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 Potri.004G050200.1
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family ARF
Protein Properties Length: 763aa    MW: 83372.1 Da    PI: 7.1137
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.004G050200.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B378.57.2e-25151252199
                         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  
  Potri.004G050200.1 151 FCKTLTASDTSTHGGFSVPRRAAEDCfppldytQ--QRPSQELVAKDLHGSEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL- 238
                         99****************************9743..345679************************************************. PP

                         -SSSEE..EEEEE-S CS
                  B3  85 dgrsefelvvkvfrk 99 
                          + +++el+++v+r+
  Potri.004G050200.1 239 -RGEDGELRLGVRRA 252
                         .449999*****996 PP
2Auxin_resp118.45.7e-39277358182
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                         +a+a+s++s+F+++YnPras+seF+++++k++k+l++++s+GmR+km+feted++err++G+++g+s+ldp+rWp+SkW++L
  Potri.004G050200.1 277 VANAISMRSAFRIYYNPRASSSEFIIPFNKFLKSLDQSFSAGMRVKMRFETEDAAERRYTGLITGISELDPTRWPGSKWKCL 358
                         689******************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.96E-42145270IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.9E-40146253IPR015300DNA-binding pseudobarrel domain
CDDcd100171.00E-22149251No hitNo description
SMARTSM010192.7E-23151253IPR003340B3 DNA binding domain
PfamPF023621.2E-22151252IPR003340B3 DNA binding domain
PROSITE profilePS5086313.535151253IPR003340B3 DNA binding domain
PfamPF065076.9E-34277358IPR010525Auxin 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 763 aa     Download sequence    Send to blast
MIDLNTTEED ETTPSSGSLS SPSSSSAASA LSASGSGSGT SPVCLELWHA CAGPLISLPK  60
RGSIVVYVPQ GHLEQLPDLP LGIYDLPPHV FCRVVDVKLH AEAASDDVYA QVSLVPESEE  120
IEQKLREGVF EGDGEEEDVE ATVKTTTPHM FCKTLTASDT STHGGFSVPR RAAEDCFPPL  180
DYTQQRPSQE LVAKDLHGSE WKFRHIYRGQ PRRHLLTTGW SAFVNKKKLV SGDAVLFLRG  240
EDGELRLGVR RAAQVKCGPT FPALWNQQLN QSSLADVANA ISMRSAFRIY YNPRASSSEF  300
IIPFNKFLKS LDQSFSAGMR VKMRFETEDA AERRYTGLIT GISELDPTRW PGSKWKCLLV  360
RWDDTEANRH SRVSPWEVEP SGSVSGSGSG SISSSNNSMA PGLKRSRSGL PSLKAEFPIP  420
DGIGASDFRV SSRFQEVLQG QEIMSFNTLY DDVDGQNQHP SEIRSRFPGS HGSGIAAIGS  480
GIRGSIPTSE NSFKGIGFNE SYRFHKVLQG QEIFPRSPYR RIPNANKARE NCGLGLSDGV  540
QRSSSRNGWS TMMQGYNTQM RPPTQVSSPS SVLMFQHASN QVSNPTSIFN SNDHEEQTTN  600
TQSWFYPETH GGKFKLSSHS DPGLRGDSQC STNPYVLSHE HLQHGISQPV VAQSAFRSSQ  660
DMVLCKSSCR LFGFSLTEDR HVVNKEDNIA SITSPLNPES SFLPRVGEQL HPKPPAINNA  720
VGSSCTKSFV HEYKTSVTAS LATQMANFSM IGAKVKGGIV CF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-114263872361Auxin response factor 1
4ldy_B1e-114263872361Auxin response factor 1
Search in ModeBase
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.004G050200.1
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
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024455530.10.0auxin response factor 3 isoform X1
SwissprotO236610.0ARFC_ARATH; Auxin response factor 3
TrEMBLA0A1L6K4990.0A0A1L6K499_POPTO; Auxin response factor
STRINGPOPTR_0004s04970.10.0(Populus trichocarpa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF45763355
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. 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]
  2. Thoma R,Chandler JW
    Polarity in the early floral meristem of Arabidopsis.
    Plant Signal Behav, 2015. 10(4): p. e992733
    [PMID:25806573]
  3. 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]
  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. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  15. 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]
  16. 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]
  17. 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]
  18. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.
    [PMID:29440299]
  19. 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]
  20. 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]