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

RrC1813_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

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: 607aa MW: 69036.4 Da PI: 8.1635

Description

FAR1 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1813_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	FAR1	77.7	2.2e-24	71	180	2	91
FAR1 2 fYneYAkevGFsvrkskskkskrngeitkrtfvCskegkreeekkk...............tekerr.........traetrtgCkaklkvkkekdgkw 76 fY+eY++ +GF++ +++s++sk+++e+++++f Cs++g+++e ++k + + +ra +t+Cka+++vk++++gkw RrC1813_p1 71 FYQEYSRAIGFNTAIQNSRRSKTTREFIDAKFACSRYGTKREYDNKsfnrprarqsnnnkqD----HhnmsgggggRRACAKTDCKASMHVKRRSNGKW 165 9************************************99999999*9998765430....14567777879****************** PP FAR1 77 evtkleleHnHelap 91 +v++++ eHnHel+p RrC1813_p1 166 VVHSFVREHNHELVP 180 ***********86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03101	3.2E-22	71	180	IPR004330	FAR1 DNA binding domain
PROSITE profile	PS50966	9.137	375	411	IPR007527	Zinc finger, SWIM-type
SMART	SM00575	6.7E-7	386	413	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: 607 aa Download sequence Send to blast
MDIDLHLHSG ELCKEDDNNN VLHNSDIGSK IEEDDVVMGV TTSELVDYTE SINLEPLNGM 60 EFDSHGEAYA FYQEYSRAIG FNTAIQNSRR SKTTREFIDA KFACSRYGTK REYDNKSFNR 120 PRARQSNNNK QDHHNMSGGG GGRRACAKTD CKASMHVKRR SNGKWVVHSF VREHNHELVP 180 AQAVTEQARR IYAAMAKQFA EYKLCDAKSS HEKGRSAEED FARRWWKILA KFGLKEDQSM 240 QSLYEDRRKW APTYMSDVLL AGMSTSQRGD SVNAFLDKYL HKKTSVQEFV KLYDTILQDR 300 FEEEAKAESE TWNKQPTLKS PSPFEKSVSE VYTPAVFKKF QVEVLGAIAC SPREENRDAT 360 CSTFRVQDFE NSQEFVVTWN QAKAEVSCIC RLFEYKGYLC RHTLNVLQCC HLSSIPSQYV 420 LKRWTKDAKS RQFSSGEPPQ QLQTRLQRYN DLCQRALKLS EEASCSQESY NIAFLAVEEA 480 LRNCAGVNTS GRSLPDVVSS PTQGLVSVEE DNQSRGAGGK ASKKKNPTKK RKDKLNPRTV 540 GIEGYYGAQQ SVQNMVNYAH KTNVIYSLIC VCSLWSDYVC LQVQLDLMAG ANRDNFYGNQ 600 QTIQGLV

Sequence ? help Back to Top

Protein Sequence Length: 607 aa Download sequence Send to blast

MDIDLHLHSG ELCKEDDNNN VLHNSDIGSK IEEDDVVMGV TTSELVDYTE SINLEPLNGM  60
EFDSHGEAYA FYQEYSRAIG FNTAIQNSRR SKTTREFIDA KFACSRYGTK REYDNKSFNR  120
PRARQSNNNK QDHHNMSGGG GGRRACAKTD CKASMHVKRR SNGKWVVHSF VREHNHELVP  180
AQAVTEQARR IYAAMAKQFA EYKLCDAKSS HEKGRSAEED FARRWWKILA KFGLKEDQSM  240
QSLYEDRRKW APTYMSDVLL AGMSTSQRGD SVNAFLDKYL HKKTSVQEFV KLYDTILQDR  300
FEEEAKAESE TWNKQPTLKS PSPFEKSVSE VYTPAVFKKF QVEVLGAIAC SPREENRDAT  360
CSTFRVQDFE NSQEFVVTWN QAKAEVSCIC RLFEYKGYLC RHTLNVLQCC HLSSIPSQYV  420
LKRWTKDAKS RQFSSGEPPQ QLQTRLQRYN DLCQRALKLS EEASCSQESY NIAFLAVEEA  480
LRNCAGVNTS GRSLPDVVSS PTQGLVSVEE DNQSRGAGGK ASKKKNPTKK RKDKLNPRTV  540
GIEGYYGAQQ SVQNMVNYAH KTNVIYSLIC VCSLWSDYVC LQVQLDLMAG ANRDNFYGNQ  600
QTIQGLV

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}.

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 -- 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	A0A3N6QE62	0.0	A0A3N6QE62_BRACR; 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]