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

XP_009145425.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

FAR1

Protein Properties

Length: 840aa MW: 96568.5 Da PI: 7.1622

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009145425.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	79.6	5.8e-25	83	186	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk..............tekerrtraetrtgCkaklkvkkekdgkwevtkle 82 fY+eY++++GF++ +++s++sk+++e+++++f Cs++g+++e +k+ +++ + +r+ +t+Cka+++vk++ dgkw++++++ XP_009145425.1 83 FYQEYSRTIGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKSfnrprarqskqdhpENNMSGRRTCAKTDCKASMHVKRKPDGKWVIHSFV 177 ******************************************9999998887766666669999********************* PP FAR1 83 leHnHelap 91 +HnHel p XP_009145425.1 178 RDHNHELLP 186 ****975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	7.3E-23	83	186	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	6.3E-26	284	375	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.124	564	600	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	2.9E-6	575	602	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: 840 aa Download sequence Send to blast
MDIDLRLHSG DLCKEGDDEE HRGLDNEDID ISKIEDDVTV EPHTDNNGIT LPEHNTQQQQ 60 QQGVNLEPLN GMEFNSHGEA YTFYQEYSRT IGFNTAIQNS RRSKTTREFI DAKFACSRYG 120 TKREYDKSFN RPRARQSKQD HPENNMSGRR TCAKTDCKAS MHVKRKPDGK WVIHSFVRDH 180 NHELLPAQAV SEQTRKIYAA MAKQFAEYKT VISLKSESKT SFEKGRSLSV ETGDFKLLLE 240 FLSRMQILNS NFFYAVDLGD DQRVKNVFWV DAKSRVNYGS FCDVVSLDTT YVRNKYKMPL 300 AIFVGVNQHY QYMVLGCALL SDESAATFSW LMETWLRAMG GQAPKVLITE QDPVLNSIVP 360 EVFPNTQHCL FLWHVLIKVS ENLGQVAKQH ENFTAKFEKC IYKSWKEEDF ARRWWKILAR 420 FGLKDDQWMQ SLYEDRRKWA PTYMTDVLLA GMSTSLRADS VNAFFDKYLH KKTSVQEFVK 480 LYDTILQDRF EEEAKADSET WNKPPTMKSP SPFEKSVSDV YTPAVFKKFQ IEVLGAIACS 540 PREENRDATC STFRVQDFEN NQDFVVTWSQ AKAEVSCMCR LFEYKGYLCR HTLNVLQCCH 600 LSSIPSQYIL KRWTKDARSQ HFPGEPQQLQ TRLQRYNDLC QRALKLSEEA SISQESYNIA 660 FLAIEEALGN CAGVNTSGRS LPDVVASPTQ GLISVEEDNQ SRSAVKTTSK KKNPTKKRKV 720 NSEQEVIPVT APESLQQMDK LSPRTVGLES YYGTQQSVQN LVQLNLMAPN RDNFYGNQQT 780 IQGLRQLNSI APSYDSYYTA QQGIHGQGVD FFRPPNFTYD IRDDPNVRTT QLHEDASRHT

Sequence ? help Back to Top

Protein Sequence Length: 840 aa Download sequence Send to blast

MDIDLRLHSG DLCKEGDDEE HRGLDNEDID ISKIEDDVTV EPHTDNNGIT LPEHNTQQQQ  60
QQGVNLEPLN GMEFNSHGEA YTFYQEYSRT IGFNTAIQNS RRSKTTREFI DAKFACSRYG  120
TKREYDKSFN RPRARQSKQD HPENNMSGRR TCAKTDCKAS MHVKRKPDGK WVIHSFVRDH  180
NHELLPAQAV SEQTRKIYAA MAKQFAEYKT VISLKSESKT SFEKGRSLSV ETGDFKLLLE  240
FLSRMQILNS NFFYAVDLGD DQRVKNVFWV DAKSRVNYGS FCDVVSLDTT YVRNKYKMPL  300
AIFVGVNQHY QYMVLGCALL SDESAATFSW LMETWLRAMG GQAPKVLITE QDPVLNSIVP  360
EVFPNTQHCL FLWHVLIKVS ENLGQVAKQH ENFTAKFEKC IYKSWKEEDF ARRWWKILAR  420
FGLKDDQWMQ SLYEDRRKWA PTYMTDVLLA GMSTSLRADS VNAFFDKYLH KKTSVQEFVK  480
LYDTILQDRF EEEAKADSET WNKPPTMKSP SPFEKSVSDV YTPAVFKKFQ IEVLGAIACS  540
PREENRDATC STFRVQDFEN NQDFVVTWSQ AKAEVSCMCR LFEYKGYLCR HTLNVLQCCH  600
LSSIPSQYIL KRWTKDARSQ HFPGEPQQLQ TRLQRYNDLC QRALKLSEEA SISQESYNIA  660
FLAIEEALGN CAGVNTSGRS LPDVVASPTQ GLISVEEDNQ SRSAVKTTSK KKNPTKKRKV  720
NSEQEVIPVT APESLQQMDK LSPRTVGLES YYGTQQSVQN LVQLNLMAPN RDNFYGNQQT  780
IQGLRQLNSI APSYDSYYTA QQGIHGQGVD FFRPPNFTYD IRDDPNVRTT QLHEDASRHT

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	XP_009145425.1

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009145425.1	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_009145426.1	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_009145427.1	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Swissprot	Q9LIE5	0.0	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	M4ERA7	0.0	M4ERA7_BRARP; Uncharacterized protein
STRING	Bra031330.1-P	0.0	(Brassica rapa)

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]