PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Salvia

Family

ARF

Protein Properties

Length: 1062aa MW: 117688 Da PI: 5.9219

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
SMil_00003923-RA_Salv	genome	NDCTCM	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	76.2	3.7e-24	155	256	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvF 82 f+k+lt sd++++g +++p++ ae+ ++++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv a++L++gD v+F SMil_00003923-RA_Salv 155 FCKTLTASDTSTHGGFSVPRRAAEKLfpqldySMQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSMFVGAKRLRAGDAVLF 241 99*******************999*9555554.49********************************************* PP EE-SSSEE..EEEEE-S CS B3 83 kldgrsefelvvkvfrk 99 ++++ +l+++v+r+ SMil_00003923-RA_Salv 242 I--RDEKSQLLLGVRRA 256 *..45677789999997 PP
2	Auxin_resp	115.6	4.3e-38	281	364	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++seFv++++k++ka++ +++s+GmRf ++fete+s +rr++Gt++g+sd+dp+rWpnSkWrsL+ SMil_00003923-RA_Salv 281 AAHAAANRSPFTIFYNPRACPSEFVIPLAKYRKAVYgTQLSIGMRFGIMFETEESTKRRYMGTIIGISDIDPLRWPNSKWRSLQ 364 79********************************9*******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.7E-47	142	284	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	9.3E-42	148	269	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.54E-22	154	255	No hit	No description
PROSITE profile	PS50863	13.155	155	257	IPR003340	B3 DNA binding domain
SMART	SM01019	8.9E-23	155	257	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.5E-21	155	256	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.6E-33	281	364	IPR010525	Auxin response factor
Pfam	PF02309	2.2E-8	818	907	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.528	821	904	IPR000270	PB1 domain
SuperFamily	SSF54277	2.94E-8	834	899	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: 1062 aa Download sequence Send to blast
LREGERKGEM ASVEEKLKPG GLVSGGSNLI DGMKLLKEMQ DHTGVKKAIN SELWHACAGP 60 LVTLPQVGSL VYYFPQGHSE QVAVSTNRSA TTQIPNYPNL PTQLLCQVHN VTLHADKETD 120 EIYAQMSLQC VNTEKDVFPI PDFGLKPSKH PTEFFCKTLT ASDTSTHGGF SVPRRAAEKL 180 FPQLDYSMQP PTQELVVRDL HDNTWTFRHI YRGQPKRHLL TTGWSMFVGA KRLRAGDAVL 240 FIRDEKSQLL LGVRRANRQQ TTLPSSVLSA DSMHIGILAA AAHAAANRSP FTIFYNPRAC 300 PSEFVIPLAK YRKAVYGTQL SIGMRFGIMF ETEESTKRRY MGTIIGISDI DPLRWPNSKW 360 RSLQVEWDEP GCGDKQNRVS PWEIETPESL FIFPSLTANL KRPFHSAFIG APPEWDSLMN 420 RPFLRVPDNP HGEFQCPSIS SMWSEQLLKM LAKPHGMMMT PHSMQEMKDV ALQEPRSLMQ 480 PAIKQKPEMM VPQDVCLQSE THSQSFIGQP YITNPSISPA GKPNISRNLT SPAAGHELSK 540 LDSVPAENQS GQCRSEGQLS EEKLSGKPVN PQSLNNDFVV TSQIGGSVPF QTSPCGTQSR 600 LETHSPVDPS QVESANATNA MLQYTNQVDF SPYHMMCPSP SGSFRNTGSL SMFKKPDQSP 660 LSSEVVYPML PSVGQELWDD GPKCAGNLPV LLPHHDMSNL VLKDLSDENH NQSDIYSCLN 720 LDGSNSGSTV VDPCVSSSIL DDFSALKNMD FPNPSDYMVG GFCSTQDVQS QITSASLADS 780 QTFSIQEYAD NSGGASSSNV DFDDNNLLQQ SSFQQVTPRF RTYTKIQKAG SVGRSIDVSS 840 FKTYKQLRSE IERMFGLEGL LNDPGSGWKL VYVDFESDVL LVGDDPWEEF VGCVRCIRIL 900 SPSEVKQMGE EGMQLLNSAM QNSPIINDTV VALERDPTLD KRGGVLHEGN KELSALGPDN 960 IASRISQLEE QVSQWMKMLS DKTTKRGRGR PKGTGKGMGS EPMQAVPEGS IKGHLRNAGE 1020 MGYKPRDFVV DCSNSDSMRA MNNIVHRRWS DEMDDYPDLW DC

Sequence ? help Back to Top

Protein Sequence Length: 1062 aa Download sequence Send to blast

LREGERKGEM ASVEEKLKPG GLVSGGSNLI DGMKLLKEMQ DHTGVKKAIN SELWHACAGP  60
LVTLPQVGSL VYYFPQGHSE QVAVSTNRSA TTQIPNYPNL PTQLLCQVHN VTLHADKETD  120
EIYAQMSLQC VNTEKDVFPI PDFGLKPSKH PTEFFCKTLT ASDTSTHGGF SVPRRAAEKL  180
FPQLDYSMQP PTQELVVRDL HDNTWTFRHI YRGQPKRHLL TTGWSMFVGA KRLRAGDAVL  240
FIRDEKSQLL LGVRRANRQQ TTLPSSVLSA DSMHIGILAA AAHAAANRSP FTIFYNPRAC  300
PSEFVIPLAK YRKAVYGTQL SIGMRFGIMF ETEESTKRRY MGTIIGISDI DPLRWPNSKW  360
RSLQVEWDEP GCGDKQNRVS PWEIETPESL FIFPSLTANL KRPFHSAFIG APPEWDSLMN  420
RPFLRVPDNP HGEFQCPSIS SMWSEQLLKM LAKPHGMMMT PHSMQEMKDV ALQEPRSLMQ  480
PAIKQKPEMM VPQDVCLQSE THSQSFIGQP YITNPSISPA GKPNISRNLT SPAAGHELSK  540
LDSVPAENQS GQCRSEGQLS EEKLSGKPVN PQSLNNDFVV TSQIGGSVPF QTSPCGTQSR  600
LETHSPVDPS QVESANATNA MLQYTNQVDF SPYHMMCPSP SGSFRNTGSL SMFKKPDQSP  660
LSSEVVYPML PSVGQELWDD GPKCAGNLPV LLPHHDMSNL VLKDLSDENH NQSDIYSCLN  720
LDGSNSGSTV VDPCVSSSIL DDFSALKNMD FPNPSDYMVG GFCSTQDVQS QITSASLADS  780
QTFSIQEYAD NSGGASSSNV DFDDNNLLQQ SSFQQVTPRF RTYTKIQKAG SVGRSIDVSS  840
FKTYKQLRSE IERMFGLEGL LNDPGSGWKL VYVDFESDVL LVGDDPWEEF VGCVRCIRIL  900
SPSEVKQMGE EGMQLLNSAM QNSPIINDTV VALERDPTLD KRGGVLHEGN KELSALGPDN  960
IASRISQLEE QVSQWMKMLS DKTTKRGRGR PKGTGKGMGS EPMQAVPEGS IKGHLRNAGE  1020
MGYKPRDFVV DCSNSDSMRA MNNIVHRRWS DEMDDYPDLW DC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	8	389	3	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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	KX036726	0.0	KX036726.1 Salvia miltiorrhiza auxin response factor ARF6 (ARF) gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_011083507.1	0.0	auxin response factor 5
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A191T8S8	0.0	A0A191T8S8_SALMI; Auxin response factor
STRING	XP_009778804.1	0.0	(Nicotiana sylvestris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA5859	23	34

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

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]