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 Dca12447.1
Organism
Dianthus caryophyllus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Caryophyllaceae; Caryophylleae; Dianthus
Family ARF
Protein Properties Length: 794aa    MW: 89172.7 Da    PI: 6.9967
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Dca12447.1genomeDCAView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B372.16.9e-23101202199
                 EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS
          B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 
                 f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++ ++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + +++el+
  Dca12447.1 101 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHRNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGELR 196
                 99*****************************7333.34459************************************************..449999** PP

                 EEEE-S CS
          B3  94 vkvfrk 99 
                 v+v+r+
  Dca12447.1 197 VGVRRA 202
                 ***996 PP
2Auxin_resp119.42.9e-39227309183
  Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                 a+ha++t+++F+v+Y+Pr+s+++F+v+++++ +++k+++s+GmRfkm+fe+e+++e+r++Gt+vgv+d+d  rW++SkWr+L+
  Dca12447.1 227 AWHAIKTGTMFTVYYKPRTSPAQFIVPYDQYTESVKHHYSIGMRFKMRFEGEEAPEQRFTGTIVGVEDADANRWRESKWRCLQ 309
                 89********************************************************************************7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.109.9E-4097216IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.77E-4097230IPR015300DNA-binding pseudobarrel domain
CDDcd100173.93E-2199201No hitNo description
PROSITE profilePS5086311.251101203IPR003340B3 DNA binding domain
PfamPF023629.8E-21101202IPR003340B3 DNA binding domain
SMARTSM010192.1E-22101203IPR003340B3 DNA binding domain
PfamPF065079.7E-37227309IPR010525Auxin response factor
PfamPF023093.9E-10655758IPR033389AUX/IAA domain
PROSITE profilePS5174523.537668752IPR000270PB1 domain
SuperFamilySSF542771.37E-11670745No 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: 794 aa     Download sequence    Send to blast
MSSTEVSTKQ NSEQFPPQIE TKVDPETALY RELWHACAGP LVTVPRINDL VYYFPQGHIE  60
QAEADTDEVY AQVMLQPQKE ENSVEKEPPA QPQPRFHVHS FCKTLTASDT STHGGFSVLR  120
RHADECLPPL DMSRQPPTQE LVAKDLHRNE WRFRHIFRGQ PRRHLLQSGW SVFVSSKRLV  180
AGDAFIFLRG ENGELRVGVR RAMRQQVIVP SSVISSHSMH LGVLATAWHA IKTGTMFTVY  240
YKPRTSPAQF IVPYDQYTES VKHHYSIGMR FKMRFEGEEA PEQRFTGTIV GVEDADANRW  300
RESKWRCLQV RWDETSTVPR PDRVSPWQVE PAVTPPTINP LPVSRVKRPR PNVATQSQDS  360
SAFTREGSSK LTADRSPASM LSRVLQGQEY PNMNPSLADS NESETVEKPI AWPNAVDEEK  420
TNSPSVSRKY VPEHWAPSMR PGPTYTDLLS GFGGHSDQPS GFHSSYQSAV ASPIKKSVVE  480
QDGRFNILGN PWSLNTVMSP GLSLNITDSS VKVPSQNSSI SYHVQGNGRY GSFGDIPVLH  540
GHRVDHHSGN WMMPPPGPPR FDNHPRSREM PMREPTKPKD GNCKLFGIPL ISSPVQQGSA  600
ILSRNGDESS NLLPPLLQHN GHHSEADRNS EQSKDCKQTE NLPTSNEQEK KLGSSRDCQA  660
KFHCGSTRSC TKVHKQGIAL GRSVDLSKFS DYDQFIDELD HLFDFNGELK APEKNWLIVY  720
TDDEGDMMLV GDDPWQEFCA MVRKIFIYTK EEVQKMTPKT LNSRTEDNPP AIGGSDSKEG  780
KQSLPSSASY AESH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1492833118354Auxin response factor 1
4ldw_A1e-1492833118354Auxin response factor 1
4ldw_B1e-1492833118354Auxin response factor 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1346350KRPRP
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) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255|RuleBase:RU004561, ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00574DAPTransfer from AT5G62000Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010678349.10.0PREDICTED: auxin response factor 2
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLD7SH690.0D7SH69_VITVI; Auxin response factor
STRINGXP_010678349.10.0(Beta vulgaris)
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. Tomato Genome Consortium
    The tomato genome sequence provides insights into fleshy fruit evolution.
    Nature, 2012. 485(7400): p. 635-41
    [PMID:22660326]
  2. Breitel DA, et al.
    AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening.
    PLoS Genet., 2016. 12(3): p. e1005903
    [PMID:26959229]
  3. Xu T, et al.
    SlARF2a plays a negative role in mediating axillary shoot formation.
    Sci Rep, 2016. 6: p. 33728
    [PMID:27645097]
  4. Ren Z,Liu R,Gu W,Dong X
    The Solanum lycopersicum auxin response factor SlARF2 participates in regulating lateral root formation and flower organ senescence.
    Plant Sci., 2017. 256: p. 103-111
    [PMID:28167023]