PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc11g069190.1.1
Common NameARF4
Organism
Solanum lycopersicum
Taxonomic ID
Taxonomic Lineage
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: 812aa    MW: 90330.8 Da    PI: 6.1592
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc11g069190.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.99e-24176277199
                         EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                         f+k+lt sd++++g +++p++ ae++      +++ + s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F   
  Solyc11g069190.1.1 176 FCKTLTASDTTTHGGFSVPRRAAEDCfppldyKEQ-RPSQELIAKDLHGVEWKFRHIYRGQPRRHLLTTGWSIFVSQKNLVSGDAVLFL-- 263
                         99****************************86333.45679************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + ++++l+++++r+
  Solyc11g069190.1.1 264 RGEGGNLRLGIRRA 277
                         449999*****996 PP
2Auxin_resp119.52.7e-39302383182
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                         +a+a+s ks+F+v+Y+Pras+++Fvv+++k++ka+++++ vG+Rfkm+f+ +ds+err+sG+v+g+sd+dp+rWpnSkWr+L
  Solyc11g069190.1.1 302 VATALSAKSTFHVFYSPRASHADFVVPYQKYVKAINSRIPVGTRFKMKFDLDDSPERRYSGVVTGISDMDPFRWPNSKWRCL 383
                         6899*****************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.31E-43168292IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.8E-40169289IPR015300DNA-binding pseudobarrel domain
CDDcd100175.03E-22174276No hitNo description
PROSITE profilePS5086312.915176278IPR003340B3 DNA binding domain
SMARTSM010191.3E-22176278IPR003340B3 DNA binding domain
PfamPF023621.0E-21176277IPR003340B3 DNA binding domain
PfamPF065078.4E-33303383IPR010525Auxin response factor
SuperFamilySSF542774.12E-11676762No hitNo description
PROSITE profilePS5174521.663683767IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 812 aa     Download sequence    Send to blast
MEIDLNHALV SEVEKNVCCN EECDKGGGGG CVNCSLYTST TSSCSSNVSS SSSLALTSIY  60
KELWHACAGP LTSLPKKGNV VVYFPQGHME EAVSAFPFSP VKIDLPTFGL QPQIFCRVED  120
VQLLANKEND EVYTQLTLLP LPESMAISLE GKEHEDSGTD EEGNGVNPGK SASHMFCKTL  180
TASDTTTHGG FSVPRRAAED CFPPLDYKEQ RPSQELIAKD LHGVEWKFRH IYRGQPRRHL  240
LTTGWSIFVS QKNLVSGDAV LFLRGEGGNL RLGIRRAARP RNGLPESIIK SQYSGPDVLS  300
SVATALSAKS TFHVFYSPRA SHADFVVPYQ KYVKAINSRI PVGTRFKMKF DLDDSPERRY  360
SGVVTGISDM DPFRWPNSKW RCLMVRWDED IMSNHQERVS PWEIDSSVSL PPLSIQSSPR  420
LKKLRTSQQA PSVLDSHFAG GSALLDFEES IRSSKVLQGQ ENLGLISPPY GCDKPVRPLD  480
FELQRVARHN LMPNGVENII VGDFVKTQPP TTYTGFLESN RFPKVLQGQE ICSLRSLTGK  540
GDVNFGAWGK PEFGCNVFGT YQRPRANFYP LASEGARNVF LPYNAMYRAG QDPVVPSYST  600
NFQRENPTLN QNSIQNVVRR EEVGMPKFVN EQRPPEMSKV SIPENHFKNE NDDSFNAQAP  660
CKLFGFSLTK EPSTPSSQSS GKRSCTKVHK QGSLVGRAID LSRLNGYDDL LVELERLFNM  720
EDLLRDPNKG WRILYTDSEN DMMVVGDDPW HEFCEVVSKI HIYTQEEVEK MTIEGISDDT  780
QSCLEEAPAI MDVSKSSSVG QPDSSPTVIR I*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1145840518353Auxin response factor 1
4ldw_A1e-1145840518353Auxin response factor 1
4ldw_B1e-1145840518353Auxin response factor 1
4ldy_A1e-1135840518353Auxin response factor 1
4ldy_B1e-1135840518353Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.159970.0floral bud| flower| fruit| leaf
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078}.
Functional Description ? help Back to Top
Source Description
UniProtAuxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. {ECO:0000269|PubMed:12036261}.
Function -- GeneRIF ? help Back to Top
  1. SlARF4 expression is high in pericarp tissues of immature fruit and then undergoes a dramatic decline at the onset of ripening concomitant with the increase in sugar content.
    [PMID: 23341361]
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc11g069190.1.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ3402590.0Lycopersicon esculentum auxin response factor 4 (ARF4) mRNA, complete cds
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001233771.10.0auxin response factor 4
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLQ2LAI90.0Q2LAI9_SOLLC; Auxin response factor
STRINGSolyc11g069190.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA51432234
Representative plantOGRP10049811
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60450.10.0auxin response factor 4
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. Sagar M, et al.
    SlARF4, an auxin response factor involved in the control of sugar metabolism during tomato fruit development.
    Plant Physiol., 2013. 161(3): p. 1362-74
    [PMID:23341361]
  3. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  4. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  5. Pashkovskiy PP,Kartashov AV,Zlobin IE,Pogosyan SI,Kuznetsov VV
    Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.
    Plant Physiol. Biochem., 2016. 104: p. 146-54
    [PMID:27031426]
  6. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  7. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  8. Liu Z, et al.
    ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis.
    Plant Cell Physiol., 2018. 59(1): p. 179-189
    [PMID:29145642]