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

Solyc07g042260.2.1

Common Name

LOC100191131

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 1138aa MW: 127856 Da PI: 6.6348

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc07g042260.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	72.5	5.1e-23	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 f+k+lt sd++++g +++p++ ae++ ++++++ +l+ +d++ ++W++++iyr++++r++lt+GW+ F ++++L++gD+v+F + Solyc07g042260.2.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldyaMQPPAQ--ELMARDLHDQTWTFRHIYRGQPKRHLLTTGWSVFISSKRLCAGDSVLFIR 214 99****************************5444444..8**********************************************4 PP -SSSEE..EEEEE-S CS B3 85 dgrsefelvvkvfrk 99 +++ +l++++ r+ Solyc07g042260.2.1 215 --DEKSQLLLGIKRT 227 ..4666678888775 PP
2	Auxin_resp	123.3	1.8e-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+ Solyc07g042260.2.1 252 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYAQVSLGMRFRMMFETEESGVRRYMGTITGVSDLDPIRWKSSQWRNLQ 334 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	8.76E-43	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.4E-40	118	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.98E-18	125	226	No hit	No description
PROSITE profile	PS50863	12.026	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.0E-20	126	227	IPR003340	B3 DNA binding domain
SMART	SM01019	3.6E-22	126	228	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.4E-35	252	334	IPR010525	Auxin response factor
Pfam	PF02309	1.0E-8	1001	1097	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	27.529	1011	1095	IPR000270	PB1 domain
SuperFamily	SSF54277	2.21E-9	1012	1089	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: 1138 aa Download sequence Send to blast
MKAPSNGYLP NSGEGERKLM NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE 60 TDGIPSYPNL PSKLICMLHN VTLHADTETD EVYAQMTLQP VNKYDQEALL LSEMGLKQNR 120 QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDYAMQ PPAQELMARD LHDQTWTFRH 180 IYRGQPKRHL LTTGWSVFIS SKRLCAGDSV LFIRDEKSQL LLGIKRTNRQ QPALSSSVIS 240 SDSMHIGILA AAAHAAANNS PFTIFYNPRA SPSEFVIPLA KYNKAMYAQV SLGMRFRMMF 300 ETEESGVRRY MGTITGVSDL DPIRWKSSQW RNLQVGWDES TAGERPSRVS IWDIEPVVTP 360 FYICPPPFFR PKFPKQPSFP GDESDIENVL KRGMPWINDE LGLKDAQNSI FPGLSLVQWM 420 SMQQNNHVPV AQSGLPSVLH SNIGSDDHSK LLNFQSPALA TPGLQFNKPN QLNQPFGQIQ 480 QPPLAWTQEQ QQSLQSPVSA QQQQQQQHTL QQQQQQQQHT LQQQQQQRHT LQQQQQQQTL 540 QQQQQQQQQQ HTLQQQQQQQ HTLQHQQQHT LQQPQQHMLQ QQPQFHQQAQ QQLQQQQRPS 600 QQQQLTGNSS PVNRCVSPNQ IPNQTFPQAA VYGQLQQQQV LSASTQSQQN VPVSRNSFPS 660 TSLAQDFQFQ QQMEQQSNLL QKSQQQQTIP QQAPLQLLQQ SLMQRSQVQP SSQQSLTEQQ 720 LQLQLLNKLQ QQQQQQQAQL LSPVSSTLEP RMPQQQQNRQ PQELQFAHQQ LSSNIVTTVT 780 HLQSTHHAFN QLQNHHKSPI TIKALSGGTE GDAPSCSTSP STNNFQVSPP NFLTRNQGQA 840 ILVDESVVDP SQEQNKSECR IKHELVFSKG SELSKYKGNN TENLEAASST TSYGLDSSGF 900 NFSLPALCVD GDVQSHSRNI LPSAANNIDG LNPDALLSRD YDSGKDIQNL FSPFGNAPRD 960 IETELSDAGI NSQQFGVPNM SYKPRCANDL AVNDNGILNN NAWTNQTQRM RTYTKVQKRG 1020 SVGRTIDVTR YIGYDELRHD LARMFGIEGQ LEDPQRTEWK LVYVDHENDI LLVGDDPWEE 1080 FVSCVQSIKI LSCAEVQQMS LNGDLGNVPV PNQASSGTDS GNAWKGHYDD NSAASFN*

Sequence ? help Back to Top

Protein Sequence Length: 1138 aa Download sequence Send to blast

MKAPSNGYLP NSGEGERKLM NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE  60
TDGIPSYPNL PSKLICMLHN VTLHADTETD EVYAQMTLQP VNKYDQEALL LSEMGLKQNR  120
QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDYAMQ PPAQELMARD LHDQTWTFRH  180
IYRGQPKRHL LTTGWSVFIS SKRLCAGDSV LFIRDEKSQL LLGIKRTNRQ QPALSSSVIS  240
SDSMHIGILA AAAHAAANNS PFTIFYNPRA SPSEFVIPLA KYNKAMYAQV SLGMRFRMMF  300
ETEESGVRRY MGTITGVSDL DPIRWKSSQW RNLQVGWDES TAGERPSRVS IWDIEPVVTP  360
FYICPPPFFR PKFPKQPSFP GDESDIENVL KRGMPWINDE LGLKDAQNSI FPGLSLVQWM  420
SMQQNNHVPV AQSGLPSVLH SNIGSDDHSK LLNFQSPALA TPGLQFNKPN QLNQPFGQIQ  480
QPPLAWTQEQ QQSLQSPVSA QQQQQQQHTL QQQQQQQQHT LQQQQQQRHT LQQQQQQQTL  540
QQQQQQQQQQ HTLQQQQQQQ HTLQHQQQHT LQQPQQHMLQ QQPQFHQQAQ QQLQQQQRPS  600
QQQQLTGNSS PVNRCVSPNQ IPNQTFPQAA VYGQLQQQQV LSASTQSQQN VPVSRNSFPS  660
TSLAQDFQFQ QQMEQQSNLL QKSQQQQTIP QQAPLQLLQQ SLMQRSQVQP SSQQSLTEQQ  720
LQLQLLNKLQ QQQQQQQAQL LSPVSSTLEP RMPQQQQNRQ PQELQFAHQQ LSSNIVTTVT  780
HLQSTHHAFN QLQNHHKSPI TIKALSGGTE GDAPSCSTSP STNNFQVSPP NFLTRNQGQA  840
ILVDESVVDP SQEQNKSECR IKHELVFSKG SELSKYKGNN TENLEAASST TSYGLDSSGF  900
NFSLPALCVD GDVQSHSRNI LPSAANNIDG LNPDALLSRD YDSGKDIQNL FSPFGNAPRD  960
IETELSDAGI NSQQFGVPNM SYKPRCANDL AVNDNGILNN NAWTNQTQRM RTYTKVQKRG  1020
SVGRTIDVTR YIGYDELRHD LARMFGIEGQ LEDPQRTEWK LVYVDHENDI LLVGDDPWEE  1080
FVSCVQSIKI LSCAEVQQMS LNGDLGNVPV PNQASSGTDS GNAWKGHYDD NSAASFN*

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

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.22486	0.0	leaf

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}.

Function -- GeneRIF ? help Back to Top
SlARF7 acts as a negative regulator of fruit set until pollination and fertilization have taken place, and moderates the auxin response during fruit growth. [SlARF7] [PMID: 18778404] ARF7 mediates cross-talk between auxin and gibberellin signalling during fruit development. [ARF7] [PMID: 20937732]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc07g042260.2.1

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	EF121545	0.0	Solanum lycopersicum auxin response factor mRNA, partial cds

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004243692.1	0.0	auxin response factor 7 isoform X1
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	B5SP99	0.0	B5SP99_SOLLC; Auxin response factor (Fragment)
STRING	Solyc07g042260.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA1302	24	65
Representative plant	OGRP9033	9	14

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	Solyc07g042260.2.1
Entrez Gene	100191131

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] 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] de Jong M,Wolters-Arts M,Feron R,Mariani C,Vriezen WH The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signaling during tomato fruit set and development. Plant J., 2009. 57(1): p. 160-70 [PMID:18778404] de Jong M,Wolters-Arts M,Garc The Solanum lycopersicum AUXIN RESPONSE FACTOR 7 (SlARF7) mediates cross-talk between auxin and gibberellin signalling during tomato fruit set and development. J. Exp. Bot., 2011. 62(2): p. 617-26 [PMID:20937732] 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]