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_01070.1_g00010.1

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: 835aa MW: 94963.5 Da PI: 7.4039

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01070.1_g00010.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	77.4	2.7e-24	77	187	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk..............tekerr...........traetrtgC 62 fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e ++k + + +ra +t+C Rsa1.0_01070.1_g00010.1 77 FYQEYSRAIGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDNKsfnrprarqssnkqD----HhnmsgggggggRRACAKTDC 158 9************************************999999999998765430....135677788888***** PP FAR1 63 kaklkvkkekdgkwevtkleleHnHelap 91 ka+++vk++++gkw+v++++ eHnHel+p Rsa1.0_01070.1_g00010.1 159 KASMHVKRRSNGKWVVHSFVREHNHELVP 187 *************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	4.8E-22	77	187	IPR004330	FAR1 DNA binding domain
Pfam	PF10551	8.7E-25	279	372	IPR018289	MULE transposase domain
PROSITE profile	PS50966	8.976	555	591	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	4.2E-6	566	593	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: 835 aa Download sequence Send to blast
MDIDLHLHSG DLRKESDDNN NVLHNSDIDI GSKIEEEDDV VVMGHVTTSE LVDYTESINL 60 EPLNGMEFDS HGEAYAFYQE YSRAIGFNTA IQNSRRSKTT REFIDAKFAC SRYGTKREYD 120 NKSFNRPRAR QSSNKQDHHN MSGGGGGGGR RACAKTDCKA SMHVKRRSNG KWVVHSFVRE 180 HNHELVPAQA VTEQARRIYA AMAKQFAEYK LCDAKSSHEK GRSGVETGDF KTLLEFLERM 240 QGLSSNFYYA VDLGDDQRVK NVFWVDAKSR GGYVSFCDVV SLDTTYVRSK YKTPLAIFVG 300 VNQHYQYMVL GCALLSDESA VTFSWLMETW LKAMGGQAPK VLITEQDSVM NSVVSVVFPN 360 TRHCFFLWHV LSKVSENLGH KEDFTQKFEK CVYKSWKEED FARRWWKILA KFGLKEDQSM 420 QSLYEDRRKW APTYMSDVLL AGMSTPQRAD SVNAFLDKYL HKKTSVQEFV KLYDTILQDR 480 FEEEAKAESE TWNKQPTLKS PSPFEKSVSE VYTPAVFKKF QVEVLGAIAC SPREENRDAT 540 CSTFRVQDFE NSQEFVVTWN QAKAEVFCIC RLFEYKGYLC RHTLNVLQCC HLSSIPSQYV 600 LKRWTKDAKS RQFSSGEPPQ QLQTRLQRYN DLCQRALKLS EEASCSQESY NVAFLAVEEA 660 LRNCAGVNTS GRSVPDVVSS PTQGLVSVEE DNQSRGAGGK ASKKKNPTKK RKVNSEQEVM 720 PPVAAPESLQ QMDKLNPRTV GIEGYYGAQQ SVQNMVQLDL MGGANRDNFY GNQQTIQGLR 780 QLNSIAPSYD GYYTAQPGIH GQGVDFFRPP NFPYDIRDDP NVRTTQLHED ASRHS

Sequence ? help Back to Top

Protein Sequence Length: 835 aa Download sequence Send to blast

MDIDLHLHSG DLRKESDDNN NVLHNSDIDI GSKIEEEDDV VVMGHVTTSE LVDYTESINL  60
EPLNGMEFDS HGEAYAFYQE YSRAIGFNTA IQNSRRSKTT REFIDAKFAC SRYGTKREYD  120
NKSFNRPRAR QSSNKQDHHN MSGGGGGGGR RACAKTDCKA SMHVKRRSNG KWVVHSFVRE  180
HNHELVPAQA VTEQARRIYA AMAKQFAEYK LCDAKSSHEK GRSGVETGDF KTLLEFLERM  240
QGLSSNFYYA VDLGDDQRVK NVFWVDAKSR GGYVSFCDVV SLDTTYVRSK YKTPLAIFVG  300
VNQHYQYMVL GCALLSDESA VTFSWLMETW LKAMGGQAPK VLITEQDSVM NSVVSVVFPN  360
TRHCFFLWHV LSKVSENLGH KEDFTQKFEK CVYKSWKEED FARRWWKILA KFGLKEDQSM  420
QSLYEDRRKW APTYMSDVLL AGMSTPQRAD SVNAFLDKYL HKKTSVQEFV KLYDTILQDR  480
FEEEAKAESE TWNKQPTLKS PSPFEKSVSE VYTPAVFKKF QVEVLGAIAC SPREENRDAT  540
CSTFRVQDFE NSQEFVVTWN QAKAEVFCIC RLFEYKGYLC RHTLNVLQCC HLSSIPSQYV  600
LKRWTKDAKS RQFSSGEPPQ QLQTRLQRYN DLCQRALKLS EEASCSQESY NVAFLAVEEA  660
LRNCAGVNTS GRSVPDVVSS PTQGLVSVEE DNQSRGAGGK ASKKKNPTKK RKVNSEQEVM  720
PPVAAPESLQ QMDKLNPRTV GIEGYYGAQQ SVQNMVQLDL MGGANRDNFY GNQQTIQGLR  780
QLNSIAPSYD GYYTAQPGIH GQGVDFFRPP NFPYDIRDDP NVRTTQLHED ASRHS

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	Rsa1.0_01070.1_g00010.1

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	7e-77	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_018440787.1	0.0	PREDICTED: protein FAR-RED ELONGATED HYPOCOTYL 3-like
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]