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; Lycopersicon

Family

ARF

Protein Properties

Length: 354aa MW: 39768.9 Da PI: 9.4499

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc00g196060.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	33.1	9.7e-11	18	59	56	99
TTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS B3 56 sgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 ++r++lt+GW+ Fv+a++L +gD+v+F ++++ +l+++++r+ Solyc00g196060.2.1 18 PKRHLLTTGWSVFVSAKRLVAGDSVIFI--WNENNQLLLGIRRA 59 679***********************..7888889**997 PP
2	Auxin_resp	115.3	5.4e-38	84	167	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+t+s F++++nPra++seFv++++k+ ka++ ++vsvGmRf+m fete+ss rr++Gt++g+ dldpvrWpnS+W+s+k Solyc00g196060.2.1 84 AAHAAATNSRFTIFFNPRACPSEFVIPLAKYAKAVYhTRVSVGMRFRMLFETEESSIRRYMGTITGIGDLDPVRWPNSHWQSVK 167 79*******************************9789***************************************9975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50863	9.573	1	60	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	6.02E-13	16	87	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.6E-15	17	73	IPR015300	DNA-binding pseudobarrel domain
Pfam	PF02362	3.0E-8	17	59	IPR003340	B3 DNA binding domain
CDD	cd10017	2.27E-6	18	58	No hit	No description
Pfam	PF06507	4.0E-33	84	166	IPR010525	Auxin response factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 354 aa Download sequence Send to blast
MYNSLCIYKG INCIICQPKR HLLTTGWSVF VSAKRLVAGD SVIFIWNENN QLLLGIRRAN 60 RPQTVLPSSV LSSDSMHIGL LAAAAHAAAT NSRFTIFFNP RACPSEFVIP LAKYAKAVYH 120 TRVSVGMRFR MLFETEESSI RRYMGTITGI GDLDPVRWPN SHWQSVKVGW DESTAGERQP 180 RVSLWEIEPL TTFPMYPSPF SLRLKRPWPP GLPSFPGLSN GDMTMNSQLP WLHGGMGDQG 240 IQSLNFQGFG VTPFMQPRFD ASMLGLQPDI LQAMAALDSS KLANQPLMQF QHIPSTSASS 300 IQSQLLHPSN LQHTFLQGLP ENQLISQAQM LQQQLQCHQS YNTQQQQLQR QXXX

Sequence ? help Back to Top

Protein Sequence Length: 354 aa Download sequence Send to blast

MYNSLCIYKG INCIICQPKR HLLTTGWSVF VSAKRLVAGD SVIFIWNENN QLLLGIRRAN  60
RPQTVLPSSV LSSDSMHIGL LAAAAHAAAT NSRFTIFFNP RACPSEFVIP LAKYAKAVYH  120
TRVSVGMRFR MLFETEESSI RRYMGTITGI GDLDPVRWPN SHWQSVKVGW DESTAGERQP  180
RVSLWEIEPL TTFPMYPSPF SLRLKRPWPP GLPSFPGLSN GDMTMNSQLP WLHGGMGDQG  240
IQSLNFQGFG VTPFMQPRFD ASMLGLQPDI LQAMAALDSS KLANQPLMQF QHIPSTSASS  300
IQSQLLHPSN LQHTFLQGLP ENQLISQAQM LQQQLQCHQS YNTQQQQLQR QXXX

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	6e-75	7	188	213	388	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.6144	0.0	cell culture\| flower\| fruit\| leaf\| root

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots, culms, leaves and young panicles. {ECO:0000269\|PubMed:17408882}.

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).
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).

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc00g196060.2.1

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	HM594684	0.0	Solanum lycopersicum auxin response factor 6 (ARF6) mRNA, complete cds

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015061224.1	0.0	auxin response factor 6-like isoform X1
Refseq	XP_015061225.1	0.0	auxin response factor 6-like isoform X2
Swissprot	A2YG67	1e-148	ARFQ_ORYSI; Auxin response factor 17
Swissprot	Q653U3	1e-148	ARFQ_ORYSJ; Auxin response factor 17
TrEMBL	E0AD21	0.0	E0AD21_SOLLC; Auxin response factor
STRING	Solyc00g196060.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA5859	23	34
Representative plant	OGRP856	14	56

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G30330.2	1e-146	auxin response factor 6

Link Out ? help Back to Top
Phytozome	Solyc00g196060.2.1

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Wu J, et al. Identification, isolation and expression analysis of auxin response factor (ARF) genes in Solanum lycopersicum. Plant Cell Rep., 2011. 30(11): p. 2059-73 [PMID:21735233]