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: 738aa MW: 80405.2 Da PI: 7.7596

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kalax.0092s0025.1.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	6.3e-24	171	272	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 + Kalax.0092s0025.1.p 171 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyTLQRP-SQELVAKDLHGREWKFRHIYRGQPRRHLLTTGWSAFVNRKKLVSGDAVLFLR 259 99**************************9955544.569**********************************************4 PP -SSSEE..EEEEE-S CS B3 85 dgrsefelvvkvfrk 99 ++ l+++v+r+ Kalax.0092s0025.1.p 260 G--GDGILRLGVRRA 272 3..677778888875 PP
2	Auxin_resp	99.7	3.9e-33	297	378	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++a+st+svF++ YnPr ++s+F+++ +k+ ++l +k+s G+R+k+ eted++err++G v+gvsdldp+ Wp+SkW++L Kalax.0092s0025.1.p 297 VINAISTRSVFNISYNPRGTSSDFIIPHSKFTRSLGHKFSCGTRLKLCCETEDAAERRFTGAVTGVSDLDPIGWPGSKWKCL 378 5799*****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	8.8E-39	167	274	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.57E-40	167	280	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.95E-23	169	271	No hit	No description
Pfam	PF02362	9.9E-22	171	272	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.563	171	273	IPR003340	B3 DNA binding domain
SMART	SM01019	1.0E-23	171	273	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.1E-27	298	378	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: 738 aa Download sequence Send to blast
MICAVEGLSE ILAMAAAGRG LNLFDLNTAE EEDAAAGGSL SPSPSPTSTC SGVVPGSIGC 60 VAPSVCLELW HACVGPLVSL PKKNSFVVYF PQGQLECFGE SPAVICGVPP HVFCRVLDVK 120 LHAEVDSDDV CAQVFLIPVA QEQLPQVDKT EVDGENDDIN CGSKSMTRHM FCKTLTASDT 180 STHGGFSVPR RAAEDCFPPL DYTLQRPSQE LVAKDLHGRE WKFRHIYRGQ PRRHLLTTGW 240 SAFVNRKKLV SGDAVLFLRG GDGILRLGVR RAAQLKEKPP FPPIFREQQT HGSFSAVINA 300 ISTRSVFNIS YNPRGTSSDF IIPHSKFTRS LGHKFSCGTR LKLCCETEDA AERRFTGAVT 360 GVSDLDPIGW PGSKWKCLLV EWDDSENNLH GSRVSPWEVE PAGFVVGCCM PAPSGSKRGR 420 NGLPSTIHDL PIPDGKGLPD FRESLRFQKV LQGQEIMSLK PQNTQNHNLV ESLSCYPGTD 480 SSRIGALGNK ISRPYFGNPD FSFNNKGFGE SQWFQRVLQG QEKTSNMPYG MISCTSSHDE 540 LLGIFNGIAL PNFRRTALLH DSNSQFHAAK SSVPVSSPSS VLMFPQATSL VTYPCRVPGL 600 LEGRGIGNQG QVSPTRPYVG ELPSSYIKDN FGRFESCIPR TQFNQQDFCG HGPRPALTGS 660 QKLVPSCKNS CRLFGISLTD KEHAPNVADE TILKANQLNT GPAFRITERQ FLAQHPTVAL 720 GRLQKYDSAS DAITYGI*

Sequence ? help Back to Top

Protein Sequence Length: 738 aa Download sequence Send to blast

MICAVEGLSE ILAMAAAGRG LNLFDLNTAE EEDAAAGGSL SPSPSPTSTC SGVVPGSIGC  60
VAPSVCLELW HACVGPLVSL PKKNSFVVYF PQGQLECFGE SPAVICGVPP HVFCRVLDVK  120
LHAEVDSDDV CAQVFLIPVA QEQLPQVDKT EVDGENDDIN CGSKSMTRHM FCKTLTASDT  180
STHGGFSVPR RAAEDCFPPL DYTLQRPSQE LVAKDLHGRE WKFRHIYRGQ PRRHLLTTGW  240
SAFVNRKKLV SGDAVLFLRG GDGILRLGVR RAAQLKEKPP FPPIFREQQT HGSFSAVINA  300
ISTRSVFNIS YNPRGTSSDF IIPHSKFTRS LGHKFSCGTR LKLCCETEDA AERRFTGAVT  360
GVSDLDPIGW PGSKWKCLLV EWDDSENNLH GSRVSPWEVE PAGFVVGCCM PAPSGSKRGR  420
NGLPSTIHDL PIPDGKGLPD FRESLRFQKV LQGQEIMSLK PQNTQNHNLV ESLSCYPGTD  480
SSRIGALGNK ISRPYFGNPD FSFNNKGFGE SQWFQRVLQG QEKTSNMPYG MISCTSSHDE  540
LLGIFNGIAL PNFRRTALLH DSNSQFHAAK SSVPVSSPSS VLMFPQATSL VTYPCRVPGL  600
LEGRGIGNQG QVSPTRPYVG ELPSSYIKDN FGRFESCIPR TQFNQQDFCG HGPRPALTGS  660
QKLVPSCKNS CRLFGISLTD KEHAPNVADE TILKANQLNT GPAFRITERQ FLAQHPTVAL  720
GRLQKYDSAS DAITYGI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-98	59	401	13	354	Auxin response factor 1
4ldw_A	1e-98	59	401	13	354	Auxin response factor 1
4ldw_B	1e-98	59	401	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	A0A2N9G8C1	0.0	A0A2N9G8C1_FAGSY; 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-172	ARF family protein

Link Out ? help Back to Top
Phytozome	Kalax.0092s0025.1.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]