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

Cagra.1850s0019.1.p

Organism

Capsella grandiflora

Taxonomic ID

264402

Taxonomic Lineage

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

Family

FAR1

Protein Properties

Length: 825aa MW: 95207 Da PI: 6.8937

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cagra.1850s0019.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	89.8	3.7e-28	66	153	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtkleleHnHelap 91 fY+eYAk++GF++++++s++sk+++e+++++f Cs++g + e+++ +++r++++++t+Cka+++vk++ dgkw ++++ ++HnHel p Cagra.1850s0019.1.p 66 FYQEYAKSMGFTTSIKNSRRSKKTKEFIDAKFACSRYGVTPESESG--SSSRRSSVKKTDCKASMHVKRRADGKWIIHEFIKDHNHELLP 153 9************************************9999888..8999999******************************975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	8.4E-26	66	153	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	9.2E-26	274	367	IPR018289	MULE transposase domain
PROSITE profile	PS50966	8.988	554	590	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	2.4E-7	554	589	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	3.1E-7	565	592	IPR006564	Zinc finger, PMZ-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010018	Biological Process	far-red light signaling pathway
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: 825 aa Download sequence Send to blast
MDLQENQVSD AGDECMVDIM VESNSNRDVG IVDDLKAGGD LGFSGVLDLE PRNGIDFESN 60 DAAYLFYQEY AKSMGFTTSI KNSRRSKKTK EFIDAKFACS RYGVTPESES GSSSRRSSVK 120 KTDCKASMHV KRRADGKWII HEFIKDHNHE LLPALAYHFR IQRNVKLAEK NNIDILHAVS 180 ERTRKMYVEM SRQSGGYKNI GPLLQNDGNN HVDKGRYLAL EEGDSQVLLE YFKRIKKENP 240 KFFYAIDLNE EQRLRNLFWV DAKSRDDYLS FSDVVSFDTT YVKFNDKLPL ALFIGVNHHS 300 QPMLLGCALV ADESNETFVW LIKTWLRAMG GRAPNVILTD QDKFLMAAVS ELLPNTRHCF 360 ALWHVLEKIP EYFSHVMKRH ENFLQKFNKC IFRSWTDDEF DMRWWKMVSQ FGLENDEWLL 420 WLHEHRQKWV PTFMSDVFLA GMSTSQRSES VNAFFDKYVH KKITLKEFLR QYGAILQNRY 480 EDESVADFDT CHKQPALKSP SPWEKQMATT YTHTIFKKFQ VEVLGVVACH PRKEKEDENT 540 ETFRVQDCEK DDYFLVTWSK SKSELCCFCR MFEYKGFLCR HALMILQMCG FASIPPRYIL 600 KRWTKDAKSG VMAGEGADQI QTRVQRYNDL CSRAIELSEE GCVSEENYNI VLRTLVETLK 660 NCVDLNNARN NIAESSCQLN NGAREEENQL MAVKATKKKT VIRKRKGQQE ADQMLESQQS 720 LQPMETMSSE GMSMNGYYGP QQNVQGLLNL MEPPHEGYYV NQRTIQGLGQ LNSIAPVQDS 780 FFTNQQAMPG LGQMDFRPPP NFTYNLQEEH LRSAQLPGSS SRQL*

Sequence ? help Back to Top

Protein Sequence Length: 825 aa Download sequence Send to blast

MDLQENQVSD AGDECMVDIM VESNSNRDVG IVDDLKAGGD LGFSGVLDLE PRNGIDFESN  60
DAAYLFYQEY AKSMGFTTSI KNSRRSKKTK EFIDAKFACS RYGVTPESES GSSSRRSSVK  120
KTDCKASMHV KRRADGKWII HEFIKDHNHE LLPALAYHFR IQRNVKLAEK NNIDILHAVS  180
ERTRKMYVEM SRQSGGYKNI GPLLQNDGNN HVDKGRYLAL EEGDSQVLLE YFKRIKKENP  240
KFFYAIDLNE EQRLRNLFWV DAKSRDDYLS FSDVVSFDTT YVKFNDKLPL ALFIGVNHHS  300
QPMLLGCALV ADESNETFVW LIKTWLRAMG GRAPNVILTD QDKFLMAAVS ELLPNTRHCF  360
ALWHVLEKIP EYFSHVMKRH ENFLQKFNKC IFRSWTDDEF DMRWWKMVSQ FGLENDEWLL  420
WLHEHRQKWV PTFMSDVFLA GMSTSQRSES VNAFFDKYVH KKITLKEFLR QYGAILQNRY  480
EDESVADFDT CHKQPALKSP SPWEKQMATT YTHTIFKKFQ VEVLGVVACH PRKEKEDENT  540
ETFRVQDCEK DDYFLVTWSK SKSELCCFCR MFEYKGFLCR HALMILQMCG FASIPPRYIL  600
KRWTKDAKSG VMAGEGADQI QTRVQRYNDL CSRAIELSEE GCVSEENYNI VLRTLVETLK  660
NCVDLNNARN NIAESSCQLN NGAREEENQL MAVKATKKKT VIRKRKGQQE ADQMLESQQS  720
LQPMETMSSE GMSMNGYYGP QQNVQGLLNL MEPPHEGYYV NQRTIQGLGQ LNSIAPVQDS  780
FFTNQQAMPG LGQMDFRPPP NFTYNLQEEH LRSAQLPGSS SRQL*

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. Positive regulator of chlorophyll biosynthesis via the activation of HEMB1 gene expression. {ECO:0000269\|PubMed:11889039, ECO:0000269\|PubMed:12753585, ECO:0000269\|PubMed:18033885, ECO:0000269\|PubMed:22634759}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00434	DAP	Transfer from AT4G15090	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Cagra.1850s0019.1.p

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. {ECO:0000269\|PubMed:18033885}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF159587	0.0	AF159587.1 Arabidopsis thaliana far-red impaired response protein (FAR1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006286331.2	0.0	protein FAR-RED IMPAIRED RESPONSE 1
Swissprot	Q9SWG3	0.0	FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBL	A0A178UYQ0	0.0	A0A178UYQ0_ARATH; FAR1
STRING	Cagra.1850s0019.1.p	0.0	(Capsella grandiflora)

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
AT4G15090.1	0.0	FAR1 family protein

Link Out ? help Back to Top
Phytozome	Cagra.1850s0019.1.p

Publications ? help Back to Top
Domergue F, et al. Three Arabidopsis fatty acyl-coenzyme A reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition. Plant Physiol., 2010. 153(4): p. 1539-54 [PMID:20571114] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] 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] 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]