH 840 EDASRHS

Sequence ? help Back to Top

Protein Sequence Length: 847 aa Download sequence Send to blast

MDIDLRLHSG DLCKEGDEDR GLDNVLQNEH KLHDDADEDI DIGKIEDVTV EVQTDDSAGM  60
GVTTGELVEY TEGVNLEPLN GMEFESHGEA YSFYQEYSRA IGFNTAIQNS RRSKTTREFI  120
DAKFACSRYG TKREYDKSFN RPRARQSKQD PENMAGRRTC AKTDCKASMH VKRRPDGKWV  180
IHSFVREHNH ELLPAQAVSE QTRKIYAAMA KQFAEYKTVI SLKSDSKSSY EKGRNLSVET  240
GDFKTLLDFL SRMQILNSNF FYAVDLGDDQ RVKNVFWVDA KSRHNYGIFC DVVSLDTTYV  300
RNKYKMPLAV FVGVNQHYQY MVLGCALLSD ESAATFSWLM ETWLKAMGGQ APKVLITEHD  360
VVMNSIVPEI FPNTQHCLFL WHILITVSEN LGQVAKQHEN FTAKFEKCIY KSWKEEDFAR  420
RWWKILARFG LKEDQWMQSL YEDRRKWAPT YMTDVLLAGM STAQRADSIN AFFDKYLHKK  480
TSVQEFVKLY DTILQDRCEE EAKADSETWN KQPAMKSPSP FEKSVSEVYT PAVFKKFQIE  540
VLGAIACSPR EENRDATCST FRVQDFENNE DFVVTWNQAK AEVSCICRLF EYKGYLCRHT  600
LNVLQCCHLS SIPSQYILKR WTKDAKSRHF SGDPPQLQTR LQRYNDLCQR ALKLNEDASC  660
SQESYSIAFL AIEEALGNCA GVNTSGRSLP DVVSSPTQGL ISVEEDNQSR SAGKTSKKKN  720
PTKKRKVNSE QEVMPVAAPE SLQQMDKLSP RTVGIESYYG TQQSVQNMVQ LNLMAPNRDN  780
FYGNQQTIQG LRQLNSIAPS YDSYYTAQQG IHGQGVDFFR PPNFPYDIRD DPNVRTTQLH  840
EDASRHS

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp3g19980

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}.

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	AP001306	0.0	AP001306.1 Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone:MKA23.
GenBank	CP002686	0.0	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006406203.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_006406204.1	0.0	protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Swissprot	Q9LIE5	0.0	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	V4LYQ9	0.0	V4LYQ9_EUTSA; Uncharacterized protein
STRING	XP_006406203.1	0.0	(Eutrema salsugineum)

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	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]