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

RrC414_p2

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

ARF

Protein Properties

Length: 948aa MW: 104090 Da PI: 6.2783

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC414_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	74.8	9.7e-24	127	228	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 f+k+lt sd++++g +++p++ ae++ +++++++ +l+ +d + ++W++++i+r++++r++lt+GW+ Fv+ ++L +gD+v+F + + +++l++ RrC414_p2 127 FCKTLTASDTSTHGGFSVPRRAAEKIfpaldfSMQPPCQ-ELVAKDIHDNTWTFRHIFRGQPKRHLLTTGWSVFVSTKRLLAGDSVLFVR--DGKGQLLL 223 99***************************98888885.9********************************************5..468889 PP EEE-S CS B3 95 kvfrk 99 +++r+ RrC414_p2 224 GIRRA 228 **997 PP
2	Auxin_resp	117.1	1.5e-38	253	335	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha +++s+F+++YnPra+++eFvv+++k+ ka++ +vs+GmRf+m fete++ rr++Gtv+g++dldpvrW+nS+Wr+L+ RrC414_p2 253 AAHANANNSPFTIFYNPRAAPAEFVVPLAKYTKAMYAQVSLGMRFRMIFETEECGVRRYMGTVTGITDLDPVRWKNSQWRNLQ 335 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.83E-42	117	256	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.5E-41	121	242	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.80E-21	126	227	No hit	No description
PROSITE profile	PS50863	12.421	127	229	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.0E-22	127	228	IPR003340	B3 DNA binding domain
SMART	SM01019	2.3E-23	127	229	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.3E-33	253	335	IPR010525	Auxin response factor
Pfam	PF02309	2.4E-9	819	907	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	26.174	821	914	IPR000270	PB1 domain
SuperFamily	SSF54277	7.85E-9	834	899	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009638	Biological Process	phototropism
GO:0009723	Biological Process	response to ethylene
GO:0009733	Biological Process	response to auxin
GO:0009785	Biological Process	blue light signaling pathway
GO:0010311	Biological Process	lateral root formation
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 948 aa Download sequence Send to blast
MKAPSSNGVS PNPMEGERRN INSELWHACA GPLISLPPAG SLVVYFPQGH SEQVAASMQK 60 QTDFIPSYPN LPSKLICMLQ NVTLNADPET EEVYAQMTLQ PVNKYDREAL LASDMGLKLN 120 RQPNEFFCKT LTASDTSTHG GFSVPRRAAE KIFPALDFSM QPPCQELVAK DIHDNTWTFR 180 HIFRGQPKRH LLTTGWSVFV STKRLLAGDS VLFVRDGKGQ LLLGIRRANR QQPALSSSVI 240 SSDSMHIGVL AAAAHANANN SPFTIFYNPR AAPAEFVVPL AKYTKAMYAQ VSLGMRFRMI 300 FETEECGVRR YMGTVTGITD LDPVRWKNSQ WRNLQIGWDE SAAGDRPSRV SVWDIEPVLT 360 PFYICPPPFF RPRFAGQPGM PDDGTDMESA LKRAMPWLDN GLEMKDPSST IFPGLSLVQW 420 MSMQQQNGQV PGAAAQPGFF PSMLSPAAAL HNNLGGADDP SNKSSSNLMS KPPQDTQFSR 480 QMEQQQPSGL VQGHNQQTLV QQKTQQSQVQ QRFQQSLLEQ PHLQFQLLQR LQQQQQQQQQ 540 QQFLSPGSSS LQSQLLHQQL QSQQLQQLPS ISQGQQFPSS CTNTGLPSLQ PPQMLVSRPQ 600 DKHNPPVGGG AKAYSGITDG GDAPSSSTSP STNNCQISSS TFLNRSQSGP AILIPDPAVD 660 VSASLVQDLY SKSDMRLKHE LVSQQKPKAS LTDHQQLEAS ASGTSYGLDG GENSRQQNFL 720 SPNFGLDGDS RNSLFGGANV ENGFVPDTLL SRGYDSQKDL QNMLSNYGGV TNDIGTEMST 780 SAVRTQSFGI PNVPAISNDL AVNDAGVLGG GLWPTQAQRM RTYTKVQKRG SVGRSIDVNR 840 YRGYDELRHD LARMFGIEGQ LEDPLTSDWK LVYVDHENDI LLVGDDPWEE FVNCVQSIKI 900 LSSAEVQQMS LDGNFAGLPA TNQACSGGDN GNGWRGQYDD NSANSFNR

Sequence ? help Back to Top

Protein Sequence Length: 948 aa Download sequence Send to blast

MKAPSSNGVS PNPMEGERRN INSELWHACA GPLISLPPAG SLVVYFPQGH SEQVAASMQK  60
QTDFIPSYPN LPSKLICMLQ NVTLNADPET EEVYAQMTLQ PVNKYDREAL LASDMGLKLN  120
RQPNEFFCKT LTASDTSTHG GFSVPRRAAE KIFPALDFSM QPPCQELVAK DIHDNTWTFR  180
HIFRGQPKRH LLTTGWSVFV STKRLLAGDS VLFVRDGKGQ LLLGIRRANR QQPALSSSVI  240
SSDSMHIGVL AAAAHANANN SPFTIFYNPR AAPAEFVVPL AKYTKAMYAQ VSLGMRFRMI  300
FETEECGVRR YMGTVTGITD LDPVRWKNSQ WRNLQIGWDE SAAGDRPSRV SVWDIEPVLT  360
PFYICPPPFF RPRFAGQPGM PDDGTDMESA LKRAMPWLDN GLEMKDPSST IFPGLSLVQW  420
MSMQQQNGQV PGAAAQPGFF PSMLSPAAAL HNNLGGADDP SNKSSSNLMS KPPQDTQFSR  480
QMEQQQPSGL VQGHNQQTLV QQKTQQSQVQ QRFQQSLLEQ PHLQFQLLQR LQQQQQQQQQ  540
QQFLSPGSSS LQSQLLHQQL QSQQLQQLPS ISQGQQFPSS CTNTGLPSLQ PPQMLVSRPQ  600
DKHNPPVGGG AKAYSGITDG GDAPSSSTSP STNNCQISSS TFLNRSQSGP AILIPDPAVD  660
VSASLVQDLY SKSDMRLKHE LVSQQKPKAS LTDHQQLEAS ASGTSYGLDG GENSRQQNFL  720
SPNFGLDGDS RNSLFGGANV ENGFVPDTLL SRGYDSQKDL QNMLSNYGGV TNDIGTEMST  780
SAVRTQSFGI PNVPAISNDL AVNDAGVLGG GLWPTQAQRM RTYTKVQKRG SVGRSIDVNR  840
YRGYDELRHD LARMFGIEGQ LEDPLTSDWK LVYVDHENDI LLVGDDPWEE FVNCVQSIKI  900
LSSAEVQQMS LDGNFAGLPA TNQACSGGDN GNGWRGQYDD NSANSFNR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-165	21	356	51	388	Auxin response factor 5
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Act as a transcriptional activator of several tropic stimulus-induced (TSI) genes, including SAUR50. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Required for differential growth responses of aerial tissues. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF19. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF5. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:16371470, ECO:0000269\|PubMed:16461383, ECO:0000269\|PubMed:17259263}.

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	JN979469	0.0	JN979469.1 Brassica rapa subsp. pekinensis auxin response factor 7-1 (ARF7-1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018445241.1	0.0	PREDICTED: auxin response factor 7
Swissprot	P93022	0.0	ARFG_ARATH; Auxin response factor 7
TrEMBL	A0A3N6QIU7	0.0	A0A3N6QIU7_BRACR; Auxin response factor
STRING	AT5G20730.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2629	26	65

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G20730.2	0.0	ARF family protein

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Hu J,Zhang Y,Wang J,Zhou Y Glycerol affects root development through regulation of multiple pathways in Arabidopsis. PLoS ONE, 2014. 9(1): p. e86269 [PMID:24465999] Mellor N, et al. Modelling of Arabidopsis LAX3 expression suggests auxin homeostasis. J. Theor. Biol., 2015. 366: p. 57-70 [PMID:25446711] Gupta A,Singh M,Laxmi A Interaction between glucose and brassinosteroid during the regulation of lateral root development in Arabidopsis. Plant Physiol., 2015. 168(1): p. 307-20 [PMID:25810094] Youn JH, et al. ARF7 increases the endogenous contents of castasterone through suppression of BAS1 expression in Arabidopsis thaliana. Phytochemistry, 2016. 122: p. 34-44 [PMID:26608667] Porco S, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development, 2016. 143(18): p. 3340-9 [PMID:27578783] Carey NS,Krogan NT The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems. Plant Signal Behav, 2017. 12(4): p. e1307492 [PMID:28340328] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Sheng L, et al. Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture. Development, 2017. 144(17): p. 3126-3133 [PMID:28743799] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana. Plant Sci., 2017. 264: p. 168-178 [PMID:28969797] Nakamura M, et al. Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells. Plant Physiol., 2018. 176(1): p. 378-391 [PMID:29084900] Hong L, et al. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J., 2018. 93(2): p. 246-258 [PMID:29155478] Lee K,Park OS,Seo PJ Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal, 2018. [PMID:29184030] Prát T, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genet., 2018. 14(1): p. e1007177 [PMID:29377885] Kimura T, et al. Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 823-835 [PMID:29401292] Schoenaers S, et al. The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Curr. Biol., 2018. 28(5): p. 722-732.e6 [PMID:29478854] Huang KL, et al. The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots. Plant Physiol., 2018. 178(1): p. 413-427 [PMID:30026290] Hablak SG Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2. Tsitol. Genet., 2019. [PMID:30484609] Orosa-Puente B, et al. Root branching toward water involves posttranslational modification of transcription factor ARF7. Science, 2018. 362(6421): p. 1407-1410 [PMID:30573626]