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

XP_009147838.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

FAR1

Protein Properties

Length: 827aa MW: 95287.2 Da PI: 7.9072

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009147838.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	89.5	4.7e-28	71	159	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkktekerrtraetrtgCkaklkvkkekdgkwevtkleleHnHelap 91 fY++YAk++GF++++++s++sk+++ +++++f Cs++g++ e+++ +++ r++++++t+Cka+++vk+++dg+w ++++ +eHnHel p XP_009147838.1 71 FYQDYAKSMGFTTSIKNSRRSKKTKDFIDAKFACSRYGSTPESESG-SSSGRRSSVKKTDCKASMHVKRKSDGRWIIHEFIKEHNHELLP 159 **************************************999998.888889999*****************************975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	1.2E-25	71	159	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	1.0E-25	281	374	IPR018289	MULE transposase domain
PROSITE profile	PS50966	8.803	561	597	IPR007527	Zinc finger, SWIM-type
Pfam	PF04434	1.1E-5	563	596	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	4.9E-6	572	599	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: 827 aa Download sequence Send to blast
MVNPDVAKLK MDLQESDNNQ MSDANMVESH NNNNGDVGGG VVVDDLRTGG HLGVEPPDGI 60 DFDTHEAAYT FYQDYAKSMG FTTSIKNSRR SKKTKDFIDA KFACSRYGST PESESGSSSG 120 RRSSVKKTDC KASMHVKRKS DGRWIIHEFI KEHNHELLPA LAYHFRIQRN IKLAEKNNID 180 ILHAVSERTR KMYVEMSRQS GGYNKNNKGL LLLQTSQVDK GRRCLALEEG DSQLLLEYFK 240 RIKKENPRFF YAIDLNEEQR LRNLFWADAK SRDDYMSFND VVSFDTTYVK FNDKLPLALF 300 IGVNHHSQPM LLGCGLVADE SKETFAWLIK TWLRAMGGRA PKVILTDQDK LLMAAVSELL 360 PNTRHCFALW HVLEKLPEYF SHVMKRHENF LRKFNKCIFR SWTSDQFDMR WWKMVSQFGL 420 ENDEWLLWLH EHRQKWVPTF MSEVFLAGMS TSQRAESVNS FFDKYVHKKI TLKEFLRQYG 480 VMLQNRYEEE SVADFDTCHK QPALKSPSPW EKQMAATYTH TIFKKFQVEV LGVVACHPRK 540 EKEDENMVTF RVQDCEKDDE FLVTWSKTQS ELCCFCHMFE YKGFLCRHAL MILQMCGFAS 600 VPPRYILKRW TKDAKSGGAD QVQTRVQRYN DLCCRAIELS EEGCVSEENY NIVLRTLVET 660 LKNCVDLNHA RNNFAESNSQ LNNGAHEEEN HVLAGVKATK KKTVVRKRKG QPEAGQMLES 720 QPSLQPMENI SSEGMSISGY YGPQQNVQGL LNLMEPPHEG YYVNQRTIQG LGQLNSIAPV 780 QDSFFTNQQA MPGLGQMDFR PPPNFAYNLQ DEHLRSAQLP GNSSRQL

Sequence ? help Back to Top

Protein Sequence Length: 827 aa Download sequence Send to blast

MVNPDVAKLK MDLQESDNNQ MSDANMVESH NNNNGDVGGG VVVDDLRTGG HLGVEPPDGI  60
DFDTHEAAYT FYQDYAKSMG FTTSIKNSRR SKKTKDFIDA KFACSRYGST PESESGSSSG  120
RRSSVKKTDC KASMHVKRKS DGRWIIHEFI KEHNHELLPA LAYHFRIQRN IKLAEKNNID  180
ILHAVSERTR KMYVEMSRQS GGYNKNNKGL LLLQTSQVDK GRRCLALEEG DSQLLLEYFK  240
RIKKENPRFF YAIDLNEEQR LRNLFWADAK SRDDYMSFND VVSFDTTYVK FNDKLPLALF  300
IGVNHHSQPM LLGCGLVADE SKETFAWLIK TWLRAMGGRA PKVILTDQDK LLMAAVSELL  360
PNTRHCFALW HVLEKLPEYF SHVMKRHENF LRKFNKCIFR SWTSDQFDMR WWKMVSQFGL  420
ENDEWLLWLH EHRQKWVPTF MSEVFLAGMS TSQRAESVNS FFDKYVHKKI TLKEFLRQYG  480
VMLQNRYEEE SVADFDTCHK QPALKSPSPW EKQMAATYTH TIFKKFQVEV LGVVACHPRK  540
EKEDENMVTF RVQDCEKDDE FLVTWSKTQS ELCCFCHMFE YKGFLCRHAL MILQMCGFAS  600
VPPRYILKRW TKDAKSGGAD QVQTRVQRYN DLCCRAIELS EEGCVSEENY NIVLRTLVET  660
LKNCVDLNHA RNNFAESNSQ LNNGAHEEEN HVLAGVKATK KKTVVRKRKG QPEAGQMLES  720
QPSLQPMENI SSEGMSISGY YGPQQNVQGL LNLMEPPHEG YYVNQRTIQG LGQLNSIAPV  780
QDSFFTNQQA MPGLGQMDFR PPPNFAYNLQ DEHLRSAQLP GNSSRQL

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bra.22707	0.0	root

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	XP_009147838.1

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_009147838.1	0.0	PREDICTED: protein FAR-RED IMPAIRED RESPONSE 1 isoform X1
Swissprot	Q9SWG3	0.0	FAR1_ARATH; Protein FAR-RED IMPAIRED RESPONSE 1
TrEMBL	A0A3P5YT17	0.0	A0A3P5YT17_BRACM; Uncharacterized protein
TrEMBL	M4FHW7	0.0	M4FHW7_BRARP; Uncharacterized protein
STRING	Bra040696.1-P	0.0	(Brassica rapa)

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]