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

PGSC0003DMP400004262

Common Name

LOC102594021

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: 1158aa MW: 130147 Da PI: 6.6074

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400004262	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	70.8	1.8e-22	126	226	1	98
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvF 82 f+k+lt sd++++g +++p++ ae++ ++++++ +l+ +d++ + W++++iyr++++r++lt+GW+ F ++++L++gD+v+F PGSC0003DMP400004262 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldyaMQPPAQ--ELMARDLHDQAWTFRHIYRGQPKRHLLTTGWSVFISSKRLCAGDSVLF 212 99****************************5444444..8********************************************* PP EE-SSSEE..EEEEE- CS B3 83 kldgrsefelvvkvfr 98 +d ++ +l++++ r PGSC0003DMP400004262 213 IRD--DKSQLLLGIKR 226 *54..45556888776 PP
2	Auxin_resp	123.5	1.5e-40	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFv++++k++ka++ +vs+GmRf+m+fete+s rr++Gt++gvsdldp+rW+ S+Wr+L+ PGSC0003DMP400004262 252 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYAQVSLGMRFRMMFETEESGVRRYMGTITGVSDLDPIRWKSSEWRNLQ 334 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.7E-42	114	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.8E-39	118	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.71E-17	125	226	No hit	No description
SMART	SM01019	1.0E-20	126	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.899	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.6E-19	126	226	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.3E-35	252	334	IPR010525	Auxin response factor
Pfam	PF02309	2.4E-9	1020	1116	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	27.484	1030	1123	IPR000270	PB1 domain
SuperFamily	SSF54277	1.28E-9	1031	1108	No hit	No description
CDD	cd05992	1.49E-4	1034	1116	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: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: 1158 aa Download sequence Send to blast
MKAPSNGYLP NSGEGERKLM NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE 60 TDGIPSYPNL PSKLICMLHN VTLHADTETD EVYAQMTLQP VNKYDQEALL LSDMGLKQNR 120 QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDYAMQ PPAQELMARD LHDQAWTFRH 180 IYRGQPKRHL LTTGWSVFIS SKRLCAGDSV LFIRDDKSQL LLGIKRTNRQ QPALSSSVIS 240 SDSMHIGILA AAAHAAANNS PFTIFYNPRA SPSEFVIPLA KYNKAMYAQV SLGMRFRMMF 300 ETEESGVRRY MGTITGVSDL DPIRWKSSEW RNLQVGWDES TAGERPSRVS IWDIEPVVTP 360 FYICPPPFFR PKFPKQPNFP GDESDIENVL KRGMPWINDE LGLKDSQNSI FPGLSLVQWM 420 SMQQNNHVPV AQSGLPSVLH SNIGSDDHSK LLNFQSPTLA TPGLQFNKPN QLNQPFGQIQ 480 QPPLAWAQQQ QQSLQSPVSA QQQQPTLQQQ QQQHTLQQQQ PTLQQQQHTL QQQQHTLQQQ 540 QQQQQQQQHT LQQQQQQQHT LQQQQQQHTL QQQQQQQHTL QHQQQHTLQQ SQQHMLQQQP 600 QLHQQAQQQL QQQQRPSQQQ QLTGNSSPVN RCVSPNQIPN QTFPQAAVYG QLQQQQVLSA 660 STQSQQNVPV NRNPFPSTSL AQDFQFQQQV EQQSNLLQKS QQQQTIPQQV PLQLLQQSLM 720 QRPQVQPSSQ QSLTEQQLQL QLLNKLQQQQ QQQQQQAQLL SPVSSTLEPR MPQQQQNRQP 780 QELQIAHQQL SSNIVTTATH LQSTHHAFNQ LQSQHKSPIT IKALSGGTDG DAPSCSTSPS 840 TNNFQVSPPN FLTKNQGQAI LVDESVVDPS QEQNKSEFRI KHELVFSKGS EQSKYKGNNT 900 ENLEAASSTT SYGLDSSGFN FSLPALCVDG DVQSHSRNSL PSAANNIDGL NPDALLSRDY 960 DSGKDMQNLF SPFGNAPRDI ETELSDAGIN SQQFGVPNMA YKPRCTNDLA VNDNGVLNNN 1020 AWTNQTQRMR TYTKVQKRGS VGRTIDVTRY IGYDELRHDL ARMFGIEGQL EDPQRTEWKL 1080 VYVDHENDML LVGDDPWEEF VSCVQSIKIL SSAEVQQMSL DGDLGNVPVP NQASSGTDSG 1140 NAWKGHYDDN SAASFNR*

Sequence ? help Back to Top

Protein Sequence Length: 1158 aa Download sequence Send to blast

MKAPSNGYLP NSGEGERKLM NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE  60
TDGIPSYPNL PSKLICMLHN VTLHADTETD EVYAQMTLQP VNKYDQEALL LSDMGLKQNR  120
QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDYAMQ PPAQELMARD LHDQAWTFRH  180
IYRGQPKRHL LTTGWSVFIS SKRLCAGDSV LFIRDDKSQL LLGIKRTNRQ QPALSSSVIS  240
SDSMHIGILA AAAHAAANNS PFTIFYNPRA SPSEFVIPLA KYNKAMYAQV SLGMRFRMMF  300
ETEESGVRRY MGTITGVSDL DPIRWKSSEW RNLQVGWDES TAGERPSRVS IWDIEPVVTP  360
FYICPPPFFR PKFPKQPNFP GDESDIENVL KRGMPWINDE LGLKDSQNSI FPGLSLVQWM  420
SMQQNNHVPV AQSGLPSVLH SNIGSDDHSK LLNFQSPTLA TPGLQFNKPN QLNQPFGQIQ  480
QPPLAWAQQQ QQSLQSPVSA QQQQPTLQQQ QQQHTLQQQQ PTLQQQQHTL QQQQHTLQQQ  540
QQQQQQQQHT LQQQQQQQHT LQQQQQQHTL QQQQQQQHTL QHQQQHTLQQ SQQHMLQQQP  600
QLHQQAQQQL QQQQRPSQQQ QLTGNSSPVN RCVSPNQIPN QTFPQAAVYG QLQQQQVLSA  660
STQSQQNVPV NRNPFPSTSL AQDFQFQQQV EQQSNLLQKS QQQQTIPQQV PLQLLQQSLM  720
QRPQVQPSSQ QSLTEQQLQL QLLNKLQQQQ QQQQQQAQLL SPVSSTLEPR MPQQQQNRQP  780
QELQIAHQQL SSNIVTTATH LQSTHHAFNQ LQSQHKSPIT IKALSGGTDG DAPSCSTSPS  840
TNNFQVSPPN FLTKNQGQAI LVDESVVDPS QEQNKSEFRI KHELVFSKGS EQSKYKGNNT  900
ENLEAASSTT SYGLDSSGFN FSLPALCVDG DVQSHSRNSL PSAANNIDGL NPDALLSRDY  960
DSGKDMQNLF SPFGNAPRDI ETELSDAGIN SQQFGVPNMA YKPRCTNDLA VNDNGVLNNN  1020
AWTNQTQRMR TYTKVQKRGS VGRTIDVTRY IGYDELRHDL ARMFGIEGQL EDPQRTEWKL  1080
VYVDHENDML LVGDDPWEEF VSCVQSIKIL SSAEVQQMSL DGDLGNVPVP NQASSGTDSG  1140
NAWKGHYDDN SAASFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-171	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	PGSC0003DMP400004262

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	EF121545	0.0	EF121545.1 Solanum lycopersicum auxin response factor mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006353789.1	0.0	PREDICTED: auxin response factor 7-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	M0ZQX0	0.0	M0ZQX0_SOLTU; Auxin response factor
STRING	PGSC0003DMT400006151	0.0	(Solanum tuberosum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA1302	24	65

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

Link Out ? help Back to Top
Phytozome	PGSC0003DMP400004262
Entrez Gene	102594021

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] Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] 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]