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

PGSC0003DMP400032526

Organism

Solanum tuberosum

Taxonomic ID

4113

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum

Family

ARF

Protein Properties

Length: 238aa MW: 26785.9 Da PI: 10.6669

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400032526	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	35	2.6e-11	14	58	53	99
EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS B3 53 rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 +++++r++lt+GW+ Fv+a++L +gD+v+F ++++ +l+++++r+ PGSC0003DMP400032526 14 EGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI--WNEKNQLFLGIRRA 58 678999***********************..8889999**997 PP
2	Auxin_resp	118.8	4.3e-39	83	166	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+t+s F+v++nPras+seFv++++k+ ka++ ++vsvGmRf+m fete+ss rr++Gt++g+ dldpvrW nS+Wrs+k PGSC0003DMP400032526 83 AAHAAATNSCFTVFFNPRASPSEFVIPLSKYIKAVYhTRVSVGMRFRMLFETEESSVRRYMGTITGIGDLDPVRWANSHWRSVK 166 79*******************************9789****************************************985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50863	9.925	1	59	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	2.35E-14	11	86	IPR015300	DNA-binding pseudobarrel domain
Pfam	PF02362	6.1E-9	14	58	IPR003340	B3 DNA binding domain
Gene3D	G3DSA:2.40.330.10	1.3E-15	15	72	IPR015300	DNA-binding pseudobarrel domain
Pfam	PF06507	2.0E-34	83	166	IPR010525	Auxin response factor

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:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 238 aa Download sequence Send to blast
MKLSTSGMGQ QAHEGQPKRH LLTTGWSVFV SAKRLVAGDS VLFIWNEKNQ LFLGIRRATR 60 PQTVMPSSVL SSDSMHIGLL AAAAHAAATN SCFTVFFNPR ASPSEFVIPL SKYIKAVYHT 120 RVSVGMRFRM LFETEESSVR RYMGTITGIG DLDPVRWANS HWRSVKVGWD ESTAGERQPR 180 VSLWEIEPLT TFPMYPSLFP LRLKRPWYPG TSSFQGILRT QCYAVRKVKL YNPEVSL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	9e-74	13	187	214	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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Regulates both stamen and gynoecium maturation. Promotes jasmonic acid production. Partially redundant with ARF8. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:16107481}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00033	PBM	Transfer from AT5G37020	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	PGSC0003DMP400032526

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by miR167. {ECO:0000269\|PubMed:17021043}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HM560979	0.0	HM560979.1 Solanum lycopersicum auxin response factor 8-1 (ARF8-1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006343312.1	1e-142	PREDICTED: auxin response factor 8-like isoform X1
Refseq	XP_006343313.1	1e-143	PREDICTED: auxin response factor 8-like isoform X2
Refseq	XP_015162339.1	1e-143	PREDICTED: auxin response factor 8-like isoform X2
Swissprot	Q9ZTX8	1e-124	ARFF_ARATH; Auxin response factor 6
TrEMBL	M1BLU5	1e-175	M1BLU5_SOLTU; Auxin response factor
STRING	PGSC0003DMT400048034	1e-143	(Solanum tuberosum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G30330.1	1e-125	auxin response factor 6

Link Out ? help Back to Top
Phytozome	PGSC0003DMP400032526

Publications ? help Back to Top
Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] Liu N, et al. Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato. J. Exp. Bot., 2014. 65(9): p. 2507-20 [PMID:24723401] Oh E, et al. Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl. Elife, 2015. [PMID:24867218] Minato N, et al. The phytoplasmal virulence factor TENGU causes plant sterility by downregulating of the jasmonic acid and auxin pathways. Sci Rep, 2014. 4: p. 7399 [PMID:25492247] Ortega-Amaro MA, et al. Overexpression of AtGRDP2, a novel glycine-rich domain protein, accelerates plant growth and improves stress tolerance. Front Plant Sci, 2014. 5: p. 782 [PMID:25653657] Asahina M,Satoh S Molecular and physiological mechanisms regulating tissue reunion in incised plant tissues. J. Plant Res., 2015. 128(3): p. 381-8 [PMID:25736731] Batista VG,Pinheiro MP,Melo Filho PA,Santos RC,Lima LM Temporal and tissue expression of genes involved in buds of earliness cotton cultivar. Genet. Mol. Res., 2015. 14(3): p. 7386-94 [PMID:26214417] Li P, et al. Ca(2+) -regulated and diurnal rhythm-regulated Na(+) /Ca(2+) exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis. Plant Cell Environ., 2016. 39(2): p. 377-92 [PMID:26296956] Barik S, et al. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species. Sci Rep, 2015. 5: p. 14611 [PMID:26459056] 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] 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] Zhang GZ, et al. Ectopic expression of UGT84A2 delayed flowering by indole-3-butyric acid-mediated transcriptional repression of ARF6 and ARF8 genes in Arabidopsis. Plant Cell Rep., 2017. 36(12): p. 1995-2006 [PMID:29027578] 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]