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

676740286

Organism

Sisymbrium irio

Taxonomic ID

3730

Taxonomic Lineage

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

Family

FAR1

Protein Properties

Length: 865aa MW: 98831.1 Da PI: 6.8368

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
676740286	genome	VEGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	80.4	3.2e-25	100	203	1	91
FAR1 1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk.............tekerrtraetrtgCkaklkvkkekdgkwevtkleleHnH 87 +fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e +k+ +++ +r+ +t+Cka+++vk++ dgkw++++++ +HnH 676740286 100 SFYQEYSRAIGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDKTfnrprarqskqepENNMAGRRTCAKTDCKASMHVKRRPDGKWVIHSFVRDHNH 199 5******************************************99999887655544444599999**************************** PP FAR1 88 elap 91 el p 676740286 200 ELLP 203 *975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	4.2E-23	100	203	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	8.5E-26	301	392	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.137	581	617	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	1.3E-6	592	619	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: 865 aa Download sequence Send to blast
VMDIDLRLHS GDLCKQGDEE SRGLDNVSHN EHKLQAAASA GGGEEDLDIG KIEDVTVEVH 60 TEDDSAGMAV PTGELVEYTE GMNLEPLNGM EFESHGEAYS FYQEYSRAIG FNTAIQNSRR 120 SKTTREFIDA KFACSRYGTK REYDKTFNRP RARQSKQEPE NNMAGRRTCA KTDCKASMHV 180 KRRPDGKWVI HSFVRDHNHE LLPAQAVSEQ TRKIYAAMAK QFAEYKTVIS LKTDSKSSFE 240 KGRSLSVETG DFKVLLDFVS RMQILNSNFF YAVDLGDDQR VKNVFWVDAK SRHNYVSFCD 300 VVSLDTTYVR NKYKMPLAVF VGVNQHYQYM VLGCALLSDE SAATFSWLME TWLRAMGGQA 360 PKVLITEQDV VMNSIVPEVF PNTQHCLFLW HVLIKVSEHL GQVAKQHENF TAKFEKCIYK 420 SWKEEDFARR WWKILARFGL KDDHWMQSLY EDRRKWAPTY MTDVLLAGMS TSQRADSINA 480 FFDKYLHRKT SVQEFVKLYD TILQDRCEEE AKADSETWNK PPAMKSPSPF EKSVSEVYTP 540 AVFKKFQIEV LGAIACSPRE ENRDATCSTF RVQDFENNQD FVVTWNQAKA EVSCICRLFE 600 FKGYLCRHTL NVLQCCHLSS IPSQYILKRW TKDAKSRHFS GEPQQLQTRL QRYNDLCQRA 660 LKLAEDASIS QESYNIAFLA IEESLGNCAG VNTSGRSLPD VVTSPTQGLI SVEEDNQSRS 720 AGKTSKKKNP TKKRKSYDPD YGLQVNSEQD VMPVAAPESL QQMDKLSPRT VGIESYYGTQ 780 QSVQNMVQLN LMAPTRDSFY GNQQTIQGLR QLNSIAPSYD SYYTAQQGIH GQGVDFFRPP 840 NFPYDIRDDP NVRTTQLHED ASRHT

Sequence ? help Back to Top

Protein Sequence Length: 865 aa Download sequence Send to blast

VMDIDLRLHS GDLCKQGDEE SRGLDNVSHN EHKLQAAASA GGGEEDLDIG KIEDVTVEVH  60
TEDDSAGMAV PTGELVEYTE GMNLEPLNGM EFESHGEAYS FYQEYSRAIG FNTAIQNSRR  120
SKTTREFIDA KFACSRYGTK REYDKTFNRP RARQSKQEPE NNMAGRRTCA KTDCKASMHV  180
KRRPDGKWVI HSFVRDHNHE LLPAQAVSEQ TRKIYAAMAK QFAEYKTVIS LKTDSKSSFE  240
KGRSLSVETG DFKVLLDFVS RMQILNSNFF YAVDLGDDQR VKNVFWVDAK SRHNYVSFCD  300
VVSLDTTYVR NKYKMPLAVF VGVNQHYQYM VLGCALLSDE SAATFSWLME TWLRAMGGQA  360
PKVLITEQDV VMNSIVPEVF PNTQHCLFLW HVLIKVSEHL GQVAKQHENF TAKFEKCIYK  420
SWKEEDFARR WWKILARFGL KDDHWMQSLY EDRRKWAPTY MTDVLLAGMS TSQRADSINA  480
FFDKYLHRKT SVQEFVKLYD TILQDRCEEE AKADSETWNK PPAMKSPSPF EKSVSEVYTP  540
AVFKKFQIEV LGAIACSPRE ENRDATCSTF RVQDFENNQD FVVTWNQAKA EVSCICRLFE  600
FKGYLCRHTL NVLQCCHLSS IPSQYILKRW TKDAKSRHFS GEPQQLQTRL QRYNDLCQRA  660
LKLAEDASIS QESYNIAFLA IEESLGNCAG VNTSGRSLPD VVTSPTQGLI SVEEDNQSRS  720
AGKTSKKKNP TKKRKSYDPD YGLQVNSEQD VMPVAAPESL QQMDKLSPRT VGIESYYGTQ  780
QSVQNMVQLN LMAPTRDSFY GNQQTIQGLR QLNSIAPSYD SYYTAQQGIH GQGVDFFRPP  840
NFPYDIRDDP NVRTTQLHED ASRHT

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	676740286

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]