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 30111.m000734
Common NameRCOM_1400470
Organism
Ricinus communis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
Family ARF
Protein Properties Length: 810aa    MW: 89964.3 Da    PI: 6.8159
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
30111.m000734genomeJCVIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.84.7e-24159260199
                    EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS
             B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 
                    f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F   + +++
  30111.m000734 159 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyK-QQRPSQELVAKDLHGVEWRFRHIYRGQPRRHLLTTGWSIFVSQKNLVSGDAVLFL--RGEDG 251
                    99****************************963.3445679************************************************..44999 PP

                    ..EEEEE-S CS
             B3  91 elvvkvfrk 99 
                    el+++++r+
  30111.m000734 252 ELRLGIRRA 260
                    9*****996 PP
2Auxin_resp123.91.1e-40285366182
     Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                    +a+a+stks+F+v+Y+Pras+++Fvv+++k++k++ ++v++G+Rfkm+fe++ds+err+sG+v+g+sdl+p+rWpnSkWr+L
  30111.m000734 285 VANAISTKSMFNVLYSPRASHADFVVPYKKYMKSIMNPVCIGTRFKMRFEMDDSPERRCSGVVTGISDLNPYRWPNSKWRCL 366
                    689******************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.7E-44151271IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.5E-41153271IPR015300DNA-binding pseudobarrel domain
CDDcd100175.52E-23157259No hitNo description
SMARTSM010195.4E-24159261IPR003340B3 DNA binding domain
PROSITE profilePS5086312.999159261IPR003340B3 DNA binding domain
PfamPF023623.4E-22159260IPR003340B3 DNA binding domain
PfamPF065073.0E-34285366IPR010525Auxin response factor
PfamPF023099.3E-7658750IPR033389AUX/IAA domain
SuperFamilySSF542771.96E-10658745No hitNo description
PROSITE profilePS5174522.354666750IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
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: 810 aa     Download sequence    Send to blast
MEIDLNHAVT EVEKNNNAFY TNNGDSSSSS CSSNSSQSPV TSSIYLELWH ACAGPLTSLP  60
KKGNVVVYFP QGHLEQVAPS SPFSPMEMPT FDLQPQIFCK VVNVQLLANK ENDEVYTQLA  120
LLPQPELVGP NLEVKELEEL GVDEEGGGGL PAKSTPHMFC KTLTASDTST HGGFSVPRRA  180
AEDCFPPLDY KQQRPSQELV AKDLHGVEWR FRHIYRGQPR RHLLTTGWSI FVSQKNLVSG  240
DAVLFLRGED GELRLGIRRA VRPRNGLPDS VIGKQNSYPS VLSVVANAIS TKSMFNVLYS  300
PRASHADFVV PYKKYMKSIM NPVCIGTRFK MRFEMDDSPE RRCSGVVTGI SDLNPYRWPN  360
SKWRCLMVRW DEDIGNDHQE RVSPWEIDPS VSLPPLSIQS SPRLKKLRTS LQATPPDNPI  420
TGGGGFLDFE ESGRSSKVLQ GQENVGFVSP LYGCDTMNRP PDFEMRSPVH QNLVSTGREK  480
ANIGEITRTR PTTYTGFAET DRFPKVLQGQ EICPLRSLTS KGDFNLGAWV KRNVGCGSFN  540
MYQAPRRNFY PLGPESLQNV YFPYGDVYKT GQDARMRSYA TNFPRENFQF GAPSIQAGVS  600
RDEVGKPNQL SDLKTQEPGS ASPALGVNLR SQKDNSFGGT SSGCKLFGFS LTAESPNPNS  660
QNSGKRSCTK VHKQGSLVGR AIDLSRLNGY SDLLSELERL FSMEGLLQDP NKGWRILYTD  720
SENDVMVVGD DPWHEFCNVV SKIHIYTQEE VEKMTIGVIG DDTQSCLDQA HVVMEASKSS  780
SVGQPDSSPH RTYYAQVRIV ALERMVTEVC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-123303892354Auxin response factor 1
4ldy_B1e-123303892354Auxin 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMap30111.m000734
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015579153.10.0auxin response factor 4 isoform X1
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLB9SK500.0B9SK50_RICCO; Auxin response factor
STRINGXP_002526369.10.0(Ricinus communis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF52363252
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]