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

Solyc08g060840.1.1

Common Name

LOC101258392

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

FAR1

Protein Properties

Length: 827aa MW: 94634.5 Da PI: 7.5858

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc08g060840.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	87.7	1.7e-27	67	152	2	90
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtkleleHnHela 90 fY+eYAk++GF++++++s++sk+++e+++++f Cs++g++ e+++ ++r+ ++++t+Cka+++vk+++dgkw+v+++ ++HnH l Solyc08g060840.1.1 67 FYQEYAKSMGFTTSIKNSRRSKKSKEFIDAKFACSRYGTTPESDTG---SSRRPSVKKTDCKASMHVKRKRDGKWYVHEFIKDHNHGLL 152 9*************************************999877...77888899***************************997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	5.2E-25	67	153	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	6.5E-25	273	365	IPR018289	MULE transposase domain
PROSITE profile	PS50966	10.039	553	589	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	8.1E-7	563	588	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	1.2E-8	564	591	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:0010018	Biological Process	far-red light signaling pathway
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: 827 aa Download sequence Send to blast
MVDHGDVVQS SVQLTGDMVD AVDKSCLSRD GGVSRSPKRS ITGVEEHADF EPHDGIEFES 60 HEAAYAFYQE YAKSMGFTTS IKNSRRSKKS KEFIDAKFAC SRYGTTPESD TGSSRRPSVK 120 KTDCKASMHV KRKRDGKWYV HEFIKDHNHG LLPALAYHFR IHRNVKLAEK NNIDILNAVS 180 ERTRKMYVEM SRQCGGSQEV GLLTNDLNYQ FDKGRCLSLE EGDAHIMLEY FMHVQKENPC 240 FFYATDLNED QRLRNLFWID AKSRKDYVSF NDVVFFDTSY MKSNEKMPFA LLIGVNHHCQ 300 PMLLGCALIA DETKPTFVWL MKTWLRAVGG KAPKVIIADQ DKSLKSALEE VFPCSSHCFA 360 LWHVLERIPE TLAHVVKQHE NFMQKFSKCI FKSLTDEQFD LRWWKMVSRF ELQENEWIHT 420 LYEDRKKWIP AYMRGSFMAG MSTAQRSESI SSFFDKYIHK KISLKEFMRQ YGMILQNRYE 480 EEAIADFDTL HKLPALKSPS PWEKQMSTIY THTIFKKFQV EVLGVVGCHP KKEAVNGENV 540 TFRVDDCEKD ENFMVTWNEA RSDVSCSCLL FEYNGFLCRH AMIVLQMCGL SIIPSQYILK 600 RWTKDAKNIQ LISEGTERIR NRVQRYNDLC RRAIELGVEG SLSEESYGVA FRALDEALKN 660 CVNVNNRSSA LTECSSSAVG LRDLEEDTQG IHAIKTSRKK NTNKKRKMHS EPEAAIVEAK 720 DSLQQMDSLT VGGMTLNGYY GTHQNVQGLI QLNLMEPPHD GYYVNQQNMQ GLGQLNTIAP 780 GHDGFFGSQQ SIPGLGHLDF RQPSFTYGLQ DEPSLRAAQL HGNNAR*

Sequence ? help Back to Top

Protein Sequence Length: 827 aa Download sequence Send to blast

MVDHGDVVQS SVQLTGDMVD AVDKSCLSRD GGVSRSPKRS ITGVEEHADF EPHDGIEFES  60
HEAAYAFYQE YAKSMGFTTS IKNSRRSKKS KEFIDAKFAC SRYGTTPESD TGSSRRPSVK  120
KTDCKASMHV KRKRDGKWYV HEFIKDHNHG LLPALAYHFR IHRNVKLAEK NNIDILNAVS  180
ERTRKMYVEM SRQCGGSQEV GLLTNDLNYQ FDKGRCLSLE EGDAHIMLEY FMHVQKENPC  240
FFYATDLNED QRLRNLFWID AKSRKDYVSF NDVVFFDTSY MKSNEKMPFA LLIGVNHHCQ  300
PMLLGCALIA DETKPTFVWL MKTWLRAVGG KAPKVIIADQ DKSLKSALEE VFPCSSHCFA  360
LWHVLERIPE TLAHVVKQHE NFMQKFSKCI FKSLTDEQFD LRWWKMVSRF ELQENEWIHT  420
LYEDRKKWIP AYMRGSFMAG MSTAQRSESI SSFFDKYIHK KISLKEFMRQ YGMILQNRYE  480
EEAIADFDTL HKLPALKSPS PWEKQMSTIY THTIFKKFQV EVLGVVGCHP KKEAVNGENV  540
TFRVDDCEKD ENFMVTWNEA RSDVSCSCLL FEYNGFLCRH AMIVLQMCGL SIIPSQYILK  600
RWTKDAKNIQ LISEGTERIR NRVQRYNDLC RRAIELGVEG SLSEESYGVA FRALDEALKN  660
CVNVNNRSSA LTECSSSAVG LRDLEEDTQG IHAIKTSRKK NTNKKRKMHS EPEAAIVEAK  720
DSLQQMDSLT VGGMTLNGYY GTHQNVQGLI QLNLMEPPHD GYYVNQQNMQ GLGQLNTIAP  780
GHDGFFGSQQ SIPGLGHLDF RQPSFTYGLQ DEPSLRAAQL HGNNAR*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.8437	0.0	callus\| flower

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. Positive regulator of chlorophyll biosynthesis via the activation of HEMB1 gene expression. {ECO:0000269\|PubMed:11889039, ECO:0000269\|PubMed:12753585, ECO:0000269\|PubMed:18033885, ECO:0000269\|PubMed:22634759}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00434	DAP	Transfer from AT4G15090	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc08g060840.1.1

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. {ECO:0000269\|PubMed:18033885}.

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_004245025.1	0.0	protein FAR-RED IMPAIRED RESPONSE 1 isoform X1
Refseq	XP_010324981.1	0.0	protein FAR-RED IMPAIRED RESPONSE 1 isoform X1
Refseq	XP_010324983.1	0.0	protein FAR-RED IMPAIRED RESPONSE 1 isoform X1
Swissprot	Q9SWG3	0.0	FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBL	K4CKM9	0.0	K4CKM9_SOLLC; Uncharacterized protein
STRING	Solyc08g060840.1.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA496	21	103
Representative plant	OGRP13457	3	4

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G15090.1	0.0	FAR1 family protein

Link Out ? help Back to Top
Phytozome	Solyc08g060840.1.1
Entrez Gene	101258392

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] Domergue F, et al. Three Arabidopsis fatty acyl-coenzyme A reductases, FAR1, FAR4, and FAR5, generate primary fatty alcohols associated with suberin deposition. Plant Physiol., 2010. 153(4): p. 1539-54 [PMID:20571114] Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] 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] 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]