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_22509_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: 352aa    MW: 39619.4 Da    PI: 7.8293
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_22509_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B331.92.4e-10101161156
                     EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEET CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkks 56 
                     f+k+lt sd++++g +++p++ ae+        ++++ + ++l+++d++ ++W++++iyr+ +
  Neem_22509_f_1 101 FCKTLTASDTSTHGGFSVPRRAAEKLfppldytMQPP-T-QELVVRDLHDNTWTFRHIYRGEG 161
                     99*********************999*****954444.4.38****************97654 PP

2Auxin_resp119.72.3e-39210293183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     aahaas++s+F+++YnPra++seFv++++k++k+++ +++svGmRf m+fete+s +rr++Gt+vg+sdldp+rWp+SkWr+L+
  Neem_22509_f_1 210 AAHAASNRSPFTIFYNPRACPSEFVIPLAKYRKSVYgTQISVGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRNLQ 293
                     79**********************************9*********************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.44E-3188213IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.2E-2094161IPR015300DNA-binding pseudobarrel domain
CDDcd100179.29E-10100163No hitNo description
SMARTSM010190.0038101191IPR003340B3 DNA binding domain
PfamPF023623.4E-8101161IPR003340B3 DNA binding domain
PfamPF065073.2E-34210293IPR010525Auxin response factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009733Biological Processresponse to auxin
GO:0009908Biological Processflower development
GO:0009942Biological Processlongitudinal axis specification
GO:0010305Biological Processleaf vascular tissue pattern formation
GO:0048364Biological Processroot development
GO:0048507Biological Processmeristem development
GO:0005634Cellular Componentnucleus
GO:0016020Cellular Componentmembrane
GO:0042802Molecular Functionidentical protein binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 352 aa     Download sequence    Send to blast
MVQPGAIRSV AFILTYDFMY YVRFFDQVAV STKRSATSQI PNYPNLPSQL MCQVHNVTLH  60
ADKDTDEIYA QMSLQPVSCE KDVFPIPDFG LKPSKHPSEF FCKTLTASDT STHGGFSVPR  120
RAAEKLFPPL DYTMQPPTQE LVVRDLHDNT WTFRHIYRGE GSQRDTFSPQ VGVCLLAQKG  180
LELVILFCLL ALPSSVLSAD SMHIGVLAAA AHAASNRSPF TIFYNPRACP SEFVIPLAKY  240
RKSVYGTQIS VGMRFGMMFE TEESGKRRYM GTIVGISDLD PLRWPGSKWR NLQVEWDEPG  300
CSDKQKRVSS WEIETPESLF IFPSLTSGLK RPFHSGFLGE FSFVLVSTKH AF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1652631882392Auxin response factor 5
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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:14973283, ECO:0000269|PubMed:17553903}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00153DAPTransfer from AT1G19850Download
Motif logo
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKF7394011e-50KF739401.1 Dimocarpus longan cultivar Honghezi auxin response factor mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021692668.10.0auxin response factor 5-like
SwissprotP930241e-172ARFE_ARATH; Auxin response factor 5
TrEMBLA0A3R5SIX40.0A0A3R5SIX4_POPTO; Auxin response factor
STRINGXP_006435146.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM58082746
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G19850.11e-173ARF family protein
Publications ? help Back to Top
  1. Chen MK,Wilson RL,Palme K,Ditengou FA,Shpak ED
    ERECTA family genes regulate auxin transport in the shoot apical meristem and forming leaf primordia.
    Plant Physiol., 2013. 162(4): p. 1978-91
    [PMID:23821653]
  2. Huang JB, et al.
    ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis.
    Plant Cell, 2014. 26(9): p. 3501-18
    [PMID:25217509]
  3. Qi J, et al.
    Auxin depletion from leaf primordia contributes to organ patterning.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(52): p. 18769-74
    [PMID:25512543]
  4. Crawford BC, et al.
    Plant development. Genetic control of distal stem cell fate within root and embryonic meristems.
    Science, 2015. 347(6222): p. 655-9
    [PMID:25612610]
  5. Zhang Y, et al.
    Regulation of oncogene expression in T-DNA-transformed host plant cells.
    PLoS Pathog., 2015. 11(1): p. e1004620
    [PMID:25615824]
  6. Robert HS, et al.
    Plant embryogenesis requires AUX/LAX-mediated auxin influx.
    Development, 2015. 142(4): p. 702-11
    [PMID:25617434]
  7. Krogan NT,Berleth T
    The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development.
    Plant Signal Behav, 2015. 10(4): p. e992748
    [PMID:25830553]
  8. Ckurshumova W,Berleth T
    Overcoming recalcitrance - Auxin response factor functions in plant regeneration.
    Plant Signal Behav, 2015. 10(7): p. e993293
    [PMID:26098229]
  9. Wendrich JR, et al.
    A set of domain-specific markers in the Arabidopsis embryo.
    Plant Reprod, 2015. 28(3-4): p. 153-60
    [PMID:26216537]
  10. Wu MF, et al.
    Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate.
    Elife, 2015. 4: p. e09269
    [PMID:26460543]
  11. Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D
    AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis.
    Plant Physiol., 2016. 170(1): p. 283-93
    [PMID:26537561]
  12. Müller CJ, et al.
    PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis.
    Plant Physiol., 2016. 170(2): p. 956-70
    [PMID:26637548]
  13. Herud O,Weijers D,Lau S,Jürgens G
    Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS.
    Plant J., 2016. 85(2): p. 269-77
    [PMID:26714008]
  14. Luo S, et al.
    Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis.
    Front Plant Sci, 2015. 6: p. 1156
    [PMID:26734051]
  15. 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]
  16. Krogan NT,Marcos D,Weiner AI,Berleth T
    The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes.
    New Phytol., 2016. 212(1): p. 42-50
    [PMID:27441727]
  17. Fendrych M,Leung J,Friml J
    TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls.
    Elife, 2018.
    [PMID:27627746]
  18. Matthes M,Torres-Ruiz RA
    Boronic acid treatment phenocopies monopteros by affecting PIN1 membrane stability and polar auxin transport in Arabidopsis thaliana embryos.
    Development, 2016. 143(21): p. 4053-4062
    [PMID:27697905]
  19. Bhatia N, et al.
    Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis.
    Curr. Biol., 2016. 26(23): p. 3202-3208
    [PMID:27818174]
  20. 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]
  21. Möller BK, et al.
    Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539
    [PMID:28265057]
  22. Carey NS,Krogan NT
    The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems.
    Plant Signal Behav, 2017. 12(4): p. e1307492
    [PMID:28340328]
  23. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  24. Gaillochet C, et al.
    Control of plant cell fate transitions by transcriptional and hormonal signals.
    Elife, 2018.
    [PMID:29058667]
  25. Zheng K, et al.
    Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 1813
    [PMID:29114256]
  26. 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]