PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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: 864aa MW: 96107 Da PI: 6.9769

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sme2.5_06398.1_g00002.1	genome	EGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	74.8	9.9e-24	146	247	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 f+k+lt sd++++g +++ +++a+e+ + + + +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD + Sme2.5_06398.1_g00002.1 146 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAF 230 99***************************7333.34459***************************************** PP EEEE-SSSEE..EEEEE-S CS B3 81 vFkldgrsefelvvkvfrk 99 +F + +++el+v+v+r+ Sme2.5_06398.1_g00002.1 231 IFL--RGENGELRVGVRRA 247 ..449999****996 PP
2	Auxin_resp	79.5	8.1e-27	272	332	1	61
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsG 61 a+ha++tk++F+v+Y+Pr+s++eF+++++++++++k+++s+GmRfkm+fe+e+++e+r+++ Sme2.5_06398.1_g00002.1 272 AWHAIQTKTMFTVYYKPRTSPAEFIIPYDHYMESVKNNYSIGMRFKMRFEGEEAPEQRYAA 332 89********************************************************865 PP
3	Auxin_resp	26.1	3.7e-10	344	370	57	83
Auxin_resp 57 rrlsGtvvgvsdldpvrWpnSkWrsLk 83 ++++Gt+vg++d+dp rW +SkWr+Lk Sme2.5_06398.1_g00002.1 344 KSFTGTIVGIEDTDPQRWLDSKWRCLK 370 689**********************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.22E-40	142	275	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.1E-41	142	261	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	7.97E-22	144	246	No hit	No description
PROSITE profile	PS50863	12.012	146	248	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.2E-21	146	247	IPR003340	B3 DNA binding domain
SMART	SM01019	2.0E-23	146	248	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.3E-29	272	370	IPR010525	Auxin response factor
Pfam	PF02309	4.5E-10	734	823	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	3.38E-12	734	815	No hit	No description
PROSITE profile	PS51745	23.891	738	822	IPR000270	PB1 domain

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: 864 aa Download sequence Send to blast
MAASEVSIKG YSEPSDGSRT VSETVWSTSG VGKVDADTAL YTELWRSCAG PLVTVPREGE 60 LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVAN VLLKAEPDTD EVYAQVTLMP 120 EPNQDANAVK KEPMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ 180 PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL 240 RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT SPAEFIIPYD 300 HYMESVKNNY SIGMRFKMRF EGEEAPEQRY AAVYFVEVIS LLFKSFTGTI VGIEDTDPQR 360 WLDSKWRCLK VRWDENSSIP RPDRVSPWKI EPALSPPALN APPVARTKRP RSNILPSSPD 420 SSVLTREGSS RVTADHSQAS GFSRVLQGQE LTTSRGGFAE SNETDLSEKP MLWQPSVNDE 480 KNDNYSASKR HHSGKWLPLG RPESSLTDLL SGFGVPNNSS LGFCLPSADQ AAFGASLVKQ 540 QTQDQEKDFS LLGKPWSLSP SSLSLNLMDS GSKAPGLRGE TPYQMRGDAR YSAFGEFSVL 600 PGHRLANQQG SWVPQPVSPY MKLSHSREMM HKPTVVKQPE AVKPKEGNCK LFGIPLTSSV 660 CTDPVMMQKS SLHDPVSDKN FGIHPHQSPA TDSDQRAEQS KGSKVDDGIA ANDHDKQFQT 720 FHLAGRERDG KGHSSSTRSC TKVHKQGTAL GRSVDLAKFN NYDELIAELD GLFDFNGELK 780 ARSKSWLVVY TDDEGDMMLV GDDPWQEFCG MVRKIFIYTK EEVQRMNPGT LNSKGEDTSS 840 VAEGSDAKEV KNQLLPSESC QEEY

Sequence ? help Back to Top

Protein Sequence Length: 864 aa Download sequence Send to blast

MAASEVSIKG YSEPSDGSRT VSETVWSTSG VGKVDADTAL YTELWRSCAG PLVTVPREGE  60
LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVAN VLLKAEPDTD EVYAQVTLMP  120
EPNQDANAVK KEPMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ  180
PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL  240
RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT SPAEFIIPYD  300
HYMESVKNNY SIGMRFKMRF EGEEAPEQRY AAVYFVEVIS LLFKSFTGTI VGIEDTDPQR  360
WLDSKWRCLK VRWDENSSIP RPDRVSPWKI EPALSPPALN APPVARTKRP RSNILPSSPD  420
SSVLTREGSS RVTADHSQAS GFSRVLQGQE LTTSRGGFAE SNETDLSEKP MLWQPSVNDE  480
KNDNYSASKR HHSGKWLPLG RPESSLTDLL SGFGVPNNSS LGFCLPSADQ AAFGASLVKQ  540
QTQDQEKDFS LLGKPWSLSP SSLSLNLMDS GSKAPGLRGE TPYQMRGDAR YSAFGEFSVL  600
PGHRLANQQG SWVPQPVSPY MKLSHSREMM HKPTVVKQPE AVKPKEGNCK LFGIPLTSSV  660
CTDPVMMQKS SLHDPVSDKN FGIHPHQSPA TDSDQRAEQS KGSKVDDGIA ANDHDKQFQT  720
FHLAGRERDG KGHSSSTRSC TKVHKQGTAL GRSVDLAKFN NYDELIAELD GLFDFNGELK  780
ARSKSWLVVY TDDEGDMMLV GDDPWQEFCG MVRKIFIYTK EEVQRMNPGT LNSKGEDTSS  840
VAEGSDAKEV KNQLLPSESC QEEY

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-170	32	392	12	354	Auxin response factor 1
4ldw_A	1e-170	32	392	12	354	Auxin response factor 1
4ldw_B	1e-170	32	392	12	354	Auxin response factor 1
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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) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255\|RuleBase:RU004561, ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

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	DQ340255	0.0	DQ340255.1 Lycopersicon esculentum auxin response factor 2 (ARF2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006341482.1	0.0	PREDICTED: auxin response factor 2-like
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	M1B469	0.0	M1B469_SOLTU; Auxin response factor
STRING	PGSC0003DMT400036765	0.0	(Solanum tuberosum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA2618	24	44

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G62000.3	0.0	auxin response factor 2

Publications ? help Back to Top
Tomato Genome Consortium The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 2012. 485(7400): p. 635-41 [PMID:22660326] Breitel DA, et al. AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening. PLoS Genet., 2016. 12(3): p. e1005903 [PMID:26959229] Xu T, et al. SlARF2a plays a negative role in mediating axillary shoot formation. Sci Rep, 2016. 6: p. 33728 [PMID:27645097] Ren Z,Liu R,Gu W,Dong X The Solanum lycopersicum auxin response factor SlARF2 participates in regulating lateral root formation and flower organ senescence. Plant Sci., 2017. 256: p. 103-111 [PMID:28167023]