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_30902_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: 772aa    MW: 86086.1 Da    PI: 7.3779
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_30902_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.27.4e-24169270199
                     EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                     f+k+lt sd++++g +++p++ ae++      +++ + s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F   ++++
  Neem_30902_f_1 169 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyEQQ-RPSQELIAKDLHGVEWRFRHIYRGQPRRHLLTTGWSIFVSQKNLVSGDAVLFL--RSEN 260
                     99****************************97433.45679************************************************..4589 PP

                     E..EEEEE-S CS
              B3  90 felvvkvfrk 99 
                     +el+++++r+
  Neem_30902_f_1 261 GELRLGIRRA 270
                     999****996 PP

2Auxin_resp124.76.5e-41295376182
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                     ++ha+stksvF+v+Y+Pras++eFv++++k+ ++++++++vG+Rfkm+fe++d++err+ G+v+g+sdldp+rWpnSkWr+L
  Neem_30902_f_1 295 VSHAISTKSVFHVFYSPRASHAEFVIPYQKYITSITNPICVGTRFKMRFEMDDAPERRCNGIVTGMSDLDPYRWPNSKWRCL 376
                     689******************************************************************************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.88E-44162282IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.4E-41163280IPR015300DNA-binding pseudobarrel domain
CDDcd100173.43E-22167269No hitNo description
PfamPF023629.3E-22169270IPR003340B3 DNA binding domain
SMARTSM010199.5E-24169271IPR003340B3 DNA binding domain
PROSITE profilePS5086313.211169271IPR003340B3 DNA binding domain
PfamPF065071.3E-34295376IPR010525Auxin response factor
SuperFamilySSF542771.63E-8651725No hitNo description
PROSITE profilePS5174516.997655740IPR000270PB1 domain
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:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 772 aa     Download sequence    Send to blast
MEIDLNHAAT TEVEKIAFCN GDCQKNSGCV YCLNSSPSSS SSSNSGSPSL SSSIYFELWH  60
ACAGPLTSLP KKGNVVVYFP QGNLEQVASS SPFPPIEVPN FDLQPQIFCK VVDVQLLANK  120
ENDEVYTQVA LLPQPELEGL NLKDKELEEL GVDEEGGGGS PRKSTPHMFC KTLTASDTST  180
HGGFSVPRRA AEDCFPPLDY EQQRPSQELI AKDLHGVEWR FRHIYRGQPR RHLLTTGWSI  240
FVSQKNLVSG DAVLFLRSEN GELRLGIRRA VRPRNGLPDS ILTKQNSYPN VLSQVSHAIS  300
TKSVFHVFYS PRASHAEFVI PYQKYITSIT NPICVGTRFK MRFEMDDAPE RRCNGIVTGM  360
SDLDPYRWPN SKWRCLMVRW DEDIGSDHQE RVSPWEIDRS VSLPPLNIQS SPRLKKLRTS  420
LQATPPVYRV NAGGNGFLDF EESVRSSKVL QGQENVGFLS PLYGCDTASH ALDFEMRTPA  480
HQSLPLAGVR KDNVREFVRA RPTTYTGFME SNRFPKVLQG QEICPLRSLT RKVDLNLGTW  540
GKPNLGCNSF DMYQASKPSF YALPSESLQN MFFPYGDVHK TSKNHAVAVA GDEVRKANLL  600
SEHQSLESTL TPSLKTNIRN QKDGSFNGTA AGCKLFGFSL TAETPTPSSQ SSGKRSCTKV  660
HKQGSLVGRA IDLSRLNGYG DLLSELEQLF NMEGLLGDPE KGWRILYTDS ENDMMVVGDD  720
PWHAFSYGNT CAPRIFVIFQ LCFSFLSNTK MFRYTSKHNI FGAYAEGHVN AE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-121394072356Auxin response factor 1
4ldw_A1e-121394072356Auxin response factor 1
4ldw_B1e-121394072356Auxin response factor 1
4ldx_A1e-121394072356Auxin response factor 1
4ldx_B1e-121394072356Auxin 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. {ECO:0000269|PubMed:12036261}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006424619.10.0auxin response factor 4 isoform X2
RefseqXP_006488136.10.0auxin response factor 4 isoform X2
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLA0A067GCZ50.0A0A067GCZ5_CITSI; Auxin response factor
STRINGXP_006424619.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95302636
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60450.10.0auxin response factor 4
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. 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]
  3. Pashkovskiy PP,Kartashov AV,Zlobin IE,Pogosyan SI,Kuznetsov VV
    Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.
    Plant Physiol. Biochem., 2016. 104: p. 146-54
    [PMID:27031426]
  4. 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]
  5. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  6. 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]