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 RrC4660_p2
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family ARF
Protein Properties Length: 887aa    MW: 98077.9 Da    PI: 6.6085
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC4660_p2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.46.4e-24127228199
                 EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
          B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                 f+k+lt sd++++g +++p++ ae+        ++++++  +l+ +d++ ++W++++i+r++++r++lt+GW+ Fv+a++L +gD+v+F   ++++ +l
  RrC4660_p2 127 FCKTLTASDTSTHGGFSVPRRAAEKVfppldytQQPPAQ--ELMARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI--WNDKNQL 221
                 99*****************************96555555..8************************************************..7888889 PP

                 EEEEE-S CS
          B3  93 vvkvfrk 99 
                 +++++r+
  RrC4660_p2 222 LLGIRRA 228
                 ****997 PP
2Auxin_resp116.62.2e-38253336183
  Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                 aahaa+t+s F+++YnPra++seFv++++k++ka++ ++vsvGmRf+m fete+ss rr++Gt++g+ dldp rW nS+Wrs+k
  RrC4660_p2 253 AAHAAATNSRFTIFYNPRACPSEFVIPLAKYVKAVYhTRVSVGMRFRMLFETEESSVRRYMGTITGICDLDPARWANSHWRSVK 336
                 79*********************************9789******************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.32E-48112256IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.3E-41121242IPR015300DNA-binding pseudobarrel domain
CDDcd100171.00E-20126227No hitNo description
PfamPF023627.7E-22127228IPR003340B3 DNA binding domain
SMARTSM010192.3E-24127229IPR003340B3 DNA binding domain
PROSITE profilePS5086312.435127229IPR003340B3 DNA binding domain
PfamPF065072.3E-33253336IPR010525Auxin response factor
PfamPF023091.6E-6556836IPR033389AUX/IAA domain
SuperFamilySSF542773.86E-7741822No hitNo description
PROSITE profilePS5174524747831IPR000270PB1 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 887 aa     Download sequence    Send to blast
MRLSSAGFDT HPHEGEKRVL NSELWHACAG PLVSLPPLGS RVVYFPQGHS EQVAASTNKE  60
VDAHTPNYPS LQPQLICQLH NVTMHADVET DEVYAQMTLQ PLNAQEQKDP YLPAELGVPN  120
RQPTNYFCKT LTASDTSTHG GFSVPRRAAE KVFPPLDYTQ QPPAQELMAR DLHDNEWKFR  180
HIFRGQPKRH LLTTGWSVFV SAKRLVAGDS VLFIWNDKNQ LLLGIRRANR PQTVMPSSVL  240
SSDSMHLGLL AAAAHAAATN SRFTIFYNPR ACPSEFVIPL AKYVKAVYHT RVSVGMRFRM  300
LFETEESSVR RYMGTITGIC DLDPARWANS HWRSVKVGWD ESTAGDRQPR VSLWEIEPLT  360
TFPMYPSPFP LRLKRPWPPP GLPSFHGLRE DDLGMGMSMS SPLMWDRGLQ SMNFQGMGVN  420
PWIQQRLDAS GLLGVQNDVY QAMAAAALQD MRGIDPAKAA ASLLQFQSPS GFSMQSPSLV  480
QPQLLQQQLS QQQQQQHQAY LPETHQPQSQ AQSQPNNILS QQQQQVVDNH NQSASSPTTA  540
TRAMAQFGSA SQSNTSLLQS MTSLCHQQIF SDTNGGNNPI TPLHTLLSNF PQDESSQLLN  600
LTRTNSAMTS SGWPSKRQAV DSSFQHSGAG NNNNNQSVME QLGQTHMSNV PPNIISLPPF  660
PSGRECVQEE NPSDPHSHLL FGVNIDSSSP LMPNGMSNLR SIGIEGTLPF TSSTFNNEFS  720
GNLAMTTPSS CIDEQGSLQS SENQQSNTFV KVYKSGSFGR SLDIKKFSSY NELRSELARM  780
FGLEGQLEDP VRSGWQLVFV DRENDVLLLG DDPWPEFVSS VWCIKILSPQ EVQKMGKRGL  840
ELLNSAPPSS NNVDKVPSNG NCDDFGNRSD PRSLGNGIAS VGGSFNY
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1601635747388Auxin 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. Regulates both stamen and gynoecium maturation. Promotes jasmonic acid production. Partially redundant with ARF8. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:16107481}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by miR167. {ECO:0000269|PubMed:17021043}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794680.0JN979468.1 Brassica rapa subsp. pekinensis auxin response factor 6 (ARF6) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018450596.10.0PREDICTED: auxin response factor 6-like isoform X1
SwissprotQ9ZTX80.0ARFF_ARATH; Auxin response factor 6
TrEMBLV4L2540.0V4L254_EUTSA; Auxin response factor
STRINGAT1G30330.20.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM13442894
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G30330.10.0auxin response factor 6
Publications ? help Back to Top
  1. Liu N, et al.
    Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato.
    J. Exp. Bot., 2014. 65(9): p. 2507-20
    [PMID:24723401]
  2. Oh E, et al.
    Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl.
    Elife, 2015.
    [PMID:24867218]
  3. Minato N, et al.
    The phytoplasmal virulence factor TENGU causes plant sterility by downregulating of the jasmonic acid and auxin pathways.
    Sci Rep, 2014. 4: p. 7399
    [PMID:25492247]
  4. Ortega-Amaro MA, et al.
    Overexpression of AtGRDP2, a novel glycine-rich domain protein, accelerates plant growth and improves stress tolerance.
    Front Plant Sci, 2014. 5: p. 782
    [PMID:25653657]
  5. Asahina M,Satoh S
    Molecular and physiological mechanisms regulating tissue reunion in incised plant tissues.
    J. Plant Res., 2015. 128(3): p. 381-8
    [PMID:25736731]
  6. Batista VG,Pinheiro MP,Melo Filho PA,Santos RC,Lima LM
    Temporal and tissue expression of genes involved in buds of earliness cotton cultivar.
    Genet. Mol. Res., 2015. 14(3): p. 7386-94
    [PMID:26214417]
  7. Li P, et al.
    Ca(2+) -regulated and diurnal rhythm-regulated Na(+) /Ca(2+) exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis.
    Plant Cell Environ., 2016. 39(2): p. 377-92
    [PMID:26296956]
  8. Barik S, et al.
    Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.
    Sci Rep, 2015. 5: p. 14611
    [PMID:26459056]
  9. 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]
  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. Zhang GZ, et al.
    Ectopic expression of UGT84A2 delayed flowering by indole-3-butyric acid-mediated transcriptional repression of ARF6 and ARF8 genes in Arabidopsis.
    Plant Cell Rep., 2017. 36(12): p. 1995-2006
    [PMID:29027578]
  12. 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]