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 evm_27.model.AmTr_v1.0_scaffold00016.128
Common NameAMTR_s00016p00168950
Organism
Amborella trichopoda
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella
Family ARF
Protein Properties Length: 839aa    MW: 92618.1 Da    PI: 6.9662
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00016.128genomeTAGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B370.81.7e-22143244199
                                               EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-T CS
                                        B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltk 63 
                                               f+k+lt sd++++g +++ k++a+e+      g +++ +++l+ +d++g +W++++i+r++++r++l++
  evm_27.model.AmTr_v1.0_scaffold00016.128 143 FCKTLTASDTSTHGGFSVLKRHADEClppldmGRQPP-TQELIAKDLHGIEWRFRHIFRGQPRRHLLQS 210
                                               99*****************************755544.469**************************** PP

                                               THHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
                                        B3  64 GWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 
                                               GW+ Fv +++L +gD ++F   + +++el+v+v+r+
  evm_27.model.AmTr_v1.0_scaffold00016.128 211 GWSVFVGSKKLVAGDAFIFL--RGENGELRVGVRRA 244
                                               ********************..449999*****996 PP
2Auxin_resp119.62.5e-39269351183
                                Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdl 69 
                                               a+ha+st+++F+v+Y+Pr s+seF+v+++++++alk+++s+GmRfkm+fe+e+++e+r++Gtvvg+ d+
  evm_27.model.AmTr_v1.0_scaffold00016.128 269 AMHAISTGTMFTVYYKPRISPSEFIVPCNQYLEALKQNYSIGMRFKMRFEGEEAPEQRFTGTVVGIGDV 337
                                               78******************************************************************* PP

                                Auxin_resp  70 dpvrWpnSkWrsLk 83 
                                               dp +Wp+SkWr+Lk
  evm_27.model.AmTr_v1.0_scaffold00016.128 338 DPDKWPGSKWRCLK 351
                                               ************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.57E-39138272IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.0E-39139258IPR015300DNA-binding pseudobarrel domain
CDDcd100171.08E-20141243No hitNo description
PROSITE profilePS5086311.448143245IPR003340B3 DNA binding domain
SMARTSM010193.6E-22143245IPR003340B3 DNA binding domain
PfamPF023622.4E-20143244IPR003340B3 DNA binding domain
PfamPF065074.9E-37269351IPR010525Auxin response factor
PROSITE profilePS5174524.301703787IPR000270PB1 domain
SuperFamilySSF542774.07E-11706780No hitNo description
PfamPF023091.2E-6750789IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009734Biological Processauxin-activated signaling pathway
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: 839 aa     Download sequence    Send to blast
MASCDVPLKG SSGNGGSERF SSPCGNVGMT RSEDALYTEL WHACAGPLVT VPHTGERVFY  60
FPQGHIEQVE ASTNQVADQQ MPVYKDLPWK ILCRVINVKL KAEPDTDEVF AQVTLVPEAK  120
QDDSSLEKEP VQPPPARAHV HSFCKTLTAS DTSTHGGFSV LKRHADECLP PLDMGRQPPT  180
QELIAKDLHG IEWRFRHIFR GQPRRHLLQS GWSVFVGSKK LVAGDAFIFL RGENGELRVG  240
VRRAMKQQSN VPSSVISSHS MHLGVLATAM HAISTGTMFT VYYKPRISPS EFIVPCNQYL  300
EALKQNYSIG MRFKMRFEGE EAPEQRFTGT VVGIGDVDPD KWPGSKWRCL KVRWDETASV  360
PRPERVSPWK IEPALAPAAL NPLPVPRPKR PRGNMVAPST DVSPLPREGS SNPVDSSQPY  420
IFPRASQVHE AMNRHSFTDT GDSDAPQKLN SWGPSVLDDD KSEPASQKRL GSENWMPHFM  480
HEPPSYATPH GFGSEDPNLL KKHMIQDYEG KVNLKANPWP MILKDTSPNL KMSSQINEIP  540
YQKTGNPRYG GLGGYPPVHN LGSNSPSGNW LMSLMPSSNG IDGGAKKPQF EPSNGKIAAN  600
GGARPSDGNC KLFGIDLFNH SVAPEQALGQ TKAREEAEVH SGPSFYRSSQ QASEADQISE  660
PSKCSKSGDG YCGGSEQEKP SQYCNHHNPS KETQCKAQSG AVRSCTKVHK QGSALGRSVD  720
LTKFKGYDEL TLELDQMFDF GGELMSPNKA WLVVYTDNEG DLMLVGDDPW PEFCNMVRKI  780
FIYTREEVQK MNPGSLNHHR SEEREEPSSP HGEVVVGSKE TKHQQTSPSV PTPDRDYC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1753437317354Auxin response factor 1
4ldw_A1e-1753437317354Auxin response factor 1
4ldw_B1e-1753437317354Auxin 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
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020522960.10.0auxin response factor 2 isoform X1
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLW1PGL10.0W1PGL1_AMBTC; Auxin response factor
STRINGERN062150.0(Amborella trichopoda)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP5501582
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. Amborella Genome Project
    The Amborella genome and the evolution of flowering plants.
    Science, 2013. 342(6165): p. 1241089
    [PMID:24357323]
  4. 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]
  5. Lyons R, et al.
    Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.
    PLoS ONE, 2015. 10(4): p. e0121902
    [PMID:25849296]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]
  12. 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]
  13. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  14. 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]
  15. 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]