PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_013612785.1
Organism
Brassica oleracea
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: 743aa    MW: 82661 Da    PI: 6.4194
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013612785.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.46.3e-24148249199
                     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   ++++
  XP_013612785.1 148 FCKTLTASDTSTHGGFSVPRRAAEDCfapldyK-QQRPSQELIAKDLHGVEWKFRHIYRGQPRRHLLTTGWSIFVSQKSLVSGDAVLFL--RDEN 239
                     99****************************963.3445679************************************************..5689 PP

                     E..EEEEE-S CS
              B3  90 felvvkvfrk 99 
                     +el+++++r+
  XP_013612785.1 240 GELRLGIRRS 249
                     999****986 PP
2Auxin_resp120.61.2e-39273354182
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                     +a+a+s+ks+F+v+Y+Pra++seFv+++ek+ +++k+++ +G+Rf+m+fe++ds+err++G+v+gv d+dp+rWpnSkWr+L
  XP_013612785.1 273 VANAVSNKSMFDVFYSPRATHSEFVIPYEKYITSIKNPIGIGTRFRMRFEMDDSPERRCAGVVTGVCDMDPYRWPNSKWRCL 354
                     689******************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.5E-40139260IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.19E-42142264IPR015300DNA-binding pseudobarrel domain
CDDcd100172.85E-21146248No hitNo description
PfamPF023628.3E-22148249IPR003340B3 DNA binding domain
PROSITE profilePS5086313.422148250IPR003340B3 DNA binding domain
SMARTSM010193.7E-23148250IPR003340B3 DNA binding domain
PfamPF065071.7E-33273354IPR010525Auxin response factor
SuperFamilySSF542773.53E-10619697No hitNo description
PROSITE profilePS5174522.181622704IPR000270PB1 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: 743 aa     Download sequence    Send to blast
MEFDLNTEFA EVEEEENDEG GGARVEKASA SSIYSELWHA CAGPLTSLPK KGNVVVYFPQ  60
GHLEQGVMVS YSSPLDVPKL DLSPQIFCRV AAVHLLANKE TDEVYTQVTL LPLQELSMLN  120
GEGKEVKELG GDEEKNGSSS VKKTPHMFCK TLTASDTSTH GGFSVPRRAA EDCFAPLDYK  180
QQRPSQELIA KDLHGVEWKF RHIYRGQPRR HLLTTGWSIF VSQKSLVSGD AVLFLRDENG  240
ELRLGIRRSA RPRNGLPDSI IQKYSSSSIL SLVANAVSNK SMFDVFYSPR ATHSEFVIPY  300
EKYITSIKNP IGIGTRFRMR FEMDDSPERR CAGVVTGVCD MDPYRWPNSK WRCLLVRWDE  360
SFMSDHQERV SPWEIDPSGS LPPLSIQSSP RPKRPWAGLL GTTTPQGNPI TAERGVFLDF  420
EESVRPSKVL QGQENTGSAS SSPLQGFDVM NRRILDFAGM QQSHANPVLL SGRVKDRFGE  480
FVDSTSLDLD RFPRVLQGQE ICSLRSFPQI AGFTPASASG SPNPFAYQAN KSSFYPLASQ  540
GIRSSHIPYQ SPYNAGDKSS SRKFDAQREG GLPKNVPFKI DMMGTEKGRE VNMNASTTGC  600
KLFGFSLPVE TPASNQQSSS KRICTKVHKQ GSLVGRAIDL SRLNGYNDLL TELERLFNME  660
GLLRDPEKGW RILYTDSEND MMVVGDDPWH DFCSVVLKIH LYTKEEVENG NDDNRSCLEQ  720
AALMMEASKS SSVSQPDSSP TGH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1123038016357Auxin response factor 1
4ldy_B1e-1123038016357Auxin response factor 1
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
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). 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
PlantRegMapXP_013612785.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794640.0JN979464.1 Brassica rapa subsp. pekinensis auxin response factor 4 (ARF4) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013612785.10.0PREDICTED: auxin response factor 4 isoform X3
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLA0A0D3ED440.0A0A0D3ED44_BRAOL; Auxin response factor
STRINGBo9g143570.10.0(Brassica oleracea)
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]