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

Sopen07g021880.1

Organism

Solanum pennellii

Taxonomic ID

28526

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: 1143aa MW: 128611 Da PI: 6.6347

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sopen07g021880.1	genome	spenn	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-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 f+k+lt sd++++g +++p++ ae++ ++++++ +l+ +d++ ++W++++iyr++++r++lt+GW+ F ++++L++gD+v+F + Sopen07g021880.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldyaMQPPAQ--ELMARDLHDQTWTFRHIYRGQPKRHLLTTGWSVFISSKRLCAGDSVLFIR-- 214 99****************************5444444..8**********************************************4.. PP SSEE..EEEEE-S CS B3 87 rsefelvvkvfrk 99 +++ +l++++ r+ Sopen07g021880.1 215 DEKSQLLLGIKRT 227 4666678888775 PP
2	Auxin_resp	121.1	8.1e-40	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFv++++k++ka++ +vs+GmRf+m++ete+s rr++Gt++gvsdldp+rW+ S+Wr+L+ Sopen07g021880.1 252 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYAQVSLGMRFRMMVETEESGVRRYMGTITGVSDLDPIRWKSSQWRNLQ 334 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	8.89E-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	4.01E-18	125	226	No hit	No description
PROSITE profile	PS50863	12.026	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.1E-20	126	227	IPR003340	B3 DNA binding domain
SMART	SM01019	3.6E-22	126	228	IPR003340	B3 DNA binding domain
Pfam	PF06507	4.5E-35	252	334	IPR010525	Auxin response factor
Pfam	PF02309	7.7E-9	1006	1103	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	27.529	1017	1101	IPR000270	PB1 domain
SuperFamily	SSF54277	2.21E-9	1018	1095	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: 1143 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 SLGMRFRMMV 300 ETEESGVRRY MGTITGVSDL DPIRWKSSQW RNLQVGWDES TAGERPSRVS IWDIEPVVTP 360 FYICPPPFFR PKFPKQPSFP GDESDIENVL KRGMPWINDE LGLKDAQNSI FPGLSLVQWM 420 SMQQNNHVPV AQSGLPSVLH SNIGSDDHSK LLNFQSPTLA TPGLQFNKPN QLNQPFGQIQ 480 QPPLAWTQQQ QQSLQSPVSA QQQQQQQQQH TLQQQQQQQQ QQHTLQQQQQ QQHTLQQQQQ 540 QQTLLQQQQQ QQQQQQHSLQ QQQQQQHTLQ HQQQHTLQQP QQHMLQQQPQ LHQQAQQQLQ 600 QQQRPSQQQQ LTGNSSPVNR CVSPNQIPNQ TFPQATVYGQ LQQQQVLSAS TQSQQNVPVS 660 RNSFPSTSLA QDFQFQQQME QQSNLLQKSQ QQQTIPQQAP LQLLQQSLMQ RSQVQPSSQQ 720 SLTEQQLQLQ LLNKLQQQQQ QQQAQLLSPV SSTLEPRMPQ QQQNRQPQEL QFAHQQLSSN 780 IVTTVTHLQS THHAFNQLQN HHKSPITIKA LSGGTEGDAP SCSTSPSTNN FQVSPPNFLT 840 RSQGQAILVD ESVVDPSQEQ NKSECRIKHE LVFSKGSELS KYKGNYTENL EAASSTTSYG 900 LDSSGFNFSL PALCVDGDVQ SHSRNILPSA ANNIDGLNPD ALLSRDYDSG KDIQNLFSPF 960 GNAPRDIETE LSDAGVNSQQ FGVPNMSYKP RCVNDLAVND NSILNNNAWT NQTQRMRTYT 1020 KVQKRGSVGR TIDVTRYIGY DELRHDLARM FGIEGQLEDP QRTEWKLVYV DHENDILLVG 1080 DDPWEEFVSC VQSIKILSCA EVQQMSLNGD LGNVPVPNQA SSGTDSGNAW KGHYDDNSAA 1140 SFN

Sequence ? help Back to Top

Protein Sequence Length: 1143 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 SLGMRFRMMV  300
ETEESGVRRY MGTITGVSDL DPIRWKSSQW RNLQVGWDES TAGERPSRVS IWDIEPVVTP  360
FYICPPPFFR PKFPKQPSFP GDESDIENVL KRGMPWINDE LGLKDAQNSI FPGLSLVQWM  420
SMQQNNHVPV AQSGLPSVLH SNIGSDDHSK LLNFQSPTLA TPGLQFNKPN QLNQPFGQIQ  480
QPPLAWTQQQ QQSLQSPVSA QQQQQQQQQH TLQQQQQQQQ QQHTLQQQQQ QQHTLQQQQQ  540
QQTLLQQQQQ QQQQQQHSLQ QQQQQQHTLQ HQQQHTLQQP QQHMLQQQPQ LHQQAQQQLQ  600
QQQRPSQQQQ LTGNSSPVNR CVSPNQIPNQ TFPQATVYGQ LQQQQVLSAS TQSQQNVPVS  660
RNSFPSTSLA QDFQFQQQME QQSNLLQKSQ QQQTIPQQAP LQLLQQSLMQ RSQVQPSSQQ  720
SLTEQQLQLQ LLNKLQQQQQ QQQAQLLSPV SSTLEPRMPQ QQQNRQPQEL QFAHQQLSSN  780
IVTTVTHLQS THHAFNQLQN HHKSPITIKA LSGGTEGDAP SCSTSPSTNN FQVSPPNFLT  840
RSQGQAILVD ESVVDPSQEQ NKSECRIKHE LVFSKGSELS KYKGNYTENL EAASSTTSYG  900
LDSSGFNFSL PALCVDGDVQ SHSRNILPSA ANNIDGLNPD ALLSRDYDSG KDIQNLFSPF  960
GNAPRDIETE LSDAGVNSQQ FGVPNMSYKP RCVNDLAVND NSILNNNAWT NQTQRMRTYT  1020
KVQKRGSVGR TIDVTRYIGY DELRHDLARM FGIEGQLEDP QRTEWKLVYV DHENDILLVG  1080
DDPWEEFVSC VQSIKILSCA EVQQMSLNGD LGNVPVPNQA SSGTDSGNAW KGHYDDNSAA  1140
SFN

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}.

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_015082066.1	0.0	auxin response factor 7-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19

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

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] 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]