PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Saxifragales; Crassulaceae; Kalanchoe

Family

ARF

Protein Properties

Length: 696aa MW: 75491.5 Da PI: 7.6733

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kaladp0010s0049.2.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	75.6	5.8e-24	160	261	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 f+k+lt sd++++g +++p++ ae++ ++ + s++l+ +d++gr+W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + Kaladp0010s0049.2.p 160 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyTLQRP-SQELVAKDLHGREWKFRHIYRGQPRRHLLTTGWSAFVNRKKLVSGDAVLFLR 248 99**************************9955544.569**********************************************4 PP -SSSEE..EEEEE-S CS B3 85 dgrsefelvvkvfrk 99 ++ l+++v+r+ Kaladp0010s0049.2.p 249 G--GDGILRLGVRRA 261 3..677778888875 PP
2	Auxin_resp	102.6	5e-34	286	367	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++a+st+svF++ YnPr ++s+F+++ +k+ ++l +k+s G+R+km eted++err++G v+gvsdldp+ Wp+SkW++L Kaladp0010s0049.2.p 286 VINAISTRSVFNISYNPRGTSSDFIIPHSKFTRSLVHKFSCGTRLKMCCETEDAAERRFTGAVTGVSDLDPIGWPGSKWKCL 367 5799*****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.44E-40	156	269	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	8.0E-39	156	263	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	7.80E-23	158	260	No hit	No description
SMART	SM01019	1.0E-23	160	262	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.1E-22	160	261	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.563	160	262	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.4E-28	287	367	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: 696 aa Download sequence Send to blast
MAATGRGLNL FDLNTAEEED AAAGGSLSPS PSPSPTSTCS GVVPGSTGCV APSVCLELWH 60 ACVGPLVSLP KKNSLVVYFP QGQLECFGES PAVICGVPPH VFCRVLDVKL HAEVDSDEVC 120 AQVFLIPVAQ EQLPQVDKTE VDGEDDDINC GSKSMTRHMF CKTLTASDTS THGGFSVPRR 180 AAEDCFPPLD YTLQRPSQEL VAKDLHGREW KFRHIYRGQP RRHLLTTGWS AFVNRKKLVS 240 GDAVLFLRGG DGILRLGVRR AAQLKEKPPF PPIFREQQSH GSFSAVINAI STRSVFNISY 300 NPRGTSSDFI IPHSKFTRSL VHKFSCGTRL KMCCETEDAA ERRFTGAVTG VSDLDPIGWP 360 GSKWKCLLVE WDDSENNLHG GRVSPWEVEP AGFVVGCCMP APSGSKRGRN GLPSTIHNSP 420 IPDGKGLPDF RESLRFQKVL QGQEIMSLKP QNTQNHNLAE SLSCYPGTDS SRIGALGNKI 480 SRPYFGNPDF SFNNKGFGES QWFQRVLQGQ EKTSNMPYGM ISCTSSHDEL LGIFNGIALP 540 NFRQTALLHD SNSQFHAAKS SVPVSSPSSV LMFPQATSLV PNPCRVPGLL EGRGIGNQGQ 600 FNQQDLCGHG PRPALSGSQK LVPSCKNSCR LFGISLTDKE HAPNVADETI LKANQLNTGP 660 AFRITERQFL AQHPTMALGC LQKLDSASDA ITYGI*

Sequence ? help Back to Top

Protein Sequence Length: 696 aa Download sequence Send to blast

MAATGRGLNL FDLNTAEEED AAAGGSLSPS PSPSPTSTCS GVVPGSTGCV APSVCLELWH  60
ACVGPLVSLP KKNSLVVYFP QGQLECFGES PAVICGVPPH VFCRVLDVKL HAEVDSDEVC  120
AQVFLIPVAQ EQLPQVDKTE VDGEDDDINC GSKSMTRHMF CKTLTASDTS THGGFSVPRR  180
AAEDCFPPLD YTLQRPSQEL VAKDLHGREW KFRHIYRGQP RRHLLTTGWS AFVNRKKLVS  240
GDAVLFLRGG DGILRLGVRR AAQLKEKPPF PPIFREQQSH GSFSAVINAI STRSVFNISY  300
NPRGTSSDFI IPHSKFTRSL VHKFSCGTRL KMCCETEDAA ERRFTGAVTG VSDLDPIGWP  360
GSKWKCLLVE WDDSENNLHG GRVSPWEVEP AGFVVGCCMP APSGSKRGRN GLPSTIHNSP  420
IPDGKGLPDF RESLRFQKVL QGQEIMSLKP QNTQNHNLAE SLSCYPGTDS SRIGALGNKI  480
SRPYFGNPDF SFNNKGFGES QWFQRVLQGQ EKTSNMPYGM ISCTSSHDEL LGIFNGIALP  540
NFRQTALLHD SNSQFHAAKS SVPVSSPSSV LMFPQATSLV PNPCRVPGLL EGRGIGNQGQ  600
FNQQDLCGHG PRPALSGSQK LVPSCKNSCR LFGISLTDKE HAPNVADETI LKANQLNTGP  660
AFRITERQFL AQHPTMALGC LQKLDSASDA ITYGI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-101	48	390	13	354	Auxin response factor 1
4ldw_A	1e-101	48	390	13	354	Auxin response factor 1
4ldw_B	1e-101	48	390	13	354	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}.

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_010655464.1	0.0	PREDICTED: auxin response factor 3
Refseq	XP_019078171.1	0.0	PREDICTED: auxin response factor 3
Swissprot	O23661	1e-171	ARFC_ARATH; Auxin response factor 3
TrEMBL	F6HM45	0.0	F6HM45_VITVI; Auxin response factor
STRING	VIT_10s0003g00420.t01	0.0	(Vitis vinifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	1e-173	ARF family protein

Link Out ? help Back to Top
Phytozome	Kaladp0010s0049.2.p

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]