PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Dalbergieae; Arachis

Family

ARF

Protein Properties

Length: 699aa MW: 76401 Da PI: 6.864

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Aradu.PZ2UH	genome	NCGR_PGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	79.8	2.9e-25	162	263	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 f+k+lt sd++++g +++p++ ae++ + +++ s++l+ +d++gr+W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + ++el Aradu.PZ2UH 162 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGREWKFRHIYRGQPRRHLLTTGWSAFVNKKQLVSGDAVLFL--RGADGEL 256 99**************************963.3445679********************************************..3489999 PP EEEEE-S CS B3 93 vvkvfrk 99 +++++r+ Aradu.PZ2UH 257 RLGIRRA 263 *9986 PP
2	Auxin_resp	115.1	6.3e-38	288	369	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++a+s++++F+v YnPr+s+s+F+++v+k++k+l+ ++svGmRf+m+feted++ rr++G+++g++d+dpvrWp+SkWr+L Aradu.PZ2UH 288 VINALSSRCAFSVHYNPRVSSSDFIIPVHKFLKSLDYSYSVGMRFRMRFETEDAADRRITGLIIGINDVDPVRWPGSKWRCL 369 5799*****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.44E-42	156	275	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.3E-40	157	264	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.18E-23	160	262	No hit	No description
SMART	SM01019	8.1E-24	162	264	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.2E-23	162	263	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.719	162	264	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.3E-32	289	369	IPR010525	Auxin response factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009725	Biological Process	response to hormone
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 699 aa Download sequence Send to blast
MAGLIDLNTT EDDETPSYGS YAASPSSSSS HSGTSTASVS ASAPVVPGSS SNSVCLELWH 60 ACAGSMISLP KKGTLVVYFP QGHSEQQLHD FPLSNNNNSI PPHVFCRVLD VKLHAEEGSD 120 EVYCQVLLVP ENEQKFQEGD IEADGEEEDT DAVMKATTPH MFCKTLTASD TSTHGGFSVP 180 RRAAEDCFPP LDYSQQRPSQ ELVAKDLHGR EWKFRHIYRG QPRRHLLTTG WSAFVNKKQL 240 VSGDAVLFLR GADGELRLGI RRAGQLKSDG KFSALPHQQL NHSTPVEVIN ALSSRCAFSV 300 HYNPRVSSSD FIIPVHKFLK SLDYSYSVGM RFRMRFETED AADRRITGLI IGINDVDPVR 360 WPGSKWRCLL VRWDDLETTR HNRVSPWEIE PSGSASTASS LMTAGLKRSK IGLPSVQLEF 420 PVPNGISTSD FGESLRFQKV LQGQEILGVN NPVNGINAQC HQLSELRRCY PGFTTAGHGT 480 IPQVSSDASC NGIGFGESFR FQKVLQGQEI LPSQPYGNGR LGAFDGYQML RSRNGWSAHM 540 NSNSSHLHAP FSSGQLSSPS SVLMFQQAFN PVSNSDYSNK ANQVKGGKAL QRGSYASEVD 600 GGTNASFPSY ETTFHGKAQE GKNSFTFLNL HDQLGGSPRS PDSRSEPRGS QELVSSCKSN 660 CRVFGFSLTE GAPVANEETD PSTVTFQLNS GPSFTRHCQ

Sequence ? help Back to Top

Protein Sequence Length: 699 aa Download sequence Send to blast

MAGLIDLNTT EDDETPSYGS YAASPSSSSS HSGTSTASVS ASAPVVPGSS SNSVCLELWH  60
ACAGSMISLP KKGTLVVYFP QGHSEQQLHD FPLSNNNNSI PPHVFCRVLD VKLHAEEGSD  120
EVYCQVLLVP ENEQKFQEGD IEADGEEEDT DAVMKATTPH MFCKTLTASD TSTHGGFSVP  180
RRAAEDCFPP LDYSQQRPSQ ELVAKDLHGR EWKFRHIYRG QPRRHLLTTG WSAFVNKKQL  240
VSGDAVLFLR GADGELRLGI RRAGQLKSDG KFSALPHQQL NHSTPVEVIN ALSSRCAFSV  300
HYNPRVSSSD FIIPVHKFLK SLDYSYSVGM RFRMRFETED AADRRITGLI IGINDVDPVR  360
WPGSKWRCLL VRWDDLETTR HNRVSPWEIE PSGSASTASS LMTAGLKRSK IGLPSVQLEF  420
PVPNGISTSD FGESLRFQKV LQGQEILGVN NPVNGINAQC HQLSELRRCY PGFTTAGHGT  480
IPQVSSDASC NGIGFGESFR FQKVLQGQEI LPSQPYGNGR LGAFDGYQML RSRNGWSAHM  540
NSNSSHLHAP FSSGQLSSPS SVLMFQQAFN PVSNSDYSNK ANQVKGGKAL QRGSYASEVD  600
GGTNASFPSY ETTFHGKAQE GKNSFTFLNL HDQLGGSPRS PDSRSEPRGS QELVSSCKSN  660
CRVFGFSLTE GAPVANEETD PSTVTFQLNS GPSFTRHCQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	1e-108	48	396	13	359	Auxin response factor 1
4ldy_B	1e-108	48	396	13	359	Auxin response factor 1
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). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Involved in the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269\|PubMed:10952886, ECO:0000269\|PubMed:12036261}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Aradu.PZ2UH

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269\|PubMed:19956801}.

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_015956412.1	0.0	auxin response factor 3 isoform X1
Refseq	XP_015956413.1	0.0	auxin response factor 3 isoform X1
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A445DQW8	0.0	A0A445DQW8_ARAHY; Auxin response factor
STRING	GLYMA07G32300.2	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4576	33	55

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	0.0	ARF family protein

Publications ? help Back to Top
Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors. Mol. Gen. Mikrobiol. Virusol., 2013. [PMID:24003511] Thoma R,Chandler JW Polarity in the early floral meristem of Arabidopsis. Plant Signal Behav, 2015. 10(4): p. e992733 [PMID:25806573] Lora J,Hormaza JI,Herrero M Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). New Phytol., 2015. 208(2): p. 584-95 [PMID:25991552] Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Cabrera J, et al. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. New Phytol., 2016. 209(4): p. 1625-40 [PMID:26542733] Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 2015. 27(12): p. 3321-35 [PMID:26589551] Yamaguchi N,Wu MF,Winter CM,Wagner D LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development. Plants (Basel), 2014. 3(2): p. 251-65 [PMID:27135503] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Simonini S, et al. A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2016. 30(20): p. 2286-2296 [PMID:27898393] Pfannebecker KC,Lange M,Rupp O,Becker A An Evolutionary Framework for Carpel Developmental Control Genes. Mol. Biol. Evol., 2017. 34(2): p. 330-348 [PMID:28049761] Wójcikowska B,Gaj MD Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis. Plant Cell Rep., 2017. 36(6): p. 843-858 [PMID:28255787] Su Z, et al. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr. Biol., 2017. 27(11): p. 1597-1609.e2 [PMID:28552357] Simonini S,Bencivenga S,Trick M,Østergaard L Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell, 2017. 29(8): p. 1864-1882 [PMID:28804059] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Simonini S, et al. Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2017. 31(17): p. 1821 [PMID:28982764] Zhang K, et al. AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling. Plant Cell, 2018. 30(2): p. 324-346 [PMID:29371438] Vial-Pradel S, et al. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). Plant Cell Physiol., 2018. 59(7): p. 1385-1397 [PMID:29415182] Simonini S,Stephenson P,Østergaard L A molecular framework controlling style morphology in Brassicaceae. Development, 2018. [PMID:29440299] Andres-Robin A, et al. Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics. Plant Physiol., 2018. 178(3): p. 1222-1232 [PMID:30237208] 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]