PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc02g077560.2.1
Organism
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: 748aa    MW: 81462.8 Da    PI: 7.3884
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc02g077560.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.72.5e-24160261199
                         EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 
                         f+k+lt sd++++g +++p++ ae++       +  ++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F +
  Solyc02g077560.2.1 160 FCKTLTASDTSTHGGFSVPRRAAEDCfapldyrQ--QRPSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFLR 248
                         99****************************9743..345679************************************************4 PP

                         -SSSEE..EEEEE-S CS
                  B3  85 dgrsefelvvkvfrk 99 
                           + ++el+++v+r+
  Solyc02g077560.2.1 249 --TGDGELRLGVRRA 261
                         ..4788899999986 PP

2Auxin_resp117.31.3e-38286367182
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                         a++ +s++++F+++YnPr s+s+F+v+++k++k+l +++s+GmRfkm++eted++e+r++G+vvgvs++dpvrWp+SkWr+L
  Solyc02g077560.2.1 286 AVNVISSRNAFNICYNPRDSSSDFIVPYHKFSKTLAHPFSAGMRFKMRVETEDAAEQRFTGLVVGVSNVDPVRWPGSKWRCL 367
                         68999****************************************************************************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.0E-39154266IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019365.89E-40157264IPR015300DNA-binding pseudobarrel domain
CDDcd100176.77E-21158260No hitNo description
SMARTSM010191.3E-21160262IPR003340B3 DNA binding domain
PfamPF023623.4E-22160261IPR003340B3 DNA binding domain
PROSITE profilePS5086313.507160262IPR003340B3 DNA binding domain
PfamPF065072.0E-33286367IPR010525Auxin response factor
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:0010582Biological Processfloral meristem determinacy
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 748 aa     Download sequence    Send to blast
MMCGLIDLNT VDNDDAGEET TAPVSLDSPA SSSAASGSSD LTSSTTPAVA SVCMELWHAC  60
AGPLISLPKK GSAVVYLPQG HLEHLSEYPS IACNLPPHVF CRVVDVKLQA DAATDEVYAQ  120
VSLVPDNQQI EQKWKDGDID ADIEEEEIEG AGKSITPHMF CKTLTASDTS THGGFSVPRR  180
AAEDCFAPLD YRQQRPSQEL VAKDLHGIEW KFRHIYRGQP RRHLLTTGWS AFVNKKKLVS  240
GDAVLFLRTG DGELRLGVRR AAQAKTCSSY LAPCSKPLNV SGIVDAVNVI SSRNAFNICY  300
NPRDSSSDFI VPYHKFSKTL AHPFSAGMRF KMRVETEDAA EQRFTGLVVG VSNVDPVRWP  360
GSKWRCLLVR WDDLDVSRHN RVSPWEIEPS GSAPVPSSLV MPSAKRTRVG FPISKADFPI  420
PREGIAVSDF GEPSRFQKVL QGQEILRMHA PYGGLDARSP RPAGTRCFPG FPSSGISRMG  480
NSIRPLFGDT DKSHESIGFS ESLRFNKVLQ GQEIFTSPPY GRAQAGIQMQ EKSRTGIFVG  540
IQVPNHGNRW PAPNQDNNTP CKPINPVSAS SPPSALNFQH PSPPASKFQA MFNHKHDLVN  600
QASLDLSENC CRYPYLSSGS HTEDISQKEG TQGISSFGFL KEQKQTGLSY LSLGTQSSFK  660
GNQNLVSTCK TGCRIFGFPL TESKISATRA DTPSEAVYSH GLETTFLPSS DGKLQPGPPL  720
MTNVVGTNFT KVNDLYAARD VLLDIAL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1095139218357Auxin response factor 1
4ldy_B1e-1095139218357Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.121650.0flower| fruit| stem| trichome
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Detected during gynoecium development.
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078, ECO:0000269|PubMed:9409666}.
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. Involved in the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269|PubMed:10952886, ECO:0000269|PubMed:12036261}.
Function -- GeneRIF ? help Back to Top
  1. The physiological function of SlARF3 was studied by using the RNA interference strategy. SlARF3-down-regulated plants exhibited decreased density of epidermal pavement cells and obviously reduced density of type I, V and VI trichomes of leaves, which indicates the important role of SlARF3 in the formation of trichomes and epidermal cells in tomato.
    [PMID: 26412778]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00021PBMTransfer from AT2G33860Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc02g077560.2.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269|PubMed:19956801}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ3402540.0Lycopersicon esculentum auxin response factor 3 (ARF3) mRNA, complete cds
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010315886.10.0auxin response factor 3 isoform X1
SwissprotO236610.0ARFC_ARATH; Auxin response factor 3
TrEMBLA0A3Q7F3J70.0A0A3Q7F3J7_SOLLC; Auxin response factor
STRINGSolyc02g077560.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA61012333
Representative plantOGRP66851018
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.10.0ARF family protein
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. 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]
  3. Thoma R,Chandler JW
    Polarity in the early floral meristem of Arabidopsis.
    Plant Signal Behav, 2015. 10(4): p. e992733
    [PMID:25806573]
  4. Lora J,Hormaza JI,Herrero M
    Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT).
    New Phytol., 2015. 208(2): p. 584-95
    [PMID:25991552]
  5. 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]
  6. Zhang X, et al.
    Auxin Response Gene SlARF3 Plays Multiple Roles in Tomato Development and is Involved in the Formation of Epidermal Cells and Trichomes.
    Plant Cell Physiol., 2015. 56(11): p. 2110-24
    [PMID:26412778]
  7. Cabrera J, et al.
    Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs.
    New Phytol., 2016. 209(4): p. 1625-40
    [PMID:26542733]
  8. Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC
    The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity.
    Plant Cell, 2015. 27(12): p. 3321-35
    [PMID:26589551]
  9. Yamaguchi N,Wu MF,Winter CM,Wagner D
    LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development.
    Plants (Basel), 2014. 3(2): p. 251-65
    [PMID:27135503]
  10. 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]
  11. Simonini S, et al.
    A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis.
    Genes Dev., 2016. 30(20): p. 2286-2296
    [PMID:27898393]
  12. Pfannebecker KC,Lange M,Rupp O,Becker A
    An Evolutionary Framework for Carpel Developmental Control Genes.
    Mol. Biol. Evol., 2017. 34(2): p. 330-348
    [PMID:28049761]
  13. Wójcikowska B,Gaj MD
    Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis.
    Plant Cell Rep., 2017. 36(6): p. 843-858
    [PMID:28255787]
  14. Su Z, et al.
    The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module.
    Curr. Biol., 2017. 27(11): p. 1597-1609.e2
    [PMID:28552357]
  15. Simonini S,Bencivenga S,Trick M,Østergaard L
    Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis.
    Plant Cell, 2017. 29(8): p. 1864-1882
    [PMID:28804059]
  16. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  17. Simonini S, et al.
    Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis.
    Genes Dev., 2017. 31(17): p. 1821
    [PMID:28982764]
  18. Zhang K, et al.
    AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling.
    Plant Cell, 2018. 30(2): p. 324-346
    [PMID:29371438]
  19. Vial-Pradel S, et al.
    Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3).
    Plant Cell Physiol., 2018. 59(7): p. 1385-1397
    [PMID:29415182]
  20. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.
    [PMID:29440299]
  21. Andres-Robin A, et al.
    Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics.
    Plant Physiol., 2018. 178(3): p. 1222-1232
    [PMID:30237208]
  22. Hablak SG
    Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2.
    Tsitol. Genet., 2019.
    [PMID:30484609]