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 Cucsa.156920.1
Common NameCsa_1G000580, LOC101206845
Organism
Cucumis sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Cucumis
Family ARF
Protein Properties Length: 769aa    MW: 85514.6 Da    PI: 7.1233
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cucsa.156920.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3758.4e-2476177199
                     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++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + ++
  Cucsa.156920.1  76 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGEN 167
                     99*****************************7333.34459************************************************..4499 PP

                     E..EEEEE-S CS
              B3  90 felvvkvfrk 99 
                     +el+v+v+r+
  Cucsa.156920.1 168 GELRVGVRRA 177
                     99*****996 PP
2Auxin_resp118.94e-39202284183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     a+ha+st++ F+v+Y+Pr+s+seF+v+++++++++k+++++GmRfkm+fe+e+++e+r++Gt++g +d+dp rW++SkWr+Lk
  Cucsa.156920.1 202 AWHAISTGTLFTVYYKPRTSPSEFIVPYDQYMESIKKSYTIGMRFKMRFEGEEAPEQRFTGTIIGCEDADPKRWKDSKWRCLK 284
                     89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.105.3E-4173191IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.35E-4073205IPR015300DNA-binding pseudobarrel domain
CDDcd100171.43E-2174176No hitNo description
SMARTSM010192.0E-2376178IPR003340B3 DNA binding domain
PfamPF023629.9E-2276177IPR003340B3 DNA binding domain
PROSITE profilePS5086312.01276178IPR003340B3 DNA binding domain
PfamPF065072.0E-36202284IPR010525Auxin response factor
SuperFamilySSF542779.81E-12642720No hitNo description
PROSITE profilePS5174526.111643727IPR000270PB1 domain
PfamPF023091.9E-6690728IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009734Biological Processauxin-activated signaling pathway
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: 769 aa     Download sequence    Send to blast
MKVEASTSQV ADQQMPVYNL PSKILCRVIN VHLKAEPDTD EVFAQITLLP EANQDEHAVD  60
KEPPPPPPRR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ PPTQELVAKD  120
LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL RVGVRRAMRQ  180
HGNVPSSVIS SHSMHLGVLA TAWHAISTGT LFTVYYKPRT SPSEFIVPYD QYMESIKKSY  240
TIGMRFKMRF EGEEAPEQRF TGTIIGCEDA DPKRWKDSKW RCLKVRWDET STISRPEKVS  300
PWKIEPALAP PALNPLPMTR PKRPRSNMVS TSPDSSVLTR EGSSRVTVDP SPASAFTRVL  360
QGQEFSTLRG NFIDGSDPDA AEKSVMWPPS LDDEKVDVVS TSKKHGADSW IPPGRSEPTY  420
ADLLSGFGTD MDSSHGVRAA MGDSALVTAN SIRKHAMEHD GKFSFLGGSS WSVLPSGLSL  480
NLVDSSQKGH IRAGDLSYQV RGNATFNGFG DHSISHCHRT EQPHGNWLMP PPSSHFDYPI  540
HSSELMSKPM LFQNQDILKP KDGNCKLFGI SLVKNPAIPD PVGLNRNMMN EADVMHPNVH  600
QIHSSESGLK SELPRVLKLD KSVAISEADK LQQTCKSQGT SARSCTKVHK QGIALGRSVD  660
LSRFNNYDEL VAELDQLFEF GGELQAPKKN WLIVYTDDEG DMMLVGDDPW REFCGMVRKI  720
FIYTREEVQK MNPGSLNLKG DENPSVEGEE VKETKSQAVP SMSAPESS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-155230651354Auxin response factor 1
4ldw_A1e-155230651354Auxin response factor 1
4ldw_B1e-155230651354Auxin response factor 1
4ldx_A1e-155230651354Auxin response factor 1
4ldx_B1e-155230651354Auxin 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) (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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKU3234080.0KU323408.1 UNVERIFIED: Trichosanthes dioica clone TdARF_6 auxin response factor-like mRNA, partial sequence.
GenBankKU3234220.0KU323422.1 UNVERIFIED: Trichosanthes dioica clone TdARF_30 auxin response factor-like mRNA, partial sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004138020.10.0PREDICTED: auxin response factor 2
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLA0A0A0LR270.0A0A0A0LR27_CUCSA; Auxin response factor
STRINGXP_004138020.10.0(Cucumis sativus)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF32813366
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. Ren Y, et al.
    An integrated genetic and cytogenetic map of the cucumber genome.
    PLoS ONE, 2009. 4(6): p. e5795
    [PMID:19495411]
  2. Guo S, et al.
    Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types.
    BMC Genomics, 2010. 11: p. 384
    [PMID:20565788]
  3. Li Z, et al.
    RNA-Seq improves annotation of protein-coding genes in the cucumber genome.
    BMC Genomics, 2011. 12: p. 540
    [PMID:22047402]
  4. Tomato Genome Consortium
    The tomato genome sequence provides insights into fleshy fruit evolution.
    Nature, 2012. 485(7400): p. 635-41
    [PMID:22660326]
  5. 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]
  6. Xu T, et al.
    SlARF2a plays a negative role in mediating axillary shoot formation.
    Sci Rep, 2016. 6: p. 33728
    [PMID:27645097]
  7. 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]