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: 709aa MW: 76822.1 Da PI: 7.4384

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kaladp0010s0049.6.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	75.5	5.9e-24	173	274	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 + Kaladp0010s0049.6.p 173 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyTLQRP-SQELVAKDLHGREWKFRHIYRGQPRRHLLTTGWSAFVNRKKLVSGDAVLFLR 261 99**************************9955544.569**********************************************4 PP -SSSEE..EEEEE-S CS B3 85 dgrsefelvvkvfrk 99 ++ l+++v+r+ Kaladp0010s0049.6.p 262 G--GDGILRLGVRRA 274 3..677778888875 PP
2	Auxin_resp	102.5	5.2e-34	299	380	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 Kaladp0010s0049.6.p 299 VINAISTRSVFNISYNPRGTSSDFIIPHSKFTRSLVHKFSCGTRLKMCCETEDAAERRFTGAVTGVSDLDPIGWPGSKWKCL 380 5799*****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.57E-40	169	282	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	8.3E-39	169	276	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.15E-23	171	273	No hit	No description
SMART	SM01019	1.0E-23	173	275	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.563	173	275	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.3E-22	173	274	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.5E-28	300	380	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: 709 aa Download sequence Send to blast
MICAVEGLSE ILAMAATGRG LNLFDLNTAE EEDAAAGGSL SPSPSPSPTS TCSGVVPGST 60 GCVAPSVCLE LWHACVGPLV SLPKKNSLVV YFPQGQLECF GESPAVICGV PPHVFCRVLD 120 VKLHAEVDSD EVCAQVFLIP VAQEQLPQVD KTEVDGEDDD INCGSKSMTR HMFCKTLTAS 180 DTSTHGGFSV PRRAAEDCFP PLDYTLQRPS QELVAKDLHG REWKFRHIYR GQPRRHLLTT 240 GWSAFVNRKK LVSGDAVLFL RGGDGILRLG VRRAAQLKEK PPFPPIFREQ QSHGSFSAVI 300 NAISTRSVFN ISYNPRGTSS DFIIPHSKFT RSLVHKFSCG TRLKMCCETE DAAERRFTGA 360 VTGVSDLDPI GWPGSKWKCL LVEWDDSENN LHGGRVSPWE VEPAGFVVGC CMPAPSGSKR 420 GRNGLPSTIH NSPIPDGKGL PDFRESLRFQ KVLQGQEIMS LKPQNTQNHN LAESLSCYPG 480 TDSSRIGALG NKISRPYFGN PDFSFNNKGF GESQWFQRVL QGQEKTSNMP YGMISCTSSH 540 DELLGIFNGI ALPNFRQTAL LHDSNSQFHA AKSSVPVSSP SSVLMFPQAT SLVPNPCRVP 600 GLLEGRGIGN QGQFNQQDLC GHGPRPALSG SQKLVPSCKN SCRLFGISLT DKEHAPNVAD 660 ETILKANQLN TGPAFRITER QFLAQHPTMA LGCLQKLDSA SDAITYGI*

Sequence ? help Back to Top

Protein Sequence Length: 709 aa Download sequence Send to blast

MICAVEGLSE ILAMAATGRG LNLFDLNTAE EEDAAAGGSL SPSPSPSPTS TCSGVVPGST  60
GCVAPSVCLE LWHACVGPLV SLPKKNSLVV YFPQGQLECF GESPAVICGV PPHVFCRVLD  120
VKLHAEVDSD EVCAQVFLIP VAQEQLPQVD KTEVDGEDDD INCGSKSMTR HMFCKTLTAS  180
DTSTHGGFSV PRRAAEDCFP PLDYTLQRPS QELVAKDLHG REWKFRHIYR GQPRRHLLTT  240
GWSAFVNRKK LVSGDAVLFL RGGDGILRLG VRRAAQLKEK PPFPPIFREQ QSHGSFSAVI  300
NAISTRSVFN ISYNPRGTSS DFIIPHSKFT RSLVHKFSCG TRLKMCCETE DAAERRFTGA  360
VTGVSDLDPI GWPGSKWKCL LVEWDDSENN LHGGRVSPWE VEPAGFVVGC CMPAPSGSKR  420
GRNGLPSTIH NSPIPDGKGL PDFRESLRFQ KVLQGQEIMS LKPQNTQNHN LAESLSCYPG  480
TDSSRIGALG NKISRPYFGN PDFSFNNKGF GESQWFQRVL QGQEKTSNMP YGMISCTSSH  540
DELLGIFNGI ALPNFRQTAL LHDSNSQFHA AKSSVPVSSP SSVLMFPQAT SLVPNPCRVP  600
GLLEGRGIGN QGQFNQQDLC GHGPRPALSG SQKLVPSCKN SCRLFGISLT DKEHAPNVAD  660
ETILKANQLN TGPAFRITER QFLAQHPTMA LGCLQKLDSA SDAITYGI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-101	61	403	13	354	Auxin response factor 1
4ldw_A	1e-101	61	403	13	354	Auxin response factor 1
4ldw_B	1e-101	61	403	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-170	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	Kaladp0010s0049.6.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]