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

Thecc1EG013043t1

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: 844aa MW: 96662 Da PI: 7.3737

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG013043t1	genome	CGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	85.4	8.6e-27	89	191	1	91
FAR1 1 kfYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk............tekerrtraetrtgCkaklkvkkekdgkwevtkl 81 +fY+eYA+++GF++ +++s++sk+++e+++++f Cs++g+++e +k+ +++ +r+ ++t+Cka+++vk++ dgkw+v+++ Thecc1EG013043t1 89 SFYQEYARSMGFNTAIQNSRRSKTSREFIDAKFACSRYGTKREYDKSfnrprarqskqdPDNTTGRRSCSKTDCKASMHVKRRPDGKWVVHSF 181 5*****************************************9999999987766554444558999******************** PP FAR1 82 eleHnHelap 91 ++eHnHel p Thecc1EG013043t1 182 VKEHNHELLP 191 *****975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	1.4E-24	89	191	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	5.4E-29	289	381	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.545	569	605	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	5.9E-4	579	602	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	1.8E-7	580	607	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: 844 aa Download sequence Send to blast
MDIDLRLPSG EQCKEDEEAN GIDNILDGDE KLHNGVVEAG NIAHVGQDVR PEDGVEMNSS 60 AVDMVTFKED TNLEPLSGME FESHGEAYSF YQEYARSMGF NTAIQNSRRS KTSREFIDAK 120 FACSRYGTKR EYDKSFNRPR ARQSKQDPDN TTGRRSCSKT DCKASMHVKR RPDGKWVVHS 180 FVKEHNHELL PAQAVSEQTR RMYAAMARQF AEYKNVVGLK NDPKNPFDKG RNLALEAGDV 240 KILLEFFTHM QNINSNFFYA IDLGEDQRLK SLFWVDAKSR HDYSYFCDVV SFDTTYVRNK 300 YKMPLALFIG VNHHYQFMPL GCALVSDDSA ATFSWLMQTW LKAMGGQSPR VIITDQDRIV 360 KSVVAEIFPN THHCFFLWHV LGKVSENLGH VIKQHGNFMA KFEKCIYRSW TEEEFAKRWW 420 KILDRFGLKD DEWMKSLYED RRKWVPTYIM DVLLAGMSMV QRSESVNSFF DKYVHKKTTV 480 QEFLKQYEAI LQDRYEEEAK ANSDSWSKLP TLKSPSPFEK SVAGLYTHTV FKKFQVEVVG 540 AIACHPKPEN HDATSSFFRV QDLEKNQDFI VTLNEMKSEV SCICRLYEYK GYLCRHAMVV 600 LQINGHSAIP SQYILKRWTK EAKSRHLMGD ESEQVQSRVQ RYNDLFQRAM KLIEEGSLSQ 660 ESYYIAFRSL EEAFGNCLSA NTSNKSLAEA VTSPTQGMIC IEEDNQSRST SKTNKKKNPT 720 KKRKGNSEQE VMTVPATDGL QQMDKLSSRS VGLDGYFGAQ TSVQGMVQLN LMAPRDNYYG 780 NQQTIQGLGQ LNTIAASHDG YYGPQQTMPG MGQMDFFRAP GFYIRDDTNV RAAQLHDDAS 840 RHA*

Sequence ? help Back to Top

Protein Sequence Length: 844 aa Download sequence Send to blast

MDIDLRLPSG EQCKEDEEAN GIDNILDGDE KLHNGVVEAG NIAHVGQDVR PEDGVEMNSS  60
AVDMVTFKED TNLEPLSGME FESHGEAYSF YQEYARSMGF NTAIQNSRRS KTSREFIDAK  120
FACSRYGTKR EYDKSFNRPR ARQSKQDPDN TTGRRSCSKT DCKASMHVKR RPDGKWVVHS  180
FVKEHNHELL PAQAVSEQTR RMYAAMARQF AEYKNVVGLK NDPKNPFDKG RNLALEAGDV  240
KILLEFFTHM QNINSNFFYA IDLGEDQRLK SLFWVDAKSR HDYSYFCDVV SFDTTYVRNK  300
YKMPLALFIG VNHHYQFMPL GCALVSDDSA ATFSWLMQTW LKAMGGQSPR VIITDQDRIV  360
KSVVAEIFPN THHCFFLWHV LGKVSENLGH VIKQHGNFMA KFEKCIYRSW TEEEFAKRWW  420
KILDRFGLKD DEWMKSLYED RRKWVPTYIM DVLLAGMSMV QRSESVNSFF DKYVHKKTTV  480
QEFLKQYEAI LQDRYEEEAK ANSDSWSKLP TLKSPSPFEK SVAGLYTHTV FKKFQVEVVG  540
AIACHPKPEN HDATSSFFRV QDLEKNQDFI VTLNEMKSEV SCICRLYEYK GYLCRHAMVV  600
LQINGHSAIP SQYILKRWTK EAKSRHLMGD ESEQVQSRVQ RYNDLFQRAM KLIEEGSLSQ  660
ESYYIAFRSL EEAFGNCLSA NTSNKSLAEA VTSPTQGMIC IEEDNQSRST SKTNKKKNPT  720
KKRKGNSEQE VMTVPATDGL QQMDKLSSRS VGLDGYFGAQ TSVQGMVQLN LMAPRDNYYG  780
NQQTIQGLGQ LNTIAASHDG YYGPQQTMPG MGQMDFFRAP GFYIRDDTNV RAAQLHDDAS  840
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_007036967.2	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Refseq	XP_017973538.1	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3 isoform X1
Swissprot	Q9LIE5	0.0	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	A0A061FWL4	0.0	A0A061FWL4_THECC; Far-red elongated hypocotyls 3 isoform 1
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	Thecc1EG013043t1
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]