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 Cc00_g12260
Common NameGSCOC_T00008604001
Organism
Coffea canephora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
Family ARF
Protein Properties Length: 853aa    MW: 95248.3 Da    PI: 6.8831
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cc00_g12260genomeCGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.99.7e-24146247199
                  EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                  f+k+lt sd++++g +++ +++a+e+      +  ++ +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + +++el
  Cc00_g12260 146 FCKTLTASDTSTHGGFSVLRRHADEClpqldmS-RQPPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGEL 240
                  99****************************963.3334459************************************************..449999* PP

                  EEEEE-S CS
           B3  93 vvkvfrk 99 
                  +v+v+r+
  Cc00_g12260 241 RVGVRRA 247
                  ****996 PP
2Auxin_resp118.26.8e-39272354183
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                  a+ha++t++ F+v+Y+Pr+s+seF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++++dp rWp+SkWr+Lk
  Cc00_g12260 272 AWHAIQTNTFFTVYYKPRTSPSEFIVPFDQYMESVKNSYSIGMRFKMRFEGEEAPEQRFTGTIVGTEEADPKRWPESKWRCLK 354
                  89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.1E-41140261IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.4E-40143275IPR015300DNA-binding pseudobarrel domain
CDDcd100172.64E-21144246No hitNo description
PROSITE profilePS5086312.012146248IPR003340B3 DNA binding domain
SMARTSM010191.4E-22146248IPR003340B3 DNA binding domain
PfamPF023621.1E-21146247IPR003340B3 DNA binding domain
PfamPF065072.9E-36272354IPR010525Auxin response factor
PfamPF023099.2E-11695811IPR033389AUX/IAA domain
PROSITE profilePS5174523.719726810IPR000270PB1 domain
SuperFamilySSF542773.78E-12727803No hitNo description
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: 853 aa     Download sequence    Send to blast
MAASEVSIKG YTEPSDGPRG LPEVAKSVSG AGKVDAETAL YTELWRACAG PLVTVPREKE  60
LVYYFPQGHI EQVEASTNQV ADQAMPVYNL PWKILCRVIN VQLKAEPDTD EVFAQVTLMP  120
EPDQDENAVK KEPVPPPSPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPQLDMSRQ  180
PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL  240
RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTNT FFTVYYKPRT SPSEFIVPFD  300
QYMESVKNSY SIGMRFKMRF EGEEAPEQRF TGTIVGTEEA DPKRWPESKW RCLKVRWDET  360
STIPRPDRVS PWKIEPALTP PALNPLPVPR PKRPRPNILP SSPDSSVLTR EGSSKITIDP  420
SPASGLSRVL QGQEPSTLRG TLGESNESDS LEKPVIWPPS LDDDKLDVCA SSRRYASDKW  480
LPLGRPESSF TDLLAGFGSQ INSPNEFSTT SADQSVVSAN SKKRQLQEHE GKFNYLGSPW  540
SLMSSGLSLH LMEPSVKTRG QGTDISYQTR GDARYGSFNE YPLLPSNRLD NQQANWLMPP  600
PMTSYIQMPP NSREMVHKPV LVPPHEVVKP KEGNCKLFGI PLISNSMPLE PASSHKNRTI  660
ESVGQLLPGM HTHRSSVSES DQRSEQPKGA KVADNVVASN EQDKQCQTFN QVTRDREGKV  720
SGGSTRSCTK VHKQGIALGR SVDLTKFNNY DELIAELDRL FEFNGELKYR TKHWLVVYTD  780
DEGDMMLVGD DPWQEFCGMV RKIFIYTREE VQRMNPGTLN SRGEEQSSVA EGLDAKEVKN  840
LLHPSASSPD DC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1723937618354Auxin response factor 1
4ldw_A1e-1723937618354Auxin response factor 1
4ldw_B1e-1723937618354Auxin response factor 1
4ldx_A1e-1723937618354Auxin response factor 1
4ldx_B1e-1723937618354Auxin response factor 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1391395KRPRP
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_027122786.10.0auxin response factor 2A-like
RefseqXP_027122787.10.0auxin response factor 2A-like
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLA0A068VJB60.0A0A068VJB6_COFCA; Auxin response factor
STRINGXP_009769542.10.0(Nicotiana sylvestris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA26182444
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]