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 30147.m014418
Common NameRCOM_1503930
Organism
Ricinus communis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
Family ARF
Protein Properties Length: 844aa    MW: 93835.4 Da    PI: 6.452
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
30147.m014418genomeJCVIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B341.13.2e-13158251199
                    EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS
             B3   1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 
                    f+k+lt sd++++g +++ +++a+e+  +      +++++++  +  + +i+   ++++r++l++GW+ Fv++++L +gD ++F   + +++el+v
  30147.m014418 158 FCKTLTASDTSTHGGFSVLRRHADECLPP-----LVSINSTEFVRCLIDIIMliPGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGELRV 246
                    99***********************9533.....5888888888888888777799*****************************..449999*** PP

                    EEE-S CS
             B3  95 kvfrk 99 
                    +v+r+
  30147.m014418 247 GVRRA 251
                    **996 PP
2Auxin_resp117.21.4e-38276358183
     Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                    a+ha+st++ F+v+Y+Pr+s++eF+v+++++++++k+++++GmRfkm+fe+e+++e+r++Gt+vg++d+d+ rW++SkWrsLk
  30147.m014418 276 AWHAISTGTLFTVYYKPRTSPAEFIVPFDRYMESVKNNYCIGMRFKMRFEGEEAPEQRFTGTIVGIEDADSKRWRESKWRSLK 358
                    89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019366.8E-24154279IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.109.7E-24154265IPR015300DNA-binding pseudobarrel domain
CDDcd100172.54E-13156250No hitNo description
SMARTSM010198.4E-9158252IPR003340B3 DNA binding domain
PfamPF023621.1E-10158251IPR003340B3 DNA binding domain
PROSITE profilePS508638.684212252IPR003340B3 DNA binding domain
PfamPF065076.8E-36276358IPR010525Auxin response factor
PROSITE profilePS5174525.774718802IPR000270PB1 domain
SuperFamilySSF542775.4E-12719795No hitNo description
PfamPF023091.7E-7764803IPR033389AUX/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: 844 aa     Download sequence    Send to blast
MDSSEISIKG NSSVRGGEES FSSSYSEPNV AMEGQKGHST RPVSAKDAEK ALYTELWNAC  60
AGPLVTVPRE NELVYYFPQG HIEQVEASTN QLADQQMPVY NLPSKILCRV INVQLKAEPD  120
TDEVFAQVTL LPEPIQDENA VKKDPPQPPP PRFHVHSFCK TLTASDTSTH GGFSVLRRHA  180
DECLPPLVSI NSTEFVRCLI DIIMLIPGQP RRHLLQSGWS VFVSSKRLVA GDAFIFLRGE  240
NGELRVGVRR AMRQQGNVPS SVISSHSMHL GVLATAWHAI STGTLFTVYY KPRTSPAEFI  300
VPFDRYMESV KNNYCIGMRF KMRFEGEEAP EQRFTGTIVG IEDADSKRWR ESKWRSLKVR  360
WDETSTIPRP DRVSPWSVEP ALAPPALNPL PVPRPKRPRS NMVPSSPDSS VLTRDGSSKV  420
TIDPPPPSGY SRVLQGQEFS TLRGNFAESN ESETAEKSVM WPPSVDDEKI DVSASRRHGS  480
ESWNLSGRPE PTYTDLLSGF GSNADSSHGF TSSFVDQAAT AASRKLVLDQ EGKFNLLANP  540
WSLMSSGLSL KLSESNTKVS VQGRDIPYQA RGNIRCSAFS EYPILHGHRV DQSHGNWLMP  600
PPPPSHFDNL AHAREPVSKP LQEHDIGKST DGNCKLFGIP LFSNPVAPEP ATSHRNMVNE  660
PTTAHPQSHQ PRALESDQRS EQPRVSKMAD DNEHEKQFQS GHLHTRDIQG KTQTGSTRSC  720
TKVHKQGIAL GRSVDLAKFN NYDELIAELD RLFEFGGELI SPKKNWLIVY TDDEGDMMLV  780
GDDPWQEFVG MVRKIFIYTR EEVQKMNPGT LNSKGDEHLL DVDGVDAKEV KCVPLPPAQS  840
TENC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1565138018354Auxin response factor 1
4ldw_A1e-1565138018354Auxin response factor 1
4ldw_B1e-1565138018354Auxin response factor 1
4ldx_A1e-1565138018354Auxin response factor 1
4ldx_B1e-1565138018354Auxin 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
Cis-element ? help Back to Top
SourceLink
PlantRegMap30147.m014418
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
GenBankKF0220041e-173KF022004.1 Jatropha curcas auxin response factor (ARF) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015579572.10.0LOW QUALITY PROTEIN: auxin response factor 2B
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLB9RA750.0B9RA75_RICCO; Auxin response factor
STRINGXP_002511100.10.0(Ricinus communis)
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. 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]