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

Gorai.005G134200.10

Common Name

B456_005G134200

Organism

Gossypium raimondii

Taxonomic ID

29730

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

FAR1

Protein Properties

Length: 794aa MW: 90937 Da PI: 7.3994

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.005G134200.10	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	86	5.8e-27	84	186	1	91
FAR1 1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwev 78 +fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+ e++ +r+ ++t+Cka+++vk++ dgkw++ Gorai.005G134200.10 84 SFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSfnrprarqskqdPENATGRRSCSKTDCKASMHVKRRPDGKWVI 173 5*****************************************9999999988876655555559999***************** PP FAR1 79 tkleleHnHelap 91 +++++eHnHel p Gorai.005G134200.10 174 HSFVKEHNHELLP 186 ********975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	8.9E-25	84	186	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	4.1E-29	285	376	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.507	564	600	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	1.4E-7	575	602	IPR006564	Zinc finger, PMZ-type
Pfam	PF04434	7.7E-4	575	597	IPR007527	Zinc finger, SWIM-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: 794 aa Download sequence Send to blast
MDIDLRLPSG EQCKEDEDAN GIDNMLDGDE SLHNGMVQVV GEALRAEDGG EMHSSAVDMV 60 TFKEDTNLEP LSGMEFESHG EAYSFYQEYA RSMGFNTAIQ NSRRSKTSRE FIDAKFACSR 120 YGTKREYDKS FNRPRARQSK QDPENATGRR SCSKTDCKAS MHVKRRPDGK WVIHSFVKEH 180 NHELLPAQAV SEQTRRMYAA MARQFAEYKN VVGLKNDPKN PFDKGRNLAL EAADVKILLE 240 FFTHMQSINS NFFYAVDLGE DQRLKSLFWV DSKSRHDYSY FCDAVSFDTT YVTNKYKMPL 300 ALFIGVNHHY QCIPLGCALV SDESAATFSW LMQTWLKAMG GQSPRVLITD QDRTLKSVVA 360 EIFPNTLHCF FLWHVLGKVS ENLGHVIKQY GNLMEKFEKC IYRSWTDEEF GKRWWKILDR 420 FELKDDEWMK SLYEDRKKWV PTYIMNVLLA GMSTVQRAES VNSFFDKYVH KKTTVQDFLK 480 HYEAILQDRY EEEAKANSDS WSKVPALKSP SPFEKSVAGV YTHTLFKKFQ IEVVGAIACH 540 PKPENHDSTC SIFRVQDLEK NQDFIVTLNE MKAEVSCICR LYEYKGYLCR HAMVVLQING 600 RSAIPSQYIL KRWTKEAKSR HFMGEESEQV QSRAQRYNDL FQRGMKLIEE GSLSQESYYI 660 AFRSLEEAFG NCLSANTSNK SLAEAVASPT QGMICIEEDN QSRSTSKTNK KKNPTKKRKG 720 NSEQEVMAVA PTDGLQQMDK LSSRSVALDS YFGAQPSVQG MVQLNLMAPR DNYYGNQQTI 780 QGLVLSCFIT IMS*

Sequence ? help Back to Top

Protein Sequence Length: 794 aa Download sequence Send to blast

MDIDLRLPSG EQCKEDEDAN GIDNMLDGDE SLHNGMVQVV GEALRAEDGG EMHSSAVDMV  60
TFKEDTNLEP LSGMEFESHG EAYSFYQEYA RSMGFNTAIQ NSRRSKTSRE FIDAKFACSR  120
YGTKREYDKS FNRPRARQSK QDPENATGRR SCSKTDCKAS MHVKRRPDGK WVIHSFVKEH  180
NHELLPAQAV SEQTRRMYAA MARQFAEYKN VVGLKNDPKN PFDKGRNLAL EAADVKILLE  240
FFTHMQSINS NFFYAVDLGE DQRLKSLFWV DSKSRHDYSY FCDAVSFDTT YVTNKYKMPL  300
ALFIGVNHHY QCIPLGCALV SDESAATFSW LMQTWLKAMG GQSPRVLITD QDRTLKSVVA  360
EIFPNTLHCF FLWHVLGKVS ENLGHVIKQY GNLMEKFEKC IYRSWTDEEF GKRWWKILDR  420
FELKDDEWMK SLYEDRKKWV PTYIMNVLLA GMSTVQRAES VNSFFDKYVH KKTTVQDFLK  480
HYEAILQDRY EEEAKANSDS WSKVPALKSP SPFEKSVAGV YTHTLFKKFQ IEVVGAIACH  540
PKPENHDSTC SIFRVQDLEK NQDFIVTLNE MKAEVSCICR LYEYKGYLCR HAMVVLQING  600
RSAIPSQYIL KRWTKEAKSR HFMGEESEQV QSRAQRYNDL FQRGMKLIEE GSLSQESYYI  660
AFRSLEEAFG NCLSANTSNK SLAEAVASPT QGMICIEEDN QSRSTSKTNK KKNPTKKRKG  720
NSEQEVMAVA PTDGLQQMDK LSSRSVALDS YFGAQPSVQG MVQLNLMAPR DNYYGNQQTI  780
QGLVLSCFIT IMS*

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

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_012478555.1	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3
Swissprot	Q9LIE5	0.0	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	A0A0D2REF6	0.0	A0A0D2REF6_GOSRA; Uncharacterized protein
STRING	Gorai.005G134200.1	0.0	(Gossypium raimondii)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G22170.2	0.0	far-red elongated hypocotyls 3

Link Out ? help Back to Top
Phytozome	Gorai.005G134200.10

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] 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]