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

Thecc1EG013043t10

Common Name

TCM_013043

Organism

Theobroma cacao

Taxonomic ID

3641

Taxonomic Lineage

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

Family

FAR1

Protein Properties

Length: 764aa MW: 88028.6 Da PI: 8.9354

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG013043t10	genome	CGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	85.6	7.4e-27	11	113	1	91
FAR1 1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwevtk 80 +fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+ +++ +r+ ++t+Cka+++vk++ dgkw+v++ Thecc1EG013043t10 11 SFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSfnrprarqskqdPDNTTGRRSCSKTDCKASMHVKRRPDGKWVVHS 102 5*****************************************9999999987766554444558999******************* PP FAR1 81 leleHnHelap 91 +++eHnHel p Thecc1EG013043t10 103 FVKEHNHELLP 113 ******975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	1.2E-24	11	113	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	4.7E-29	211	303	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.545	491	527	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	5.3E-4	501	524	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	1.8E-7	502	529	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:0016021	Cellular Component	integral component of membrane
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: 764 aa Download sequence Send to blast
MEFESHGEAY SFYQEYARSM GFNTAIQNSR RSKTSREFID AKFACSRYGT KREYDKSFNR 60 PRARQSKQDP DNTTGRRSCS KTDCKASMHV KRRPDGKWVV HSFVKEHNHE LLPAQAVSEQ 120 TRRMYAAMAR QFAEYKNVVG LKNDPKNPFD KGRNLALEAG DVKILLEFFT HMQNINSNFF 180 YAIDLGEDQR LKSLFWVDAK SRHDYSYFCD VVSFDTTYVR NKYKMPLALF IGVNHHYQFM 240 PLGCALVSDD SAATFSWLMQ TWLKAMGGQS PRVIITDQDR IVKSVVAEIF PNTHHCFFLW 300 HVLGKVSENL GHVIKQHGNF MAKFEKCIYR SWTEEEFAKR WWKILDRFGL KDDEWMKSLY 360 EDRRKWVPTY IMDVLLAGMS MVQRSESVNS FFDKYVHKKT TVQEFLKQYE AILQDRYEEE 420 AKANSDSWSK LPTLKSPSPF EKSVAGLYTH TVFKKFQVEV VGAIACHPKP ENHDATSSFF 480 RVQDLEKNQD FIVTLNEMKS EVSCICRLYE YKGYLCRHAM VVLQINGHSA IPSQYILKRW 540 TKEAKSRHLM GDESEQVQSR VQRYNDLFQR AMKLIEEGSL SQESYYIAFR SLEEAFGNCL 600 SANTSNKSLA EAVTSPTQGM ICIEEDNQSR STSKTNKKKN PTKKRKGNSE QEVMTVPATD 660 GLQQMDKLSS RSVGLDGYFG AQTSVQGMLN LMAPRDNYYG NQQTIQGLGQ LNTIAASHDG 720 YYGPQQTMPG MGQMDFFRAP GFYIRDDTNV RAAQLHDDAS RHA*

Sequence ? help Back to Top

Protein Sequence Length: 764 aa Download sequence Send to blast

MEFESHGEAY SFYQEYARSM GFNTAIQNSR RSKTSREFID AKFACSRYGT KREYDKSFNR  60
PRARQSKQDP DNTTGRRSCS KTDCKASMHV KRRPDGKWVV HSFVKEHNHE LLPAQAVSEQ  120
TRRMYAAMAR QFAEYKNVVG LKNDPKNPFD KGRNLALEAG DVKILLEFFT HMQNINSNFF  180
YAIDLGEDQR LKSLFWVDAK SRHDYSYFCD VVSFDTTYVR NKYKMPLALF IGVNHHYQFM  240
PLGCALVSDD SAATFSWLMQ TWLKAMGGQS PRVIITDQDR IVKSVVAEIF PNTHHCFFLW  300
HVLGKVSENL GHVIKQHGNF MAKFEKCIYR SWTEEEFAKR WWKILDRFGL KDDEWMKSLY  360
EDRRKWVPTY IMDVLLAGMS MVQRSESVNS FFDKYVHKKT TVQEFLKQYE AILQDRYEEE  420
AKANSDSWSK LPTLKSPSPF EKSVAGLYTH TVFKKFQVEV VGAIACHPKP ENHDATSSFF  480
RVQDLEKNQD FIVTLNEMKS EVSCICRLYE YKGYLCRHAM VVLQINGHSA IPSQYILKRW  540
TKEAKSRHLM GDESEQVQSR VQRYNDLFQR AMKLIEEGSL SQESYYIAFR SLEEAFGNCL  600
SANTSNKSLA EAVTSPTQGM ICIEEDNQSR STSKTNKKKN PTKKRKGNSE QEVMTVPATD  660
GLQQMDKLSS RSVGLDGYFG AQTSVQGMLN LMAPRDNYYG NQQTIQGLGQ LNTIAASHDG  720
YYGPQQTMPG MGQMDFFRAP GFYIRDDTNV RAAQLHDDAS RHA*

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_017973539.1	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X2
Swissprot	Q9LIE5	0.0	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	A0A061FW45	0.0	A0A061FW45_THECC; Far-red elongated hypocotyls 3 isoform 10
STRING	EOY21471	0.0	(Theobroma cacao)

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	Thecc1EG013043t10
Entrez Gene	18604429

Publications ? help Back to Top
Motamayor JC, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol., 2013. 14(6): p. r53 [PMID:23731509] 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]