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 Ciclev10030900m
Common NameCICLE_v10030696mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family ARF
Protein Properties Length: 666aa    MW: 74664.9 Da    PI: 7.1059
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10030900mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B356.74.3e-188713499
                     SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
               B3 34 ktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99
                     ++l  +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + +++el+v+v+r+
  Ciclev10030900m  8 QELAAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGELRVGVRRA 71
                     48999*********************************************..449999*****996 PP
2Auxin_resp124.48.1e-4196178183
       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++SkWr+Lk
  Ciclev10030900m  96 AWHAVSTGTMFTVYYKPRTSPSEFIVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWRDSKWRCLK 178
                      89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM010190.0013172IPR003340B3 DNA binding domain
PROSITE profilePS5086312.464172IPR003340B3 DNA binding domain
SuperFamilySSF1019361.96E-22299IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.6E-26285IPR015300DNA-binding pseudobarrel domain
CDDcd100171.46E-13570No hitNo description
PfamPF023629.8E-16771IPR003340B3 DNA binding domain
PfamPF065075.1E-3896178IPR010525Auxin response factor
PfamPF023097.1E-12521624IPR033389AUX/IAA domain
SuperFamilySSF542777.85E-12539617No hitNo description
PROSITE profilePS5174526.393540633IPR000270PB1 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: 666 aa     Download sequence    Send to blast
MSRQPPTQEL AAKDLHGNEW RFRHIFRGQP RRHLLQSGWS VFVSSKRLVA GDAFIFLRGE  60
NGELRVGVRR AMRQQGNVPS SVISSHSMHL GVLATAWHAV STGTMFTVYY KPRTSPSEFI  120
VPYDQYMESI KNNYSIGMRF KMRFEGEEAP EQRFTGTIVG IEDADPQRWR DSKWRCLKVR  180
WDETSTIPRP ERVSPWKIEP ALAPPALNSL PMPRPKRPRS NMLPSSPDSS VLTREGSSKL  240
NVDPSSATGF SRVLQGQEFS TLRGNFAERE SNESDTAEKS VVWPPSLDDE KIDVVSASRR  300
YGSENWVPPG RHEPVYTDLL SGFGANADPS HGFSSPFADA VPVRKSVLDQ EGKFNLVARP  360
WSLMPSGPSL KMPESNAKVP VQGGDVNYQV RGNVRYGGFG DYPMLNGNRV EHSHGNWLMP  420
PLPPSNFENS AHSRELMPKS AMVQDQEAGK SKDCKLFGIP LFSNHVMPEP VVSHRNTMND  480
PAGNLDQQFR AFESDQKSDH SKSSKLADDN QVFNEHEKLS QPSQTHTKDV RSKTQCGSTR  540
SCTKVQKQGI ALGRSVDLSK FNNYDELIAE LDQLFEFDGE LMAPKKNWII VYTDDEGDMM  600
LVGDDPWQEF CGMVRKIFIY TKEEVLKMNS VSFSSKGEDS PMNGDGIDAK EVKQPLPLAS  660
NAENF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1021200155354Auxin response factor 1
4ldw_A1e-1021200155354Auxin response factor 1
4ldw_B1e-1021200155354Auxin response factor 1
4ldx_A1e-1021200155354Auxin response factor 1
4ldx_B1e-1021200155354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Ccl.28190.0fruit
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expression increases at the orange (Or) and red (R) fruit stages. Expression is increased with ethylene at mature green (MG) stage, but only after six days post-treatment. Expression is increased three days post-treatment with plant hormone abscisic acid (ABA) at the Or stage, but not at the MG or breaker (Br) stages. No change in expression level up to six days post-treatment with ABA at the MG fruit stage (PubMed:26959229). Expressed during floral development (PubMed:21735233, PubMed:28167023, PubMed:27645097). During bud-anthesis stages flowers exhibit dynamic expression pattern in sepal, stamen, ovary and petal (PubMed:28167023). Expressed during ovary development with the highest expression on the third day after the flower fully opened (PubMed:21735233). During seed germination, expressed in the cotyledon. Expressed strongly in the pollen grain. Expressed in the developing fruits, in which mainly expressed in the vascular tissues and seeds. During growth, strongly expressed in leaf, where mainly expressed in the trichome and in the root tip and lateral root formation sites. Expressed in the vascular tissue and the epicycle of the root. Also expressed in branch (PubMed:27645097). {ECO:0000269|PubMed:21735233, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
UniprotTISSUE SPECIFICITY: Expressed in root, leaf and flower (PubMed:26716451, PubMed:27645097, PubMed:28167023, PubMed:21735233). Expressed in flower buds about three days before opening including ovary, petal and sepal with the highest in stamen (PubMed:21735233). Expressed in stem (PubMed:26716451, PubMed:28167023, PubMed:21735233). Expressed in fruit (PubMed:26716451, PubMed:27645097, PubMed:28167023). Expressed in seeds (PubMed:27645097). {ECO:0000269|PubMed:21735233, ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
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
GenBankJN6005200.0JN600520.1 Citrus sinensis auxin-response factor (ARF) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006436945.10.0auxin response factor 2B
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLV4TF440.0V4TF44_9ROSI; Auxin response factor
STRINGXP_006436945.10.0(Citrus clementina)
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]