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

Rsa1.0_05746.1_g00002.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

FAR1

Protein Properties

Length: 812aa MW: 93682.3 Da PI: 7.9171

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_05746.1_g00002.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	92.4	5.7e-29	58	147	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtkleleHnH 87 fY+eYAk++GF++++++s++sk+++ +++++f Cs++g + e+++ +++ rr++++++t+Cka+++vk+++dg+w ++++ +eHnH Rsa1.0_05746.1_g00002.1 58 FYQEYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYGATPESETGSSSGRRSSSVKKTDCKASMHVKRKSDGRWIIHEFIKEHNH 143 *****************************************9999************************************* PP FAR1 88 elap 91 el p Rsa1.0_05746.1_g00002.1 144 ELLP 147 *975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	1.4E-26	58	147	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	7.7E-26	265	358	IPR018289	MULE transposase domain
PROSITE profile	PS50966	8.926	545	581	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	1.0E-6	547	580	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	3.1E-7	556	583	IPR006564	Zinc finger, PMZ-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
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: 812 aa Download sequence Send to blast
MDLQESNNNQ MSVGSMVESH NNNGVVVVDD LRTGHVGFSD LEPPDGIDFD THEAAYTFYQ 60 EYAKSMGFTT SIKNSRRSKK TKDFIDAKFA CSRYGATPES ETGSSSGRRS SSVKKTDCKA 120 SMHVKRKSDG RWIIHEFIKE HNHELLPALA YHFRIQRNIK LAEKNNIDIL HAVSERTRKM 180 YVEMSRQSGG YKNNLGLVNN TQVDKGRCLA LEEGDSQLML DYFKRIKKEN SKFFYAIDLN 240 EEQRLRNLFW ADAKSRDDYM SFNDVVSFDT TYVKFNDKLP LALFIGVNHH SQPMLLGCAL 300 VADESKDTFA WLIKTWLRAM GGRAPKVILT DQDKLLMAAV SELLPNTRHC FALWHVLEKL 360 PEYFSHVMKR HENFLQKFNK CIFRSWTSDQ FDMRWWKMVS RFGLESDEWL LWLHEHRQKW 420 VPTFMSDVFL AGMSTSQRAE SVNSFFDKYV HKKITLKEFL RQYGVMLQNR YEEESVADFD 480 TCHKQPALKS PSPWEKQMAA TYTHTIFKKF QVEVLGVVAC HPRKEKEDEN MVTFRVQDCE 540 KDDEFLVTWS KTQSELCCFC RMFEYKGFLC RHALMILQMC GFASIPPLYI LKRWTKDAKN 600 GGADQVQTRV QRYNDLCSRA IELSEEGCVS EENYNIVLRT LVETLKNCVD LNNARNNITE 660 SNSQLNNGAQ EEESHVVAGL KATKKKKTVV RKRKGQPEAS QMLESQQSLQ PMENISSEGM 720 SISGYYGPQQ NVQGLLNLME PPHEGYYVNQ RTIQGLGQLN SLAPVQDSFF TNQQAIPGLG 780 QMDFRPPPNF TYNLQDEHLR SAQFPGSSSR QL

Sequence ? help Back to Top

Protein Sequence Length: 812 aa Download sequence Send to blast

MDLQESNNNQ MSVGSMVESH NNNGVVVVDD LRTGHVGFSD LEPPDGIDFD THEAAYTFYQ  60
EYAKSMGFTT SIKNSRRSKK TKDFIDAKFA CSRYGATPES ETGSSSGRRS SSVKKTDCKA  120
SMHVKRKSDG RWIIHEFIKE HNHELLPALA YHFRIQRNIK LAEKNNIDIL HAVSERTRKM  180
YVEMSRQSGG YKNNLGLVNN TQVDKGRCLA LEEGDSQLML DYFKRIKKEN SKFFYAIDLN  240
EEQRLRNLFW ADAKSRDDYM SFNDVVSFDT TYVKFNDKLP LALFIGVNHH SQPMLLGCAL  300
VADESKDTFA WLIKTWLRAM GGRAPKVILT DQDKLLMAAV SELLPNTRHC FALWHVLEKL  360
PEYFSHVMKR HENFLQKFNK CIFRSWTSDQ FDMRWWKMVS RFGLESDEWL LWLHEHRQKW  420
VPTFMSDVFL AGMSTSQRAE SVNSFFDKYV HKKITLKEFL RQYGVMLQNR YEEESVADFD  480
TCHKQPALKS PSPWEKQMAA TYTHTIFKKF QVEVLGVVAC HPRKEKEDEN MVTFRVQDCE  540
KDDEFLVTWS KTQSELCCFC RMFEYKGFLC RHALMILQMC GFASIPPLYI LKRWTKDAKN  600
GGADQVQTRV QRYNDLCSRA IELSEEGCVS EENYNIVLRT LVETLKNCVD LNNARNNITE  660
SNSQLNNGAQ EEESHVVAGL KATKKKKTVV RKRKGQPEAS QMLESQQSLQ PMENISSEGM  720
SISGYYGPQQ NVQGLLNLME PPHEGYYVNQ RTIQGLGQLN SLAPVQDSFF TNQQAIPGLG  780
QMDFRPPPNF TYNLQDEHLR SAQFPGSSSR QL

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	Rsa1.0_05746.1_g00002.1

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY078941	0.0	AY078941.1 Arabidopsis thaliana AT4g15090/dl3590w mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018446306.1	0.0	PREDICTED: protein FAR-RED IMPAIRED RESPONSE 1
Swissprot	Q9SWG3	0.0	FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBL	A0A397Z9K7	0.0	A0A397Z9K7_BRACM; Uncharacterized protein
STRING	Bo6g054750.1	0.0	(Brassica oleracea)

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
AT4G15090.1	0.0	FAR1 family protein

Publications ? help Back to Top
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]