PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Caricaceae; Carica

Family

ARF

Protein Properties

Length: 939aa MW: 103701 Da PI: 5.0076

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm.model.supercontig_26.24	genome	ASGPB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.9	1.1e-24	148	249	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT-- CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLk 75 f+k+lt sd++++g +++p++ ae+ ++++ + ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv +++L+ evm.model.supercontig_26.24 148 FCKTLTASDTSTHGGFSVPRRAAEKLfppldytMQPP-T-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSMFVGSKRLR 227 99*******************999*954444.4.38************************************ PP TT-EEEEEE-SSSEE..EEEEE-S CS B3 76 egDfvvFkldgrsefelvvkvfrk 99 +gD+v+F ++++ +l+v+v+r+ evm.model.supercontig_26.24 228 AGDSVLFI--RDEKSQLMVGVRRA 249 ****..4577778***97 PP
2	Auxin_resp	115.2	5.6e-38	274	357	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrs 81 aahaa+++s+F+++YnPra++seFv++++k++k++ +++svGmRf m+fete+s +rr++Gt+vg+sdldp+rWp+SkWr+ evm.model.supercontig_26.24 274 AAHAAANRSPFTIFYNPRACPSEFVIPMAKYRKSVFgTQLSVGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRN 355 79******************************988******************************************* PP Auxin_resp 82 Lk 83 L+ evm.model.supercontig_26.24 356 LQ 357 97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.23E-46	135	277	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	8.5E-42	142	262	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.87E-23	147	248	No hit	No description
Pfam	PF02362	3.8E-22	148	249	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.324	148	250	IPR003340	B3 DNA binding domain
SMART	SM01019	1.5E-24	148	250	IPR003340	B3 DNA binding domain
Pfam	PF06507	5.6E-33	274	357	IPR010525	Auxin response factor
Pfam	PF02309	6.1E-10	820	910	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.737	824	908	IPR000270	PB1 domain
SuperFamily	SSF54277	5.23E-9	835	903	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009733	Biological Process	response to auxin
GO:0009908	Biological Process	flower development
GO:0009942	Biological Process	longitudinal axis specification
GO:0010305	Biological Process	leaf vascular tissue pattern formation
GO:0048364	Biological Process	root development
GO:0048507	Biological Process	meristem development
GO:0005634	Cellular Component	nucleus
GO:0016020	Cellular Component	membrane
GO:0042802	Molecular Function	identical protein binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 939 aa Download sequence Send to blast
MASVEDNIKT SVLLTGPAQT TLFEEMKLLK EMQDPSGDRK AINSELWHAC AGPLVFLPQV 60 GSLVYYFPQG HSEQVAVSTK RTATSQIPNY PNLQSQLMCQ VHNVTLHADK DTDEIYAQMS 120 LQPVNSERDV FPIPDFGLRL SKHPSEFFCK TLTASDTSTH GGFSVPRRAA EKLFPPLDYT 180 MQPPTQELVV RDLHDNTWTF RHIYRGQPKR HLLTTGWSMF VGSKRLRAGD SVLFIRDEKS 240 QLMVGVRRAN RQQTTLPSSV LSADSMHIGV LAAAAHAAAN RSPFTIFYNP RACPSEFVIP 300 MAKYRKSVFG TQLSVGMRFG MMFETEESGK RRYMGTIVGI SDLDPLRWPG SKWRNLQVEW 360 DEPGCNDKQS RVSAWEIETP ESLFIFPSLT SGLKRSLHPG LLATETEWGN LIKRPIIRVP 420 DISNGDFPYS VSNLCSEKLM KMMLKPQLVN HPGSGAFAST LQVPVATGTS LEGATNMQAA 480 INQKSQIFQT ENRLIEKQNY PQFCPSQPTA VSSNSSKVTV PVDAHPEVKA ESSTPTGSNS 540 EKLKLEPEHS TDQLSQLTST TECNKEKFVS TSMNSESQMN QPTLNNQIHL QSNPWTMQPQ 600 LECSQQMYPA QSDSTITGLP SFPESDEWTS HLSSCQSLAT TYTSPGPVTM FGTQDSSAML 660 SEVFNPSMDQ DIWDHQLNNL KIFSQPDQFT SFMQPDPCSL NSTGLRDLSD ESNNQSGIYS 720 CLNIEAGGGG STVINPSVSN AILDEFCSLK EADFQNPTDC LIGNFSTSQD VQSQITSASL 780 AESQALSRQD FPDNSGGTSS SNIDFDESSL LQNSSWQQVA PRVRTYTKVQ KAGSVGRSID 840 VTSFKNYDEL CSAIECMFGL EGLLNDRRGS GWKLVYVDYE NDVLLVGDDP WEEFVGCVRC 900 IRILSPTEVQ QMSEEGMKLL NSAAMQGMKV AISEGGCA*

Sequence ? help Back to Top

Protein Sequence Length: 939 aa Download sequence Send to blast

MASVEDNIKT SVLLTGPAQT TLFEEMKLLK EMQDPSGDRK AINSELWHAC AGPLVFLPQV  60
GSLVYYFPQG HSEQVAVSTK RTATSQIPNY PNLQSQLMCQ VHNVTLHADK DTDEIYAQMS  120
LQPVNSERDV FPIPDFGLRL SKHPSEFFCK TLTASDTSTH GGFSVPRRAA EKLFPPLDYT  180
MQPPTQELVV RDLHDNTWTF RHIYRGQPKR HLLTTGWSMF VGSKRLRAGD SVLFIRDEKS  240
QLMVGVRRAN RQQTTLPSSV LSADSMHIGV LAAAAHAAAN RSPFTIFYNP RACPSEFVIP  300
MAKYRKSVFG TQLSVGMRFG MMFETEESGK RRYMGTIVGI SDLDPLRWPG SKWRNLQVEW  360
DEPGCNDKQS RVSAWEIETP ESLFIFPSLT SGLKRSLHPG LLATETEWGN LIKRPIIRVP  420
DISNGDFPYS VSNLCSEKLM KMMLKPQLVN HPGSGAFAST LQVPVATGTS LEGATNMQAA  480
INQKSQIFQT ENRLIEKQNY PQFCPSQPTA VSSNSSKVTV PVDAHPEVKA ESSTPTGSNS  540
EKLKLEPEHS TDQLSQLTST TECNKEKFVS TSMNSESQMN QPTLNNQIHL QSNPWTMQPQ  600
LECSQQMYPA QSDSTITGLP SFPESDEWTS HLSSCQSLAT TYTSPGPVTM FGTQDSSAML  660
SEVFNPSMDQ DIWDHQLNNL KIFSQPDQFT SFMQPDPCSL NSTGLRDLSD ESNNQSGIYS  720
CLNIEAGGGG STVINPSVSN AILDEFCSLK EADFQNPTDC LIGNFSTSQD VQSQITSASL  780
AESQALSRQD FPDNSGGTSS SNIDFDESSL LQNSSWQQVA PRVRTYTKVQ KAGSVGRSID  840
VTSFKNYDEL CSAIECMFGL EGLLNDRRGS GWKLVYVDYE NDVLLVGDDP WEEFVGCVRC  900
IRILSPTEVQ QMSEEGMKLL NSAAMQGMKV AISEGGCA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	382	5	392	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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:17553903}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00153	DAP	Transfer from AT1G19850	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	evm.model.supercontig_26.24

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021902478.1	0.0	auxin response factor 5 isoform X1
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A1R3IY13	0.0	A0A1R3IY13_COCAP; Auxin response factor
STRING	evm.model.supercontig_26.24	0.0	(Carica papaya)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5808	27	46
Representative plant	OGRP8260	12	16

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19850.1	0.0	ARF family protein

Link Out ? help Back to Top
Phytozome	evm.model.supercontig_26.24

Publications ? help Back to Top
Chen MK,Wilson RL,Palme K,Ditengou FA,Shpak ED ERECTA family genes regulate auxin transport in the shoot apical meristem and forming leaf primordia. Plant Physiol., 2013. 162(4): p. 1978-91 [PMID:23821653] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Qi J, et al. Auxin depletion from leaf primordia contributes to organ patterning. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(52): p. 18769-74 [PMID:25512543] Crawford BC, et al. Plant development. Genetic control of distal stem cell fate within root and embryonic meristems. Science, 2015. 347(6222): p. 655-9 [PMID:25612610] Zhang Y, et al. Regulation of oncogene expression in T-DNA-transformed host plant cells. PLoS Pathog., 2015. 11(1): p. e1004620 [PMID:25615824] Robert HS, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development, 2015. 142(4): p. 702-11 [PMID:25617434] Krogan NT,Berleth T The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal Behav, 2015. 10(4): p. e992748 [PMID:25830553] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Wendrich JR, et al. A set of domain-specific markers in the Arabidopsis embryo. Plant Reprod, 2015. 28(3-4): p. 153-60 [PMID:26216537] Wu MF, et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. Elife, 2015. 4: p. e09269 [PMID:26460543] Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Plant Physiol., 2016. 170(1): p. 283-93 [PMID:26537561] Müller CJ, et al. PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis. Plant Physiol., 2016. 170(2): p. 956-70 [PMID:26637548] Herud O,Weijers D,Lau S,Jürgens G Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. Plant J., 2016. 85(2): p. 269-77 [PMID:26714008] Luo S, et al. Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis. Front Plant Sci, 2015. 6: p. 1156 [PMID:26734051] 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] Krogan NT,Marcos D,Weiner AI,Berleth T The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes. New Phytol., 2016. 212(1): p. 42-50 [PMID:27441727] Fendrych M,Leung J,Friml J TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. Elife, 2018. [PMID:27627746] Matthes M,Torres-Ruiz RA Boronic acid treatment phenocopies monopteros by affecting PIN1 membrane stability and polar auxin transport in Arabidopsis thaliana embryos. Development, 2016. 143(21): p. 4053-4062 [PMID:27697905] Bhatia N, et al. Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis. Curr. Biol., 2016. 26(23): p. 3202-3208 [PMID:27818174] 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] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] 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] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Gaillochet C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. Elife, 2018. [PMID:29058667] Zheng K, et al. Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis. Front Plant Sci, 2017. 8: p. 1813 [PMID:29114256] Liu Z, et al. ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis. Plant Cell Physiol., 2018. 59(1): p. 179-189 [PMID:29145642]