PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus

Family

ARF

Protein Properties

Length: 687aa MW: 76547.2 Da PI: 6.5168

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Potri.002G172800.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	72.3	6.2e-23	116	216	1	98
EEEE-..-HHHHTT-EE--HHH.HTT.....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 f+k+lt sd++++g +++ +k+a+e+ +++ + +++l +d++g +W++k+i+r++++r++lt+GW+ Fv +++L +gD +vF + Potri.002G172800.1 116 FCKILTASDTSTHGGFSVLRKHATEClppldMSQATPTQELAARDLHGFEWRFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDAFVFLR-- 204 99**************************9555566679********************************************3.. PP SSEE..EEEEE- CS B3 87 rsefelvvkvfr 98 +++el+v+v+r Potri.002G172800.1 205 GHNRELRVGVRR 216 378889*998 PP
2	Auxin_resp	94.1	2.2e-31	242	321	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha+ t++ F v+Y+Pr+ ++++ ++k+++a+k+ +svGmRfkm+fe+eds+err++Gt+vgv d++p +W++S WrsLk Potri.002G172800.1 242 ASHAVLTQTLFVVYYKPRT--NQYIIGLNKYLEAVKNGFSVGMRFKMRFEGEDSPERRFTGTIVGVGDISP-EWSGSIWRSLK 321 68999***********6..99******************************************99.*******96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	8.11E-41	107	245	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.5E-39	109	231	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.63E-19	114	216	No hit	No description
Pfam	PF02362	6.0E-21	116	216	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.321	116	218	IPR003340	B3 DNA binding domain
SMART	SM01019	1.9E-21	116	218	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.3E-29	242	321	IPR010525	Auxin response factor
Pfam	PF02309	3.0E-6	550	607	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	1.9E-12	566	647	No hit	No description
PROSITE profile	PS51745	25.856	571	652	IPR000270	PB1 domain
Pfam	PF02309	5.6E-6	617	655	IPR033389	AUX/IAA domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 687 aa Download sequence Send to blast
MAHAERGCDD LYTELWKACA GPLVDVPKDG ERVFYFPQGH MEQLEASTNQ ELNQQIPRFN 60 LPPKILCRVV NIQLLAEQDT DEVYAQITLH PEVDQTEPTS PDPCPPEPAK PTIHSFCKIL 120 TASDTSTHGG FSVLRKHATE CLPPLDMSQA TPTQELAARD LHGFEWRFKH IFRGQPRRHL 180 LTTGWSTFVT SKRLVAGDAF VFLRGHNREL RVGVRRLARQ QSSIPSSVIS SQSMHLGVLA 240 TASHAVLTQT LFVVYYKPRT NQYIIGLNKY LEAVKNGFSV GMRFKMRFEG EDSPERRFTG 300 TIVGVGDISP EWSGSIWRSL KIQWDEPATI QRPERVSPWD IEPFAAPASP NLTQQVMKTK 360 RPRPTDIPTS AASSFWYHGS TQSHELAQLG SSNEVQSSES HVWSMRQKEI DSSLLNNSSS 420 SNTRARPEGI WPSSPNMNVS LNFFPDSVGD NNFATTRSII SGFSSPISSR QSNCLINEQV 480 EKGRKYENSV GCRLFGIDLT SNSGSSAPPE KEPGYPIVDS NGTKGLVPAA SEAERAQAMD 540 VSMYSKEQKQ VLSEAMVKES QSKQGSTTSM RTRTKVQMQG IAVGRALDLT VLKGYRDLIY 600 ELEKMFEIEG ELSTPNKWAV VFTDDEGDMM LVGDDPWPEF CKMVKKIFIY SSEEVKKTGT 660 RCKLPASSFE GEETVVSMDS DHRSDA*

Sequence ? help Back to Top

Protein Sequence Length: 687 aa Download sequence Send to blast

MAHAERGCDD LYTELWKACA GPLVDVPKDG ERVFYFPQGH MEQLEASTNQ ELNQQIPRFN  60
LPPKILCRVV NIQLLAEQDT DEVYAQITLH PEVDQTEPTS PDPCPPEPAK PTIHSFCKIL  120
TASDTSTHGG FSVLRKHATE CLPPLDMSQA TPTQELAARD LHGFEWRFKH IFRGQPRRHL  180
LTTGWSTFVT SKRLVAGDAF VFLRGHNREL RVGVRRLARQ QSSIPSSVIS SQSMHLGVLA  240
TASHAVLTQT LFVVYYKPRT NQYIIGLNKY LEAVKNGFSV GMRFKMRFEG EDSPERRFTG  300
TIVGVGDISP EWSGSIWRSL KIQWDEPATI QRPERVSPWD IEPFAAPASP NLTQQVMKTK  360
RPRPTDIPTS AASSFWYHGS TQSHELAQLG SSNEVQSSES HVWSMRQKEI DSSLLNNSSS  420
SNTRARPEGI WPSSPNMNVS LNFFPDSVGD NNFATTRSII SGFSSPISSR QSNCLINEQV  480
EKGRKYENSV GCRLFGIDLT SNSGSSAPPE KEPGYPIVDS NGTKGLVPAA SEAERAQAMD  540
VSMYSKEQKQ VLSEAMVKES QSKQGSTTSM RTRTKVQMQG IAVGRALDLT VLKGYRDLIY  600
ELEKMFEIEG ELSTPNKWAV VFTDDEGDMM LVGDDPWPEF CKMVKKIFIY SSEEVKKTGT  660
RCKLPASSFE GEETVVSMDS DHRSDA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-176	9	344	17	355	Auxin response factor 1
4ldw_A	1e-176	9	344	17	355	Auxin response factor 1
4ldw_B	1e-176	9	344	17	355	Auxin response factor 1
4ldx_A	1e-176	9	344	17	355	Auxin response factor 1
4ldx_B	1e-176	9	344	17	355	Auxin response factor 1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	359	363	KRPRP

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pth.6813	0.0	catkin

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. {ECO:0000269\|PubMed:12036261}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Potri.002G172800.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	KT164698	0.0	KT164698.1 Populus tomentosa clone Potom.002G07206 auxin response factor 11 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024451070.1	0.0	auxin response factor 18 isoform X3
Swissprot	Q9C5W9	0.0	ARFR_ARATH; Auxin response factor 18
TrEMBL	A0A2K2BK81	0.0	A0A2K2BK81_POPTR; Auxin response factor
STRING	POPTR_0002s17350.1	0.0	(Populus trichocarpa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF1511	33	96
Representative plant	OGRP550	15	82

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G59750.3	0.0	auxin response factor 1

Link Out ? help Back to Top
Phytozome	Potri.002G172800.1
Entrez Gene	18096378

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] 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]