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 Rsa1.0_00945.1_g00003.1
Organism
Raphanus sativus
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: 852aa    MW: 95004.7 Da    PI: 7.0042
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_00945.1_g00003.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B369.25.8e-22162263199
                              EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 
                              f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++  +W++++i+r++++r++l++GW+ Fv++++L +gD +
  Rsa1.0_00945.1_g00003.1 162 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHAIEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAF 246
                              99*****************************7333.34459********************************************* PP

                              EEEE-SSSEE..EEEEE-S CS
                       B3  81 vFkldgrsefelvvkvfrk 99 
                              +F   + +++el+v+v+r+
  Rsa1.0_00945.1_g00003.1 247 IFL--RGENGELRVGVRRA 263
                              ***..449999*****996 PP
2Auxin_resp120.81e-39288370183
               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
  Rsa1.0_00945.1_g00003.1 288 AWHAISTGTMFTVYYKPRTSPSEFIVPFDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDSDPTRWAKSKWRSLK 370
                              89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.107.9E-40158277IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.66E-40158291IPR015300DNA-binding pseudobarrel domain
CDDcd100175.15E-20160262No hitNo description
PROSITE profilePS5086311.166162264IPR003340B3 DNA binding domain
PfamPF023627.4E-20162263IPR003340B3 DNA binding domain
SMARTSM010191.3E-21162264IPR003340B3 DNA binding domain
PfamPF065077.7E-37288370IPR010525Auxin response factor
PfamPF023094.3E-11716817IPR033389AUX/IAA domain
PROSITE profilePS5174524.874726819IPR000270PB1 domain
SuperFamilySSF542771.42E-11727803No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009737Biological Processresponse to abscisic acid
GO:0009911Biological Processpositive regulation of flower development
GO:0010047Biological Processfruit dehiscence
GO:0010150Biological Processleaf senescence
GO:0010227Biological Processfloral organ abscission
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 852 aa     Download sequence    Send to blast
MTTSADVSMK GNRGGGGENF SSLGYSDSTV AGEAAMKTQS NRSMAAERVV DAEAALYREL  60
WHACAGPLVT VPRQDDRVFY FPQGHIEQVE ASTNQAAEQQ MPLYDLPSKI LCRVINVDLK  120
AEADTDEVYA QITLLPEPMQ DENAIEKVPP PPPPPRFQVH SFCKTLTASD TSTHGGFSVL  180
RRHADECLPP LDMSRQPPTQ ELVAKDLHAI EWRFRHIFRG QPRRHLLQSG WSVFVSSKRL  240
VAGDAFIFLR GENGELRVGV RRAMRQQGNV PSSVISSHSM HLGVLATAWH AISTGTMFTV  300
YYKPRTSPSE FIVPFDQYME SVKNNYSIGM RFKMRFEGEE APEQRFTGTI VGIEDSDPTR  360
WAKSKWRSLK VRWDETTSIP RPDRVSPWKI EPALSPPALS PVPMPRPKRP RSNIAPSTPD  420
SSMRIREGSS KANMDPLPAS GLSRVLQGQE YPTLRTKHVE SVECDAPENS IVWQSSNDDD  480
KVDVVSASRR YENWMSSTRH EQPAYTDLLS GFGANIEPPP PHGHQIPMYD RLSSSPSVAA  540
RKILSDQDGK FEYLANQWQM MHSGLSLKLH ESPKVPAASD TSFQGISNPY ALPRAVTTTE  600
NAAGNWPIRP RALNYFEEAV HAQAREHVTK RPAVVQEEAA KPRDGNCRLF GIPLVNNVNG  660
TDTATAQRNN LNDTTGLTQI ASPKVQDLSD QSKGSKSTND HREQGRPFPV SKPHPKDVQT  720
KTNSSRSCTK VHKQGIALGR SVDLSKFQNY EELVTELDRL FEFNGELMAP KKDWLIVYTD  780
DENDMMLVGD DPWQEFCCMV RKIFIYTKEE VRKMNPRTLS CRNEEDAVAG EGSDAKDAKS  840
ASNPSLSSAG NS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1785539218354Auxin response factor 1
4ldw_A1e-1785539218354Auxin response factor 1
4ldw_B1e-1785539218354Auxin 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. 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00574DAPTransfer from AT5G62000Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_00945.1_g00003.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794600.0JN979460.1 Brassica rapa subsp. pekinensis auxin response factor 2-2 (ARF2-2) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018491253.10.0PREDICTED: auxin response factor 2-like
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLA0A397Z5W50.0A0A397Z5W5_BRACM; Auxin response factor
STRINGBra010048.1-P0.0(Brassica rapa)
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]