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 XP_009115165.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family ARF
Protein Properties Length: 903aa    MW: 99578.4 Da    PI: 6.3324
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009115165.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.94.5e-24127228199
                     EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                     f+k+lt sd++++g +++p++ ae+        +++++  ++l+ +d++ ++W++++i+r++++r++lt+GW+ Fv+a++L +gD+v+F   +++
  XP_009115165.1 127 FCKTLTASDTSTHGGFSVPRRAAEKVfppldysQQPPA--QELMARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI--WND 217
                     99*****************************8544444..48************************************************..888 PP

                     EE..EEEEE-S CS
              B3  89 efelvvkvfrk 99 
                     + +l+++++r+
  XP_009115165.1 218 KNRLFLGIRRA 228
                     8889****997 PP
2Auxin_resp1187.9e-39253336183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     aahaa+t+s F+++YnPras+seFv++++k++ka++ ++vsvGmRf+m fete+ss rr++Gt++g+ dldp+rW nS+Wrs+k
  XP_009115165.1 253 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYhTRVSVGMRFRMLFETEESSVRRYMGTITGICDLDPTRWANSHWRSVK 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:2.40.330.104.1E-41120242IPR015300DNA-binding pseudobarrel domain
CDDcd100174.16E-21126222No hitNo description
PROSITE profilePS5086312.449127229IPR003340B3 DNA binding domain
PfamPF023623.4E-22127228IPR003340B3 DNA binding domain
SMARTSM010191.2E-24127229IPR003340B3 DNA binding domain
PfamPF065078.9E-34253336IPR010525Auxin response factor
PfamPF023094.9E-8753849IPR033389AUX/IAA domain
SuperFamilySSF542772.62E-7756835No hitNo description
PROSITE profilePS5174523.582760844IPR000270PB1 domain
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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 903 aa     Download sequence    Send to blast
MRLSTAGFNP QPHEGEKRVL NSELWHACAG PLVSLPPVGS RVVYFPQGHS EQVAASTNKE  60
VDAHIPNYPS LHPQLICQLH NVTMHADVET DEVYAQMTLQ PLNAQEQKDP YLPAELGVPS  120
RQPTNYFCKT LTASDTSTHG GFSVPRRAAE KVFPPLDYSQ QPPAQELMAR DLHDNEWKFR  180
HIFRGQPKRH LLTTGWSVFV SAKRLVAGDS VLFIWNDKNR LFLGIRRANR PQTVMPSSVL  240
SSDSMHLGLL AAAAHAAATN SRFTIFYNPR ASPSEFVIPL AKYVKAVYHT RVSVGMRFRM  300
LFETEESSVR RYMGTITGIC DLDPTRWANS HWRSVKVGWD ESTAGERQPR VSLWEIEPLT  360
TFPMYPSPFP LRLKRPWPPG LPSFHGLKED DMSMGMGMSS PLMWDRGLQS LNFQGMGVNP  420
WMQPRLDASG LLGMQNDVYQ AMAAAALQDM RGIDPAKAAS LLQFQNPSGF SMQPPSLMQP  480
QMLQQQLSQQ QQQQQQLSQQ QQQQSYLPVP ETHQPQSQSN TLLSQQQQQQ QVVDNHNQSA  540
STAAAVSAMS QFGSASQSMT SLCQQQSFLD TNGGNNNPMS PLHTLLSNFS QDESSQLLNL  600
TRTTNSAAMT SSGWPSKRPA VDLSSFGNNS NTQSVIEQLG QSHSTSNVPP NAVSLPPFPG  660
GGRECSIEQE GGSPSDPHSH LLFGVNIDSS SLLMPNGMSN LRSIGIEGGD STTLPFTTSN  720
FNNDFSGGNL AMTTPSSCLD EPGFLQSSEN LGSENQQSNN TFVKVYKSGS FGRSLDITKF  780
SSYHELRSEL ARMFGLEGQL EDPVRSGWQL VFVDRENDVL LLGDDPWPEF VSSVWCIKIL  840
SPQEVQQMGK RGLELLNSAP PSSNNNVVEK LPSNNGNCDD FGNRSDPRNL GNGIASVGGS  900
FNY
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1581635747388Auxin response factor 5
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in sepals at stages 11, 12 and 13 of flower development. Highly expressed in petals at stages 9-10, decreases at stage 11 and disappears after flower stage 12. In anthers, expressed at stage 11 in the tapetum, disappears early in stage 12 when the tapetum degrades and reappears throughout the anther late in stage 12 to persist at least until stage 13. In stamen filaments, expressed at stages 12 to 13, especially near the apical end of the filament. Expressed throughout the gynoecium at early stages up to stage 12, especially strongly in ovules. Expression in gynoecium decreases late in stage 12, but persists through stage 13, especially near the apical end including the style. {ECO:0000269|PubMed:16107481}.
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009115165.1
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_009115165.10.0PREDICTED: auxin response factor 6 isoform X2
SwissprotQ9ZTX80.0ARFF_ARATH; Auxin response factor 6
TrEMBLA0A3P5Y2Y20.0A0A3P5Y2Y2_BRACM; Auxin response factor
STRINGBo5g062810.10.0(Brassica oleracea)
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]