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_009109171.1

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: 826aa MW: 94211.2 Da PI: 7.7384

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009109171.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	75.8	8.4e-24	72	178	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk.................tekerrtraetrtgCkaklkvkkekdgkwevt 79 fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e ++k + +r+ +t+Cka+++vk++++gkw+++ XP_009109171.1 72 FYQEYSRAIGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYENKscnrprarqskqdhpenHMAGGCRRTCAKTDCKASMHVKRRSNGKWVIH 166 9***********************************99999888899999887776655444444449********************* PP FAR1 80 kleleHnHelap 91 +++ eHnHel+p XP_009109171.1 167 SFVREHNHELVP 178 ********86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	9.3E-22	72	178	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	4.6E-24	270	362	IPR018289	MULE transposase domain
PROSITE profile	PS50966	9.137	550	586	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	6.7E-7	561	588	IPR006564	Zinc finger, PMZ-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 826 aa Download sequence Send to blast
MDIDLRLHSG DQGDDSVRGL DNVLHNSDID ISKIEEDVLA VTTGELVDYA EAVNLEPLNG 60 MEFDSHGEAY AFYQEYSRAI GFNTAIQNSR RSKTTREFID AKFACSRYGT KREYENKSCN 120 RPRARQSKQD HPENHMAGGC RRTCAKTDCK ASMHVKRRSN GKWVIHSFVR EHNHELVPAQ 180 AVTEQARRIY AAMAKQFAEY KTVVGLKSDA KSLGRSLPVV ETGDFKALLE FLSRMQNFSY 240 AVDLGDDQRV KNVFWVDAKS RGSYVSFCDV VSLDTTYVRN KYKTPLAVFV GVNQHYQYMV 300 LGCALLSDES AATFSWLMET WLKAMGGQAP KVLITEQEAV MNSIVPVIFP NTRHCVFLWH 360 VLVKVSENLA HVAKQHEDFM PKFEKCIYKS WKEEDFARRW WKILAKFGLK EDQWMQSLYE 420 DRRKWAPTYM TDVLLAGMSS SQRGDSVNAF LDKYLHKKTS VQEFVKLYDT ILQDRFEEEA 480 KADSETLNKQ PTMKSPSPFE KSVSEVYTPA VFKKFQVEVL GAIACSPREE NRDGTCSTFR 540 VQDFENSQEF VVTWNQAKAE VSCICRLFEY KGYLCRHTLN VLQCCHLSSV PSQYILKRWT 600 KDARSRQFSG EAPPQLQTRM QRYNDLCQRA LKLSEEASCS QESYNVAFLA IEEALRNCAG 660 VNRSLPDTAS SPTQGLVSVE EDNQSRSAGG KTSKKKNPTK KRKVSSEQEV MPQVATPESL 720 QQMDKLSPRT VGIESYYGTQ QSVQTMVQLD LMGGPNRDNF YGNQQTMQGL RQLNSIAPSY 780 DSYYTAQQGI HGQGVDFFRP PNFSYDIRDD PNVRTTQLHE DAPRHS

Sequence ? help Back to Top

Protein Sequence Length: 826 aa Download sequence Send to blast

MDIDLRLHSG DQGDDSVRGL DNVLHNSDID ISKIEEDVLA VTTGELVDYA EAVNLEPLNG  60
MEFDSHGEAY AFYQEYSRAI GFNTAIQNSR RSKTTREFID AKFACSRYGT KREYENKSCN  120
RPRARQSKQD HPENHMAGGC RRTCAKTDCK ASMHVKRRSN GKWVIHSFVR EHNHELVPAQ  180
AVTEQARRIY AAMAKQFAEY KTVVGLKSDA KSLGRSLPVV ETGDFKALLE FLSRMQNFSY  240
AVDLGDDQRV KNVFWVDAKS RGSYVSFCDV VSLDTTYVRN KYKTPLAVFV GVNQHYQYMV  300
LGCALLSDES AATFSWLMET WLKAMGGQAP KVLITEQEAV MNSIVPVIFP NTRHCVFLWH  360
VLVKVSENLA HVAKQHEDFM PKFEKCIYKS WKEEDFARRW WKILAKFGLK EDQWMQSLYE  420
DRRKWAPTYM TDVLLAGMSS SQRGDSVNAF LDKYLHKKTS VQEFVKLYDT ILQDRFEEEA  480
KADSETLNKQ PTMKSPSPFE KSVSEVYTPA VFKKFQVEVL GAIACSPREE NRDGTCSTFR  540
VQDFENSQEF VVTWNQAKAE VSCICRLFEY KGYLCRHTLN VLQCCHLSSV PSQYILKRWT  600
KDARSRQFSG EAPPQLQTRM QRYNDLCQRA LKLSEEASCS QESYNVAFLA IEEALRNCAG  660
VNRSLPDTAS SPTQGLVSVE EDNQSRSAGG KTSKKKNPTK KRKVSSEQEV MPQVATPESL  720
QQMDKLSPRT VGIESYYGTQ QSVQTMVQLD LMGGPNRDNF YGNQQTMQGL RQLNSIAPSY  780
DSYYTAQQGI HGQGVDFFRP PNFSYDIRDD PNVRTTQLHE DAPRHS

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009109171.1

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. 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	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK229728	2e-74	AK229728.1 Arabidopsis thaliana mRNA for putative far-red impaired response protein, partial cds, clone: RAFL21-40-L21.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009109171.1	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3-like isoform X1
Swissprot	Q9LIE5	0.0	FHY3_ARATH; Protein FAR-RED ELONGATED HYPOCOTYL 3
TrEMBL	A0A3P5Z983	0.0	A0A3P5Z983_BRACM; Uncharacterized protein
STRING	Bo1g105420.1	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
AT3G22170.2	0.0	far-red elongated hypocotyls 3

Publications ? help Back to Top
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]