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; Brassicaceae; Arabideae; Arabis

Family

ARF

Protein Properties

Length: 1079aa MW: 119573 Da PI: 6.7942

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KFK44062.1	genome	MPIPBR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73.1	3.3e-23	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++++ +l KFK44062.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV--RDEKSQL 220 99***************************954.4444.48********************************************..4567778 PP EEEEE-S CS B3 93 vvkvfrk 99 +++++r+ KFK44062.1 221 MLGIRRA 227 **997 PP
2	Auxin_resp	118.5	5.3e-39	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha +++s+F++++nPras+seFvv+++k++kal+ +vs+GmRf+m+feted+ rr++Gtv+g+sdldpvrW++S+Wr+L+ KFK44062.1 252 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 334 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.4E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	8.0E-42	120	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.72E-21	125	226	No hit	No description
SMART	SM01019	1.0E-24	126	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.534	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.6E-21	126	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.5E-34	252	334	IPR010525	Auxin response factor
Pfam	PF02309	7.0E-10	949	1037	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.583	951	1044	IPR000270	PB1 domain
SuperFamily	SSF54277	1.63E-8	965	1029	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:0009723	Biological Process	response to ethylene
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0010311	Biological Process	lateral root formation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 1079 aa Download sequence Send to blast
MKAPSNGFHP NPTEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ 60 TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS 240 SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF 300 ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEVEPVITP 360 FYICPPPFFR PKYPRQPGMP DDDLDIENAF KRAMPWMGDD FGMKDAQSSM FPGLSLVQWM 420 SMQQNNPLSG AATTQLPSAL SSYNLPNNFG SNDPSKLLNF QSPNLSPAHS QFNKPNMGNH 480 ISQQMQAQPA MVKSQQQQQQ QQQMQQQVQM SHQQLQQHHQ QQQQGVYNTG SVNNGASVAT 540 NQVSCQNPQQ SIAFSQSQLQ QQSMLSNGAK MTHQNIVSAG NKGSPQMTSY AQEMQYQQQL 600 ELHNSSQLLR NQQEQSSLHS LQQTMSQNPQ QLQMQQQSSK PSPSQQLQLQ LLQKLQQQQQ 660 QSMPPVSSSL QPQLLQQTQS HQLQQLLSSQ NQQPLAHGNN SFSASTFMQP PPQIQVSHQP 720 QGQMNNKPLV AAGRSHSGHT DGEAPSCSTS PSANNTGHDN VSPTNFLSRN QQQVSASDSV 780 FDRASNPVQE LYTKTNSRIN QGTVNLKSAA EQFKFKGAVT DQIDVSTAGT TYCPDVVGPA 840 QQQQTFPLPS FGFDGDCQSH HPRNNLAFAG NLEAVTTDAL YSQKDFQNLV PNYGNAPRDI 900 ETELSSAAIS SQSFGIPSIP FKSGGSNEIG GINDSGIMNG GLWPNQAQRM RTYTKVQKRG 960 SVGRSIDVTR YSGYDELRHD LARMFGIEGQ LEDPQTSDWK LVYTDHENDI LLVGDDPWEE 1020 FVNCVQNIKI LSSAEVQQMS LDGDLVAIPT TNQACSETDS GNAWKVHYED TSAAASFNR

Sequence ? help Back to Top

Protein Sequence Length: 1079 aa Download sequence Send to blast

MKAPSNGFHP NPTEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS  240
SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF  300
ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEVEPVITP  360
FYICPPPFFR PKYPRQPGMP DDDLDIENAF KRAMPWMGDD FGMKDAQSSM FPGLSLVQWM  420
SMQQNNPLSG AATTQLPSAL SSYNLPNNFG SNDPSKLLNF QSPNLSPAHS QFNKPNMGNH  480
ISQQMQAQPA MVKSQQQQQQ QQQMQQQVQM SHQQLQQHHQ QQQQGVYNTG SVNNGASVAT  540
NQVSCQNPQQ SIAFSQSQLQ QQSMLSNGAK MTHQNIVSAG NKGSPQMTSY AQEMQYQQQL  600
ELHNSSQLLR NQQEQSSLHS LQQTMSQNPQ QLQMQQQSSK PSPSQQLQLQ LLQKLQQQQQ  660
QSMPPVSSSL QPQLLQQTQS HQLQQLLSSQ NQQPLAHGNN SFSASTFMQP PPQIQVSHQP  720
QGQMNNKPLV AAGRSHSGHT DGEAPSCSTS PSANNTGHDN VSPTNFLSRN QQQVSASDSV  780
FDRASNPVQE LYTKTNSRIN QGTVNLKSAA EQFKFKGAVT DQIDVSTAGT TYCPDVVGPA  840
QQQQTFPLPS FGFDGDCQSH HPRNNLAFAG NLEAVTTDAL YSQKDFQNLV PNYGNAPRDI  900
ETELSSAAIS SQSFGIPSIP FKSGGSNEIG GINDSGIMNG GLWPNQAQRM RTYTKVQKRG  960
SVGRSIDVTR YSGYDELRHD LARMFGIEGQ LEDPQTSDWK LVYTDHENDI LLVGDDPWEE  1020
FVNCVQNIKI LSSAEVQQMS LDGDLVAIPT TNQACSETDS GNAWKVHYED TSAAASFNR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-172	15	355	45	388	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). 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 ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:16461383, ECO:0000269\|PubMed:17259263}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	KFK44062.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin and ethylene. {ECO:0000269\|PubMed:16461383}.

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	AB493467	0.0	AB493467.1 Arabidopsis thaliana At1g19220 mRNA for hypothetical protein, partial cds, clone: RAAt1g19220.
GenBank	ATU53672	0.0	U53672.2 Arabidopsis thaliana early auxin-induced IAA22 mRNA, complete cds.
GenBank	AY669794	0.0	AY669794.1 Arabidopsis thaliana clone C105352 ARF19 (At1g19220) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010477125.1	0.0	PREDICTED: auxin response factor 19
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A087HPL0	0.0	A0A087HPL0_ARAAL; Auxin response factor
STRING	A0A087HPL0	0.0	(Arabis alpina)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2629	26	65

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19220.1	0.0	auxin response factor 19

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] Perilli S, et al. RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. Plant Cell, 2013. 25(11): p. 4469-78 [PMID:24285791] Sun Y, et al. Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas. Sci Rep, 2017. 7: p. 40844 [PMID:28102350] 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] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana. Plant Sci., 2017. 264: p. 168-178 [PMID:28969797] Nakamura M, et al. Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells. Plant Physiol., 2018. 176(1): p. 378-391 [PMID:29084900] Hong L, et al. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J., 2018. 93(2): p. 246-258 [PMID:29155478] Lee K,Park OS,Seo PJ Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal, 2018. [PMID:29184030] Kimura T, et al. Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 823-835 [PMID:29401292] Schoenaers S, et al. The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Curr. Biol., 2018. 28(5): p. 722-732.e6 [PMID:29478854] Huang KL, et al. The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots. Plant Physiol., 2018. 178(1): p. 413-427 [PMID:30026290]