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 Neem_25428_f_1
Organism
Azadirachta indica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family ARF
Protein Properties Length: 271aa    MW: 30861.5 Da    PI: 10.0818
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_25428_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B333.66.8e-1146885599
                    ETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
              B3 55 ksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99
                    +++r++l++GW+ Fv++++L +gD ++F   + +++el+v+v+r+
  Neem_25428_f_1 46 QPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGELRVGVRRA 88
                    6899*************************..449999*****996 PP
2Auxin_resp120.41.4e-39113195183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     a+ha+st++ F+v+Y+Pr+s++eF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp rW++SkWr+Lk
  Neem_25428_f_1 113 AWHAVSTGTLFTVYYKPRTSPAEFIVPFDQYRESIKSNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPKRWRESKWRCLK 195
                     89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.16E-1144116IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.3E-1545102IPR015300DNA-binding pseudobarrel domain
CDDcd100176.10E-74587No hitNo description
PfamPF023624.7E-84688IPR003340B3 DNA binding domain
PROSITE profilePS508638.6844989IPR003340B3 DNA binding domain
PfamPF065079.0E-37113195IPR010525Auxin response factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009725Biological Processresponse to hormone
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 271 aa     Download sequence    Send to blast
MEYHEGIADR MPSLFELICF VLLVIPFMYY SALSLSNVHD TCLPGQPRRH LLQSGWSVFV  60
SSKRLVAGDA FIFLRGENGE LRVGVRRAMR QQGNVPSSVI SSHSMHLGVL ATAWHAVSTG  120
TLFTVYYKPR TSPAEFIVPF DQYRESIKSN YSIGMRFKMR FEGEEAPEQR FTGTIVGIED  180
ADPKRWRESK WRCLKVRWDE TSTIPRPERV SPWKIEPALA PPALNPLPMP RPKRPRSSMV  240
PSSPDSSVLT REGSSKGLAR SRIFDLERQF C
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A2e-8745217182354Auxin response factor 1
4ldw_A2e-8745217182354Auxin response factor 1
4ldw_B2e-8745217182354Auxin response factor 1
4ldx_A2e-8745217182354Auxin response factor 1
4ldx_B2e-8745217182354Auxin 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. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Functions independently of ethylene and cytokinin response pathways. May act as a repressor of cell division and organ growth. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952, ECO:0000269|PubMed:16339187}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN6005202e-61JN600520.1 Citrus sinensis auxin-response factor (ARF) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002318767.21e-142auxin response factor 2
RefseqXP_011042961.11e-142PREDICTED: auxin response factor 2-like
RefseqXP_021911560.11e-142auxin response factor 2, partial
SwissprotQ94JM31e-135ARFB_ARATH; Auxin response factor 2
TrEMBLV4VCW71e-142V4VCW7_9ROSI; Auxin response factor
STRINGevm.TU.contig_31756.11e-141(Carica papaya)
STRINGPOPTR_0012s10790.11e-141(Populus trichocarpa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.31e-112auxin response factor 2
Publications ? help Back to Top
  1. Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV
    Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula).
    PLoS ONE, 2012. 7(8): p. e42839
    [PMID:22916167]
  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. Li C, et al.
    Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis.
    PLoS ONE, 2014. 9(4): p. e94830
    [PMID:24756087]
  4. Lyons R, et al.
    Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.
    PLoS ONE, 2015. 10(4): p. e0121902
    [PMID:25849296]
  5. Roodbarkelari F,Du F,Truernit E,Laux T
    ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response.
    BMC Biol., 2015. 13: p. 74
    [PMID:26358077]
  6. Meng LS,Wang ZB,Yao SQ,Liu A
    The ARF2-ANT-COR15A gene cascade regulates ABA-signaling-mediated resistance of large seeds to drought in Arabidopsis.
    J. Cell. Sci., 2015. 128(21): p. 3922-32
    [PMID:26395398]
  7. Zhao S,Zhang ML,Ma TL,Wang Y
    Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress.
    Plant Cell, 2016. 28(12): p. 3005-3019
    [PMID:27895227]
  8. Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z
    ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis .
    J Integr Plant Biol, 2017. 59(1): p. 30-43
    [PMID:28074634]
  9. 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]
  10. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]
  11. Zhang M,Hu X,Zhu M,Xu M,Wang L
    Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis.
    Sci Rep, 2017. 7(1): p. 1395
    [PMID:28469131]
  12. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  13. 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]
  14. Sarkar Das S, et al.
    Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination.
    Sci Rep, 2018. 8(1): p. 1233
    [PMID:29352229]