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

Niben101Scf05912g01012.1

Organism

Nicotiana benthamiana

Taxonomic ID

4100

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: 876aa MW: 97461.5 Da PI: 6.7408

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Niben101Scf05912g01012.1	genome	BTI	-

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	56.2	6.4e-18	146	272	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE...........................EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliy.........................rk 54 f+k+lt sd++++g +++ +++a+e+ + + + +++l+ +d++g++W++++i+ r+ Niben101Scf05912g01012.1 146 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFrddligsvkgewrswltnfcfckigRG 229 99***************************7333.34459****888888888888888888888888888888999999 PP ETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS B3 55 ksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 +++r++l++GW+ Fv++++L +gD ++F + +++el+v+v+r+ Niben101Scf05912g01012.1 230 QPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGELRVGVRRA 272 9999*********************..449999***996 PP
2	Auxin_resp	123.3	1.8e-40	297	379	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 Niben101Scf05912g01012.1 297 AWHAIQTKTMFTVYYKPRTSPAEFIVPYDQYMESMKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGTEDSDPKRWPESKWRCLK 379 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	2.5E-37	140	286	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.67E-35	142	300	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.19E-17	144	271	No hit	No description
PROSITE profile	PS50863	10.25	146	273	IPR003340	B3 DNA binding domain
SMART	SM01019	2.3E-13	146	273	IPR003340	B3 DNA binding domain
Pfam	PF02362	8.8E-9	215	272	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.6E-37	297	379	IPR010525	Auxin response factor
Pfam	PF02309	2.0E-10	740	835	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	1.47E-12	745	827	No hit	No description
PROSITE profile	PS51745	24.955	750	834	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: 876 aa Download sequence Send to blast
MATSEVSIKG YNEPIDGSRP VSETVRSAPV VGKVDAETAL YTELWRACAG PLVTVPREGE 60 LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVVN VLLKAEPDTD EVFAQVTLMP 120 EPNQDENTVK KESMRPPTPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ 180 PPTQELVAKD LHGNEWRFRH IFRDDLIGSV KGEWRSWLTN FCFCKIGRGQ PRRHLLQSGW 240 SVFVSSKRLV AGDAFIFLRG ENGELRVGVR RAMRQQGIAP SSVISSHSMH LGVLATAWHA 300 IQTKTMFTVY YKPRTSPAEF IVPYDQYMES MKNNYSIGMR FKMRFEGEEA PEQRFTGTIV 360 GTEDSDPKRW PESKWRCLKV RWDENSTTLR PDRVSPWKIE PALSPPALNA PPIARPKRPR 420 SSILPSSPDS SVLTREGSSR ITADPSQASG FSRVLQGQEL STLRGGFAES NDSDVPEKPM 480 LWPPSVDDEK IDVHSVSKRY LSDKWLPLGR LESSLTDLLS GFGVQNNSSH GFCLPSVDQT 540 AFGASLVKRQ AQDQEKDFSL LGKPWSLLSS SLSLDLMDSG SKAPGQGADT PYQMQGDARY 600 SGFGEFSVLP GHRVDNQQGS WLMPQSVSPY FQLSSHSRDL MHKPTVVQKP EAVKPKEGNC 660 KLFGIPLASN VCTDPVMTRK SSLMDSASNM NIGINSHQSP ATDSDQRSEQ SKGSKVLDDG 720 ITASDQDKQF HTSHLTARDR DAKGHSSSTR SCTKVHKQGT ALGRSVDLAK FNNYDELIAE 780 LDQIFDFNGA LKARSKSWLV VYTDDEGDMM LVGDDPWQEF CGMVRKIFIY TKEEVQRMNP 840 GTLNSKGEDT SSVAEGSEAK EVKSLQHPSE SGQEES

Sequence ? help Back to Top

Protein Sequence Length: 876 aa Download sequence Send to blast

MATSEVSIKG YNEPIDGSRP VSETVRSAPV VGKVDAETAL YTELWRACAG PLVTVPREGE  60
LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVVN VLLKAEPDTD EVFAQVTLMP  120
EPNQDENTVK KESMRPPTPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ  180
PPTQELVAKD LHGNEWRFRH IFRDDLIGSV KGEWRSWLTN FCFCKIGRGQ PRRHLLQSGW  240
SVFVSSKRLV AGDAFIFLRG ENGELRVGVR RAMRQQGIAP SSVISSHSMH LGVLATAWHA  300
IQTKTMFTVY YKPRTSPAEF IVPYDQYMES MKNNYSIGMR FKMRFEGEEA PEQRFTGTIV  360
GTEDSDPKRW PESKWRCLKV RWDENSTTLR PDRVSPWKIE PALSPPALNA PPIARPKRPR  420
SSILPSSPDS SVLTREGSSR ITADPSQASG FSRVLQGQEL STLRGGFAES NDSDVPEKPM  480
LWPPSVDDEK IDVHSVSKRY LSDKWLPLGR LESSLTDLLS GFGVQNNSSH GFCLPSVDQT  540
AFGASLVKRQ AQDQEKDFSL LGKPWSLLSS SLSLDLMDSG SKAPGQGADT PYQMQGDARY  600
SGFGEFSVLP GHRVDNQQGS WLMPQSVSPY FQLSSHSRDL MHKPTVVQKP EAVKPKEGNC  660
KLFGIPLASN VCTDPVMTRK SSLMDSASNM NIGINSHQSP ATDSDQRSEQ SKGSKVLDDG  720
ITASDQDKQF HTSHLTARDR DAKGHSSSTR SCTKVHKQGT ALGRSVDLAK FNNYDELIAE  780
LDQIFDFNGA LKARSKSWLV VYTDDEGDMM LVGDDPWQEF CGMVRKIFIY TKEEVQRMNP  840
GTLNSKGEDT SSVAEGSEAK EVKSLQHPSE SGQEES

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-167	39	401	18	354	Auxin response factor 1
4ldw_A	1e-167	39	401	18	354	Auxin response factor 1
4ldw_B	1e-167	39	401	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}.

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
Refseq	XP_016476812.1	0.0	PREDICTED: auxin response factor 2-like
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A1S4AJD8	0.0	A0A1S4AJD8_TOBAC; Auxin response factor
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]