PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID PGSC0003DMP400054999
Common NameLOC102582172
Organism
Solanum tuberosum
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
Family ARF
Protein Properties Length: 748aa    MW: 81556 Da    PI: 7.8074
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400054999genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.72.5e-24159260199
                           EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS
                    B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvF 82 
                           f+k+lt sd++++g +++p++ ae++       +  ++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F
  PGSC0003DMP400054999 159 FCKTLTASDTSTHGGFSVPRRAAEDCfapldyrQ--QRPSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLF 245
                           99****************************9743..345679*********************************************** PP

                           EE-SSSEE..EEEEE-S CS
                    B3  83 kldgrsefelvvkvfrk 99 
                            +  + ++el+++v+r+
  PGSC0003DMP400054999 246 LR--TGDGELRLGVRRA 260
                           *4..4788899999986 PP
2Auxin_resp114.31.1e-37285366182
            Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                           a++ +s+++vF+++YnPr  +s+F+v+++k++k+l +++s+GmRfkm++eted++e+r++G+vvg sd+dpvrWp+SkWr+L
  PGSC0003DMP400054999 285 AVNVISSRNVFNICYNPRGNSSDFIVPYHKFSKTLAHPFSAGMRFKMRVETEDAAEQRFTGLVVGFSDVDPVRWPGSKWRCL 366
                           68999****************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.2E-39153264IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.67E-40156262IPR015300DNA-binding pseudobarrel domain
CDDcd100176.77E-21157259No hitNo description
SMARTSM010191.3E-21159261IPR003340B3 DNA binding domain
PROSITE profilePS5086313.507159261IPR003340B3 DNA binding domain
PfamPF023623.4E-22159260IPR003340B3 DNA binding domain
PfamPF065079.9E-33285366IPR010525Auxin 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 AAPVSLDSPA SSSVASGSSD LTSSTTPAVA SVCMELWHAC  60
AGPLISLPKK GSAVVYLPQG HLEHLSEYPP IACNLPPHVF CRVVDVKLQA DAATDEVYAQ  120
VSLVPDNQIE QKWKDGDIDA DTEEEEIEGA GKSITPHMFC KTLTASDTST HGGFSVPRRA  180
AEDCFAPLDY RQQRPSQELV AKDLHGIEWK FRHIYRGQPR RHLLTTGWSA FVNKKKLVSG  240
DAVLFLRTGD GELRLGVRRA AQAKTCSSYL ARYSKPLNVS GIEDAVNVIS SRNVFNICYN  300
PRGNSSDFIV PYHKFSKTLA HPFSAGMRFK MRVETEDAAE QRFTGLVVGF SDVDPVRWPG  360
SKWRCLLVRW DDLDVSRHNR VSPWEIEPSG SAPVSSSLVM PSAKRTRVGF PISKADFPIP  420
REGIAVSDFG ESSRFQKVLQ GQEILRMHAP YGGLDARSPR PAGIRCFPGF PSSGISRMGN  480
SIRPLLGDTD KSHESIGFSE SLRFNKVLQG QEIFTSPPYG RAQAGIQMQE KGRTGIFVGI  540
QVPNHGNRWP APNQDNNTRC KPINPVSASS PPSALTFQHP SPPASKFQAM FNHKHGKHDL  600
GNQASLDMSE NCCRYLTSGS HTEDISRKEG TQGMSSFGFL KEQKQTGISY LSLGTQSSFK  660
GNQNLVSTCK TSCRIFGFPL TESKISATRA ETPSEAVYSL GLETTFLPSG DGKLQPGPPL  720
VTNVVGTNFT KVNDLYAARD VLLDIAL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1065139118357Auxin response factor 1
4ldy_B1e-1065139118357Auxin response factor 1
Search in ModeBase
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00021PBMTransfer from AT2G33860Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPGSC0003DMP400054999
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
GenBankDQ3402540.0DQ340254.1 Lycopersicon esculentum auxin response factor 3 (ARF3) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006364315.10.0PREDICTED: auxin response factor 3-like isoform X2
SwissprotO236610.0ARFC_ARATH; Auxin response factor 3
TrEMBLM1D4H80.0M1D4H8_SOLTU; Auxin response factor
STRINGPGSC0003DMT4000812820.0(Solanum tuberosum)
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. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  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. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  16. 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]
  17. 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]
  18. 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]
  19. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.
    [PMID:29440299]
  20. 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]
  21. 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]