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

XP_009769542.1

Organism

Nicotiana sylvestris

Taxonomic ID

4096

Taxonomic Lineage

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: 851aa MW: 94554.1 Da PI: 6.8243

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009769542.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	74.8	9.7e-24	146	247	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 f+k+lt sd++++g +++ +++a+e+ + + + +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F + ++ XP_009769542.1 146 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGEN 237 99***************************7333.34459********************************************..4499 PP E..EEEEE-S CS B3 90 felvvkvfrk 99 +el+v+v+r+ XP_009769542.1 238 GELRVGVRRA 247 99***996 PP
2	Auxin_resp	122.1	4e-40	272	354	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_009769542.1 272 AWHAIQTKTMFTVYYKPRTSPAEFIVPYDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGTEDSDPKRWPESKWRCLK 354 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	9.5E-42	140	261	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	2.09E-40	142	275	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	7.74E-22	144	246	No hit	No description
PROSITE profile	PS50863	12.012	146	248	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.1E-21	146	247	IPR003340	B3 DNA binding domain
SMART	SM01019	2.0E-23	146	248	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.1E-37	272	354	IPR010525	Auxin response factor
Pfam	PF02309	9.4E-11	715	810	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	1.42E-12	720	802	No hit	No description
PROSITE profile	PS51745	25.219	725	809	IPR000270	PB1 domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008285	Biological Process	negative regulation of cell proliferation
GO:0009737	Biological Process	response to abscisic acid
GO:0009911	Biological Process	positive regulation of flower development
GO:0010047	Biological Process	fruit dehiscence
GO:0010150	Biological Process	leaf senescence
GO:0010227	Biological Process	floral organ abscission
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:0048481	Biological Process	plant ovule development
GO:0005634	Cellular Component	nucleus
GO:0005515	Molecular Function	protein binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 851 aa Download sequence Send to blast
MATSEVSIKG YNEPIDGSRP VSETVRSAPV VGKVDAETAL YTELWRACAG PLVTVPREGE 60 LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVVN VLLKAEPDTD EVFAQVTLMP 120 EPNQDENTVK KESMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ 180 PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL 240 RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT SPAEFIVPYD 300 QYMESVKNNY SIGMRFKMRF EGEEAPEQRF TGTIVGTEDS DPKRWPESKW RCLKVRWDEN 360 STIPRPDRVS PWKIEPALSP PALNAPPIAR PKRPRSSILP SSPDSSVLTR EGSSRITADP 420 SQASGFSRVL QGQELSALRG GFAESNDSDV SEKPMLWPPS VDDEKIDIHS ASKRYLSDKW 480 LPLGRPESSL TDLLSGFGVQ NNSSHGFCLP SADQTAFGAS LVKRQAQDQE KDFSLLGKPW 540 LLLSSSLSLN LMDSGSKAPG QGADTPYQMQ GDARYSGFGK FSVLPGHRVD NQQGSWFMPQ 600 SVSPYFQLSS HSRDLMHKPT VVQKPEAVKP KEGNCKLFGI PLTSNVCTDP VMTRKSSLMD 660 SASNMNIGIN SHQSPATDSD QRSEQSKGSK VLDDGITAND QDKQFHTSHL AARDRDAKGH 720 SSSTRSCTKV HKQGTALGRS VDLAKFNNYD ELIAELDQLF DFNGELKARS KSWLVVYTDD 780 EGDMMLVGDD PWQEFCGMVR KIFIYTKEEV QRMNPGTLNS KGEDTSSVAE GSEAKEVKSL 840 QHPSESGQEE S

Sequence ? help Back to Top

Protein Sequence Length: 851 aa Download sequence Send to blast

MATSEVSIKG YNEPIDGSRP VSETVRSAPV VGKVDAETAL YTELWRACAG PLVTVPREGE  60
LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVVN VLLKAEPDTD EVFAQVTLMP  120
EPNQDENTVK KESMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ  180
PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL  240
RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT SPAEFIVPYD  300
QYMESVKNNY SIGMRFKMRF EGEEAPEQRF TGTIVGTEDS DPKRWPESKW RCLKVRWDEN  360
STIPRPDRVS PWKIEPALSP PALNAPPIAR PKRPRSSILP SSPDSSVLTR EGSSRITADP  420
SQASGFSRVL QGQELSALRG GFAESNDSDV SEKPMLWPPS VDDEKIDIHS ASKRYLSDKW  480
LPLGRPESSL TDLLSGFGVQ NNSSHGFCLP SADQTAFGAS LVKRQAQDQE KDFSLLGKPW  540
LLLSSSLSLN LMDSGSKAPG QGADTPYQMQ GDARYSGFGK FSVLPGHRVD NQQGSWFMPQ  600
SVSPYFQLSS HSRDLMHKPT VVQKPEAVKP KEGNCKLFGI PLTSNVCTDP VMTRKSSLMD  660
SASNMNIGIN SHQSPATDSD QRSEQSKGSK VLDDGITAND QDKQFHTSHL AARDRDAKGH  720
SSSTRSCTKV HKQGTALGRS VDLAKFNNYD ELIAELDQLF DFNGELKARS KSWLVVYTDD  780
EGDMMLVGDD PWQEFCGMVR KIFIYTKEEV QRMNPGTLNS KGEDTSSVAE GSEAKEVKSL  840
QHPSESGQEE S

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-174	39	376	18	354	Auxin response factor 1
4ldw_A	1e-174	39	376	18	354	Auxin response factor 1
4ldw_B	1e-174	39	376	18	354	Auxin response factor 1
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) (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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00574	DAP	Transfer from AT5G62000	Download

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	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_009769542.1	0.0	PREDICTED: auxin response factor 2-like isoform X1
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A1U7VNR4	0.0	A0A1U7VNR4_NICSY; Auxin response factor
STRING	XP_009769542.1	0.0	(Nicotiana sylvestris)

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]