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

Carubv10004178m

Organism

Capsella rubella

Taxonomic ID

81985

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: 786aa MW: 90772 Da PI: 6.4401

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10004178m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	89.9	3.5e-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 Carubv10004178m 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	7.8E-26	66	153	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	8.6E-26	274	367	IPR018289	MULE transposase domain
PROSITE profile	PS50966	8.988	554	590	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	2.2E-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: 786 aa Download sequence Send to blast
MDLQENQVSD AGDECMVGIM VESNSNRDVG IVDDLKAGGD LGFSGVLDLE PRNGIDFESN 60 DAAYLFYQEY AKSMGFTTSI KNSRRSKKTK EFIDAKFACS RYGVTPESES GSSSRRSSVK 120 KTDCKASMHV KRRADGKWII HEFIKDHNHE LLPALAYHFR IQRNVKLAEK NNIDILHAVS 180 ERTRKMYVEM SRQSGGYKNI GPLLQNDDNN 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 PRKEKEDENM 540 ETFRVQDCEK DDYFLVTWSK SKSELCCFCR MFEYKGFLCR HALMILQMCG FASIPPRYIL 600 KRWTKDAKSG VMAGEGADQI QTRVQRYNDL CSRAIELSEE GCVSEENYSI VLRTLVETLK 660 NCVDLNNGQQ EADQMLESQQ SLQPMETMSS EGMSMNGYYG PQQNVQGLLN LMEPPHEGYY 720 VNQRTIQGLG QLNSIAPVQD SFFTNQQAMP GLGQMDFRPP PNFTYSLQEE HLRSAQLPGS 780 SSRQL*

Sequence ? help Back to Top

Protein Sequence Length: 786 aa Download sequence Send to blast

MDLQENQVSD AGDECMVGIM VESNSNRDVG IVDDLKAGGD LGFSGVLDLE PRNGIDFESN  60
DAAYLFYQEY AKSMGFTTSI KNSRRSKKTK EFIDAKFACS RYGVTPESES GSSSRRSSVK  120
KTDCKASMHV KRRADGKWII HEFIKDHNHE LLPALAYHFR IQRNVKLAEK NNIDILHAVS  180
ERTRKMYVEM SRQSGGYKNI GPLLQNDDNN 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 PRKEKEDENM  540
ETFRVQDCEK DDYFLVTWSK SKSELCCFCR MFEYKGFLCR HALMILQMCG FASIPPRYIL  600
KRWTKDAKSG VMAGEGADQI QTRVQRYNDL CSRAIELSEE GCVSEENYSI VLRTLVETLK  660
NCVDLNNGQQ EADQMLESQQ SLQPMETMSS EGMSMNGYYG PQQNVQGLLN LMEPPHEGYY  720
VNQRTIQGLG QLNSIAPVQD SFFTNQQAMP GLGQMDFRPP PNFTYSLQEE HLRSAQLPGS  780
SSRQL*

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	Carubv10004178m

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	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.
GenBank	CP002687	0.0	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

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	Carubv10004178m

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]