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; Nicotianoideae; Nicotianeae; Nicotiana

Family

ARF

Protein Properties

Length: 859aa MW: 95739.5 Da PI: 7.0042

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_016514897.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	72.1	7.1e-23	146	255	1	99
EEEE-..-HHHHTT-EE--HHH.HTT..............---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..............ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvv 81 f+k+lt sd++++g +++ +++a+e+ + + + +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++ XP_016514897.1 146 FCKTLTASDTSTHGGFSVLRRHADEClpplfrriqllwdmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFI 239 99***********************************7333.34459****************************************** PP EEE-SSSEE..EEEEE-S CS B3 82 Fkldgrsefelvvkvfrk 99 F + +++el+v+v+r+ XP_016514897.1 240 FL--RGENGELRVGVRRA 255 ..449999*****996 PP
2	Auxin_resp	121.2	7.6e-40	280	362	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha++tk++F+v+Y+Pr+s++eF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp rWp+SkWr+Lk XP_016514897.1 280 AWHAIQTKTMFTVYYKPRTSPTEFIVPYDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGTEDSDPKRWPESKWRCLK 362 89*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.8E-38	140	269	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.83E-37	142	283	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	9.32E-21	144	254	No hit	No description
Pfam	PF02362	5.6E-21	146	255	IPR003340	B3 DNA binding domain
SMART	SM01019	4.7E-22	146	256	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.335	146	256	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.8E-37	280	362	IPR010525	Auxin response factor
Pfam	PF02309	1.5E-10	723	818	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	1.52E-12	728	810	No hit	No description
PROSITE profile	PS51745	25.301	733	817	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: 859 aa Download sequence Send to blast
MSTSEVSIKG YSEPIDGSRP VSETVRSAPV VGKVDAETAL YTELWRACAG PLVTVPREGE 60 LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVVN VLLKAEPDTD EVFAQVTLMP 120 EPNQDENTVK KESMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLFRRIQ 180 LLWDMSRQPP TQELVAKDLH GNEWRFRHIF RGQPRRHLLQ SGWSVFVSSK RLVAGDAFIF 240 LRGENGELRV GVRRAMRQQG NAPSSVISSH SMHLGVLATA WHAIQTKTMF TVYYKPRTSP 300 TEFIVPYDQY MESVKNNYSI GMRFKMRFEG EEAPEQRFTG TIVGTEDSDP KRWPESKWRC 360 LKVRWDENST IPRPDQVSPW KIEPALSPPA LNAPPIARPK RPRSSILPSS PDSSVLTREG 420 SSRITADPSQ ASGFSRVLQG QELSTLRGGF AESNDLDVSE KPMIWPPSVD DEKIDIHSAS 480 KRYLSDKWLP LGRPESSLTD LLSGFGVQNN SSHGFCLPSA DKTAFGASLV KRQAQDQEKD 540 FSLLGKPWSL LSSGLSLNLM DSGSKAPGQG GDTPYQMQGD ARYSGFGEFS VLPGHRVDNQ 600 QGSWFMPQSV SPYFQLSSHS RELRHKPTVV QKPEAVKPKE GNCKLFGIPL TSNVCTDPVM 660 TRKRSLMDSA SNMNIGINSH QSPATDSDQR SEQSKGSKVL DDGITANDQD KQFHTSHLAA 720 RDRDAKGHSS STRSCTKVHK QGTALGRSVD LAKFNNYDEL IAELDQLFDF NGELKARSKS 780 WLVVYTDDEG DMMLVGDDPW QEFCGMVRKI FIYTKDEVQR MNPGTLNSKG EDTSSVAEGS 840 EAKEVKSLQH PSESGQEES

Sequence ? help Back to Top

Protein Sequence Length: 859 aa Download sequence Send to blast

MSTSEVSIKG YSEPIDGSRP VSETVRSAPV VGKVDAETAL YTELWRACAG PLVTVPREGE  60
LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVVN VLLKAEPDTD EVFAQVTLMP  120
EPNQDENTVK KESMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLFRRIQ  180
LLWDMSRQPP TQELVAKDLH GNEWRFRHIF RGQPRRHLLQ SGWSVFVSSK RLVAGDAFIF  240
LRGENGELRV GVRRAMRQQG NAPSSVISSH SMHLGVLATA WHAIQTKTMF TVYYKPRTSP  300
TEFIVPYDQY MESVKNNYSI GMRFKMRFEG EEAPEQRFTG TIVGTEDSDP KRWPESKWRC  360
LKVRWDENST IPRPDQVSPW KIEPALSPPA LNAPPIARPK RPRSSILPSS PDSSVLTREG  420
SSRITADPSQ ASGFSRVLQG QELSTLRGGF AESNDLDVSE KPMIWPPSVD DEKIDIHSAS  480
KRYLSDKWLP LGRPESSLTD LLSGFGVQNN SSHGFCLPSA DKTAFGASLV KRQAQDQEKD  540
FSLLGKPWSL LSSGLSLNLM DSGSKAPGQG GDTPYQMQGD ARYSGFGEFS VLPGHRVDNQ  600
QGSWFMPQSV SPYFQLSSHS RELRHKPTVV QKPEAVKPKE GNCKLFGIPL TSNVCTDPVM  660
TRKRSLMDSA SNMNIGINSH QSPATDSDQR SEQSKGSKVL DDGITANDQD KQFHTSHLAA  720
RDRDAKGHSS STRSCTKVHK QGTALGRSVD LAKFNNYDEL IAELDQLFDF NGELKARSKS  780
WLVVYTDDEG DMMLVGDDPW QEFCGMVRKI FIYTKDEVQR MNPGTLNSKG EDTSSVAEGS  840
EAKEVKSLQH PSESGQEES

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-170	39	384	18	354	Auxin response factor 1
4ldw_A	1e-170	39	384	18	354	Auxin response factor 1
4ldw_B	1e-170	39	384	18	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_016514897.1	0.0	PREDICTED: auxin response factor 2-like isoform X3
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A1S4DN96	0.0	A0A1S4DN96_TOBAC; Auxin response factor
STRING	XP_009625131.1	0.0	(Nicotiana tomentosiformis)

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]