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_009130187.1
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: 853aa    MW: 95694 Da    PI: 6.632
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009130187.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B372.64.9e-23147248199
                     EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                     f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d+++++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + ++
  XP_009130187.1 147 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHSNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGEN 238
                     99*****************************7333.34459************************************************..4499 PP

                     E..EEEEE-S CS
              B3  90 felvvkvfrk 99 
                     +el+v+v+r+
  XP_009130187.1 239 GELRVGVRRA 248
                     99*****996 PP
2Auxin_resp120.81e-39273355183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     a+ha+st+++F+v+Y+Pr+s+seF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp+rW +SkWrsLk
  XP_009130187.1 273 AWHAISTGTMFTVYYKPRTSPSEFIVPFDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDSDPTRWAKSKWRSLK 355
                     89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.1E-41143262IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.14E-40144276IPR015300DNA-binding pseudobarrel domain
CDDcd100171.08E-20145247No hitNo description
PROSITE profilePS5086311.491147249IPR003340B3 DNA binding domain
PfamPF023628.0E-21147248IPR003340B3 DNA binding domain
SMARTSM010197.9E-23147249IPR003340B3 DNA binding domain
PfamPF065077.7E-37273355IPR010525Auxin response factor
PfamPF023091.6E-10691797IPR033389AUX/IAA domain
SuperFamilySSF542771.96E-11704783No hitNo description
PROSITE profilePS5174524.282706790IPR000270PB1 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: 853 aa     Download sequence    Send to blast
MEVSVKGNHG GGRGRENAVS VVAGEGQKSN LNRVVDEEAA IYRELWHACA GPLVTVPRRD  60
DRVFSFPQGH IEQVEASTNQ AAEQQMPLYD LPSKLLCRVI NVDLKAEVDT DEVYAQITLL  120
PEPNQDENAV EKEAPPPPPP RFQVHSFCKT LTASDTSTHG GFSVLRRHAD ECLPPLDMSR  180
QPPTQELVAK DLHSNEWRFR HIFRGQPRRH LLQSGWSVFV SSKRLVAGDA FIFLRGENGE  240
LRVGVRRAMR QQGNVPSSVI SSHSMHLGVL ATAWHAISTG TMFTVYYKPR TSPSEFIVPF  300
DQYMESVKNN YSIGMRFKMR FEGEEAPEQR FTGTIVGIED SDPTRWAKSK WRSLKVRWDE  360
TSSIPRPERV SPWKIEPALA PPALSPVPMT RPKRPRSNMA PSSPDSSMHI KEGSSKVNVY  420
PLPASGLSRV LQGQEYPTLR TKHTESVECD APESSVVWQS SADDDKVDVA SRRYENWMSS  480
GRHEYTDLLS GFGANVDPSQ GHQIPFHDHS SSPSVTAKKI LSDQDAKFDY LANQWQMMNS  540
GLSLKLHESP QIPSASDASF QGRGNATYGE YPVLHSLTTE TAGGNWPIRP RALNYFEEAV  600
HAQAREHVTE RPQMVQEETA KSRDGNCRLF GIPLVNNVNE TDSTMSQRNN LNENSGFTQM  660
ASPKVQDLSD HSKGSKSTND HREQGRPSQA KQPHAKDSHC KTNSNRSCTK VHKQGIALGR  720
SVDLSKFQNY EELIAELDML FEFNGELMAP KKDWLIVYTD DENDMMLVGD DPWQEFCCMV  780
RKIFIYTKEE VRNMNPRTLS CRSEEEAVVG EGSDAKDGKS ASNPSLSSEL LNQKNQHTLQ  840
AEGDVEAQIR RRV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1794037718354Auxin response factor 1
4ldw_A1e-1794037718354Auxin response factor 1
4ldw_B1e-1794037718354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.91530.0bud| leaf| silique
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the sepals and carpels of young flower buds. At stage 10 of flower development, expression in the carpels becomes restricted to the style. Also expressed in anthers and filaments. At stage 13, expressed in the region at the top of the pedicel, including the abscission zone. Expressed in developing siliques. {ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952}.
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078, ECO:0000269|PubMed:15960614}.
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. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Functions independently of ethylene and cytokinin response pathways. May act as a repressor of cell division and organ growth. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952, ECO:0000269|PubMed:16339187}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009130187.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794590.0JN979459.1 Brassica rapa subsp. pekinensis auxin response factor 2-1 (ARF2-1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009130187.10.0PREDICTED: auxin response factor 2
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLA0A078JPD80.0A0A078JPD8_BRANA; Auxin response factor
STRINGBo2g161810.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53482647
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin response factor 2
Publications ? help Back to Top
  1. Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV
    Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula).
    PLoS ONE, 2012. 7(8): p. e42839
    [PMID:22916167]
  2. 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]
  3. Li C, et al.
    Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis.
    PLoS ONE, 2014. 9(4): p. e94830
    [PMID:24756087]
  4. Lyons R, et al.
    Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.
    PLoS ONE, 2015. 10(4): p. e0121902
    [PMID:25849296]
  5. Roodbarkelari F,Du F,Truernit E,Laux T
    ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response.
    BMC Biol., 2015. 13: p. 74
    [PMID:26358077]
  6. Meng LS,Wang ZB,Yao SQ,Liu A
    The ARF2-ANT-COR15A gene cascade regulates ABA-signaling-mediated resistance of large seeds to drought in Arabidopsis.
    J. Cell. Sci., 2015. 128(21): p. 3922-32
    [PMID:26395398]
  7. Zhao S,Zhang ML,Ma TL,Wang Y
    Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress.
    Plant Cell, 2016. 28(12): p. 3005-3019
    [PMID:27895227]
  8. Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z
    ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis .
    J Integr Plant Biol, 2017. 59(1): p. 30-43
    [PMID:28074634]
  9. 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]
  10. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]
  11. Zhang M,Hu X,Zhu M,Xu M,Wang L
    Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis.
    Sci Rep, 2017. 7(1): p. 1395
    [PMID:28469131]
  12. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  13. 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]
  14. Sarkar Das S, et al.
    Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination.
    Sci Rep, 2018. 8(1): p. 1233
    [PMID:29352229]