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 Neem_11185_f_1
Organism
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: 841aa    MW: 94152.8 Da    PI: 6.7975
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_11185_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.61e-22150251199
                     EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                     f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++ ++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + ++
  Neem_11185_f_1 150 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHANEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGEN 241
                     99*****************************7333.34459************************************************..4499 PP

                     E..EEEEE-S CS
              B3  90 felvvkvfrk 99 
                     +el+v+v+r+
  Neem_11185_f_1 242 GELRVGVRRA 251
                     99*****996 PP

2Auxin_resp117.98.6e-39276358183
      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_11185_f_1 276 AWHAVSTGTLFTVYYKPRTSPAEFIVPFDQYRESIKSNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPKRWRESKWRCLK 358
                     89*******************************************************************************96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.01E-40146279IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.8E-40147265IPR015300DNA-binding pseudobarrel domain
CDDcd100171.42E-20148250No hitNo description
SMARTSM010194.1E-22150252IPR003340B3 DNA binding domain
PfamPF023621.4E-20150251IPR003340B3 DNA binding domain
PROSITE profilePS5086311.42150252IPR003340B3 DNA binding domain
PfamPF065075.5E-36276358IPR010525Auxin response factor
PfamPF023094.6E-10698804IPR033389AUX/IAA domain
PROSITE profilePS5174525.101716798IPR000270PB1 domain
SuperFamilySSF542773.24E-11716793No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009737Biological Processresponse to abscisic acid
GO:0009911Biological Processpositive regulation of flower development
GO:0010047Biological Processfruit dehiscence
GO:0010150Biological Processleaf senescence
GO:0010227Biological Processfloral organ abscission
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 841 aa     Download sequence    Send to blast
MAAASSSEVS IKSSNETSRK PMEGKNSNST SSGNKRVLDP EMALYTELWH ACAGPLVTVP  60
REGEHVYYFP QGHIEQVEAS TNQVADQQMP VYDLPSKILC RVINVQLKAE PDTDEVFAQV  120
TLLPETNQDE NAVEKEPPPP PPPRFHVHSF CKTLTASDTS THGGFSVLRR HADECLPPLD  180
MSRQPPTQEL VAKDLHANEW RFRHIFRGQP RRHLLQSGWS VFVSSKRLVA GDAFIFLRGE  240
NGELRVGVRR AMRQQGNVPS SVISSHSMHL GVLATAWHAV STGTLFTVYY KPRTSPAEFI  300
VPFDQYRESI KSNYSIGMRF KMRFEGEEAP EQRFTGTIVG IEDADPKRWR ESKWRCLKVR  360
WDETSTIPRP ERVSPWKIEP ALAPPALNPL PMPRPKRPRS SMVPSSPDSS VLTREGSSKV  420
NVDPSSATVF SRVLQGQEFS TLRGNFAERE SNESDTAEKS VVWPPSLEDE KIDVVSASRR  480
YGSENWGPSG RHEPTYTDLL SGFGANGDSP RGYNSPFADQ SVRKSMLDQE GKFNLLARPW  540
SLMPSGLSLK LSESNSKVPV QGGDVNYQVR GNVRYGGFGD YPVLHGNRSE HSHGNWLMPP  600
LPPAQFENSA HSRELMPKPV LVQDQEAGKS KDCKLFGIPL FSNPVVPEPH RNMVNEPVGN  660
IDQQFRAFES DQKSEQSKSS KLADDNKAVN DREKKLQACQ PHTKDVRSKP QSVSARSCTK  720
VHKQGIALGR SVDLSKFNNY DELIAELDQL FEFGGELMAP KKNWLIVYTD DEDDMMLVGD  780
DPWQEFCGMV RKIYIYTKEE VQKMNPGTLS SRGEENSLIG EGGDVKETKQ SLPTVSNMEN  840
C
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1794338018354Auxin response factor 1
4ldw_A1e-1794338018354Auxin response factor 1
4ldw_B1e-1794338018354Auxin response factor 1
4ldx_A1e-1794338018354Auxin response factor 1
4ldx_B1e-1794338018354Auxin 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00574DAPTransfer from AT5G62000Download
Motif logo
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN6005200.0JN600520.1 Citrus sinensis auxin-response factor (ARF) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001275789.10.0auxin-response factor
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLG9I8200.0G9I820_CITSI; Auxin response factor
STRINGXP_006436945.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53482647
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin 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]