PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Eucgr.F02090.1.p

Common Name

EUGRSUZ_F02090

Organism

Eucalyptus grandis

Taxonomic ID

71139

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Myrtales; Myrtaceae; Myrtoideae; Eucalypteae; Eucalyptus

Family

ARF

Protein Properties

Length: 840aa MW: 92274 Da PI: 5.3195

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Eucgr.F02090.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	79.3	4.1e-25	51	152	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 f+k+lt sd++++g +++p++ ae+ +++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv a++L++gD+v+F ++ Eucgr.F02090.1.p 51 FCKTLTASDTSTHGGFSVPRRAAEKLfppldfAMQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVGAKRLRAGDSVLFI--RD 140 99*******************999*9555544.49********************************************..45 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 ++ +l+v+v+r+ Eucgr.F02090.1.p 141 EKSQLMVGVRRA 152 77778***97 PP
2	Auxin_resp	113.1	2.7e-37	177	260	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s F+++YnPra++seFv+++ k++ka++ +++svGmRf m+fete+s +rr++Gt++g+sdldp+rWp+SkWr+L+ Eucgr.F02090.1.p 177 AAHAATSRSSFTIFYNPRACPSEFVIPLVKYRKAVYgTRISVGMRFGMMFETEESGKRRYMGTIIGISDLDPLRWPGSKWRNLQ 260 79********************************9*******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	7.98E-47	38	180	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	7.6E-42	44	165	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.17E-23	50	151	No hit	No description
Pfam	PF02362	5.2E-23	51	152	IPR003340	B3 DNA binding domain
SMART	SM01019	1.1E-25	51	153	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.239	51	153	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.1E-32	177	260	IPR010525	Auxin response factor
PROSITE profile	PS51745	25.174	730	814	IPR000270	PB1 domain
SuperFamily	SSF54277	4.77E-9	732	809	No hit	No description
Pfam	PF02309	8.8E-7	775	815	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: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: 840 aa Download sequence Send to blast
MCQVHNVTLH ADRETDEIYA QMCLQPVNSE KDVFPVPDFG LRPSKHPSEF FCKTLTASDT 60 STHGGFSVPR RAAEKLFPPL DFAMQPPTQE LVVRDLHDNT WTFRHIYRGQ PKRHLLTTGW 120 SLFVGAKRLR AGDSVLFIRD EKSQLMVGVR RANRQQTTLP SSVLSTDSMH IGILAAAAHA 180 ATSRSSFTIF YNPRACPSEF VIPLVKYRKA VYGTRISVGM RFGMMFETEE SGKRRYMGTI 240 IGISDLDPLR WPGSKWRNLQ VEWDEPGCGD KQNRVSPWDI ETPESLFIFP SLTSALKRPL 300 HTGFMGGETE WGSLVKRPLI QVPEGGGMNL LPFASVPNLC SEQLIKMIMK PQPQIVNHPS 360 LPQDNNPKFI PGHEVNTMQG TVNQKPQAFN TESAIPPKLI YPHLCPDQSS AMGLSSEVHV 420 TNKVPPPYKT ENQAPVETKD EKLNVDSHLK KDVLNQVPST STGELPEENI ASGPSSQQNH 480 LNHPIILNQN QGQIQSQACS WPPQPLQIPI ADSNVLHGSS PFVNPDELMF SSTNKSVAAL 540 IRSPGPFSIC GSQDPSATFG DPVGQLPLIS QELWDHQGIN LRFPSQGDQL TPLPEQDPSS 600 LCGISNSVCL KDLSAESNNQ SGIYSCLNLD ASNGGSSAID PSISSAILDD FCTIKDGPFP 660 NLSDCLVGNF SSSQDVQSQI TSASLADSQA FSRQDFPDNS GGTSSSNVDF DESSILKNST 720 WQQQVAPPMR TYTKVQKAGS VGRSIDVTNF RNYEELLSAI EYMFGLEGLL NDPRGSGWKL 780 VYVDYENDVL LVGDDPWEEF VGCVRCIRIL SPVEVQQMSE EGMKLLNASA GQVVNATTS*

Sequence ? help Back to Top

Protein Sequence Length: 840 aa Download sequence Send to blast

MCQVHNVTLH ADRETDEIYA QMCLQPVNSE KDVFPVPDFG LRPSKHPSEF FCKTLTASDT  60
STHGGFSVPR RAAEKLFPPL DFAMQPPTQE LVVRDLHDNT WTFRHIYRGQ PKRHLLTTGW  120
SLFVGAKRLR AGDSVLFIRD EKSQLMVGVR RANRQQTTLP SSVLSTDSMH IGILAAAAHA  180
ATSRSSFTIF YNPRACPSEF VIPLVKYRKA VYGTRISVGM RFGMMFETEE SGKRRYMGTI  240
IGISDLDPLR WPGSKWRNLQ VEWDEPGCGD KQNRVSPWDI ETPESLFIFP SLTSALKRPL  300
HTGFMGGETE WGSLVKRPLI QVPEGGGMNL LPFASVPNLC SEQLIKMIMK PQPQIVNHPS  360
LPQDNNPKFI PGHEVNTMQG TVNQKPQAFN TESAIPPKLI YPHLCPDQSS AMGLSSEVHV  420
TNKVPPPYKT ENQAPVETKD EKLNVDSHLK KDVLNQVPST STGELPEENI ASGPSSQQNH  480
LNHPIILNQN QGQIQSQACS WPPQPLQIPI ADSNVLHGSS PFVNPDELMF SSTNKSVAAL  540
IRSPGPFSIC GSQDPSATFG DPVGQLPLIS QELWDHQGIN LRFPSQGDQL TPLPEQDPSS  600
LCGISNSVCL KDLSAESNNQ SGIYSCLNLD ASNGGSSAID PSISSAILDD FCTIKDGPFP  660
NLSDCLVGNF SSSQDVQSQI TSASLADSQA FSRQDFPDNS GGTSSSNVDF DESSILKNST  720
WQQQVAPPMR TYTKVQKAGS VGRSIDVTNF RNYEELLSAI EYMFGLEGLL NDPRGSGWKL  780
VYVDYENDVL LVGDDPWEEF VGCVRCIRIL SPVEVQQMSE EGMKLLNASA GQVVNATTS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	285	107	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	Eucgr.F02090.1.p

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_010061492.1	0.0	PREDICTED: auxin response factor 5 isoform X2
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A059BR81	0.0	A0A059BR81_EUCGR; Auxin response factor
STRING	XP_010061491.1	0.0	(Eucalyptus grandis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5808	27	46

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	Eucgr.F02090.1.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]