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: 962aa MW: 105789 Da PI: 6.0326

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kaladp0003s0067.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	81	1.2e-25	147	248	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 f+k+lt sd++++g +++p++ ae+ ++++ + ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv+a++L++gD+v+F Kaladp0003s0067.1.p 147 FCKTLTASDTSTHGGFSVPRRAAEKLfpildytMQPP-T-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVSAKRLRQGDSVLFI 234 99*******************999*954444.4.38******************************************** PP E-SSSEE..EEEEE-S CS B3 84 ldgrsefelvvkvfrk 99 ++++ +l+v+++r+ Kaladp0003s0067.1.p 235 --RDEKSQLMVGIRRA 248 ..4577778***97 PP
2	Auxin_resp	108.9	5.5e-36	273	356	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPr+++s+Fv+++ k++ka+ +++s+GmRf m+fete+s +rr++Gt+v vsdldpvrWp+SkWr+++ Kaladp0003s0067.1.p 273 AAHAAANRSPFTIFYNPRQCPSDFVIPMPKFRKAVFgTQISMGMRFGMMFETEESGKRRYMGTIVNVSDLDPVRWPGSKWRNVQ 356 79******************************988******************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.7E-46	135	276	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	5.7E-42	140	261	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.16E-24	146	247	No hit	No description
PROSITE profile	PS50863	13.422	147	249	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.7E-23	147	248	IPR003340	B3 DNA binding domain
SMART	SM01019	4.5E-26	147	249	IPR003340	B3 DNA binding domain
Pfam	PF06507	8.1E-31	273	356	IPR010525	Auxin response factor
Pfam	PF02309	8.6E-10	835	923	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.228	837	921	IPR000270	PB1 domain
SuperFamily	SSF54277	1.31E-8	841	916	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:0009725	Biological Process	response to hormone
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: 962 aa Download sequence Send to blast
MGSVVEEKMK PGGLPNGVST NLLEEMKMVK ELQDQSGAAK TMNSELWHAC AGPLVSLPQI 60 GGLVYYFPQG HSEQVAVSTR RSATSQIPNY PNLPSQLLCQ VHNVTLHADK ETDEIYAQMS 120 LQPVNTEKDI IPVQEFGQPS KHPSEFFCKT LTASDTSTHG GFSVPRRAAE KLFPILDYTM 180 QPPTQELVVR DLHDNTWTFR HIYRGQPKRH LLTTGWSLFV SAKRLRQGDS VLFIRDEKSQ 240 LMVGIRRANR QQTTLPSSVL SADSMHIGVL AAAAHAAANR SPFTIFYNPR QCPSDFVIPM 300 PKFRKAVFGT QISMGMRFGM MFETEESGKR RYMGTIVNVS DLDPVRWPGS KWRNVQVEWD 360 EAGCSDKPNR VSSWDIETPE SLFIFPSLTS GYKRPLTAPT GFLGAETDWR SLIKRPFVRM 420 PDNGFGNLHP MASPCSEQLM KMLMKSHMVN HPTNFSSMPA DSSYNRAPVQ DVRAMEAVTK 480 QITNQLTSSG NTLAQIQNSS QSQPCPSQSA TPANSKALLQ ATHQEKALQG VKSELTSSEP 540 VTQDHGNRLK SASQIVENPA PSSMNPPVSM SSPTSLNQQM TINQLTSLSP SHGQFQPVNP 600 WQSHQPMDSS IFQSQPTEAP QSDLSTINSL LPYLETDEWI LNTSSSYQQL PGVFRSPASL 660 PMYGYQDSAP TVFPEVVNPA MSSMGHDVSE HQLNSIQSVS QSDRLVPLPL QGPGNVNLSG 720 FKELSSDINP NYSCLNYDGC NTTTAVVDHS VPSTFLDGFC KMDDPAFQNA SDCLVGAVSS 780 SQDMQSQITS ASLADSHAFS RQDFTDNSGG TSSSNVEFDD SSLLQTNSWQ QVAPPLRTYT 840 KVQKTGSVGR SIDVTSFRNY EELRSAIERM FGLEGLLKDS RGSAWKLVYV DYEKDVLLVG 900 DDPWEEFVGC VRCIRILSPT EVQQMSEEGM KLLNSTAAAA AMHGLNRALA EGGSSAWDTL 960 A*

Sequence ? help Back to Top

Protein Sequence Length: 962 aa Download sequence Send to blast

MGSVVEEKMK PGGLPNGVST NLLEEMKMVK ELQDQSGAAK TMNSELWHAC AGPLVSLPQI  60
GGLVYYFPQG HSEQVAVSTR RSATSQIPNY PNLPSQLLCQ VHNVTLHADK ETDEIYAQMS  120
LQPVNTEKDI IPVQEFGQPS KHPSEFFCKT LTASDTSTHG GFSVPRRAAE KLFPILDYTM  180
QPPTQELVVR DLHDNTWTFR HIYRGQPKRH LLTTGWSLFV SAKRLRQGDS VLFIRDEKSQ  240
LMVGIRRANR QQTTLPSSVL SADSMHIGVL AAAAHAAANR SPFTIFYNPR QCPSDFVIPM  300
PKFRKAVFGT QISMGMRFGM MFETEESGKR RYMGTIVNVS DLDPVRWPGS KWRNVQVEWD  360
EAGCSDKPNR VSSWDIETPE SLFIFPSLTS GYKRPLTAPT GFLGAETDWR SLIKRPFVRM  420
PDNGFGNLHP MASPCSEQLM KMLMKSHMVN HPTNFSSMPA DSSYNRAPVQ DVRAMEAVTK  480
QITNQLTSSG NTLAQIQNSS QSQPCPSQSA TPANSKALLQ ATHQEKALQG VKSELTSSEP  540
VTQDHGNRLK SASQIVENPA PSSMNPPVSM SSPTSLNQQM TINQLTSLSP SHGQFQPVNP  600
WQSHQPMDSS IFQSQPTEAP QSDLSTINSL LPYLETDEWI LNTSSSYQQL PGVFRSPASL  660
PMYGYQDSAP TVFPEVVNPA MSSMGHDVSE HQLNSIQSVS QSDRLVPLPL QGPGNVNLSG  720
FKELSSDINP NYSCLNYDGC NTTTAVVDHS VPSTFLDGFC KMDDPAFQNA SDCLVGAVSS  780
SQDMQSQITS ASLADSHAFS RQDFTDNSGG TSSSNVEFDD SSLLQTNSWQ QVAPPLRTYT  840
KVQKTGSVGR SIDVTSFRNY EELRSAIERM FGLEGLLKDS RGSAWKLVYV DYEKDVLLVG  900
DDPWEEFVGC VRCIRILSPT EVQQMSEEGM KLLNSTAAAA AMHGLNRALA EGGSSAWDTL  960
A*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	3	381	6	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}.

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_021285434.1	0.0	auxin response factor 5
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A1R3IY13	0.0	A0A1R3IY13_COCAP; Auxin response factor
STRING	EOY14976	0.0	(Theobroma cacao)

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	Kaladp0003s0067.1.p

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]