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 Itr_sc003239.1_g00004.1
Organism
Ipomoea trifida
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
Family ARF
Protein Properties Length: 906aa    MW: 101409 Da    PI: 7.0732
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Itr_sc003239.1_g00004.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B356.93.8e-18186306199
                              EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE.....................EEETTEEEE CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliy...................rkksgryvl 61 
                              f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++g++W++++i+                     +++r++l
  Itr_sc003239.1_g00004.1 186 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFrgiipyvlnnplpdcmmfgLSQPRRHLL 270
                              99*****************************7333.34459***************999**********99999999999999*** PP

                              -TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
                       B3  62 tkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 
                              ++GW+ Fv++++L +gD ++F   + +++el+v+v+r+
  Itr_sc003239.1_g00004.1 271 QSGWSVFVSSKRLVAGDAFIFL--RGENGELRVGVRRA 306
                              **********************..449999*****996 PP
2Auxin_resp116.42.4e-38331413183
               Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                              a+ha++tk++F+v+Y+Pr+s++eF++++++++++ k+++++GmRfkm+fe+e+++e+r++Gt+vg++d dp rW++SkWr+Lk
  Itr_sc003239.1_g00004.1 331 AWHAIQTKTIFTVYYKPRTSPAEFIIPYDQYMESEKSNYTIGMRFKMRFEGEEAPEQRFTGTIVGIEDGDPQRWQESKWRCLK 413
                              89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.83E-35182334IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.1E-38182320IPR015300DNA-binding pseudobarrel domain
CDDcd100176.93E-18184305No hitNo description
SMARTSM010195.2E-13186307IPR003340B3 DNA binding domain
PfamPF023622.4E-15186306IPR003340B3 DNA binding domain
PROSITE profilePS5086310.673186307IPR003340B3 DNA binding domain
PfamPF065077.8E-35331413IPR010525Auxin response factor
PfamPF023095.5E-11773865IPR033389AUX/IAA domain
PROSITE profilePS5174523.828780862IPR000270PB1 domain
SuperFamilySSF542778.34E-13781857No 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: 906 aa     Download sequence    Send to blast
MASRQRLTPV RRRSNSPPLL VVRLSPQRLL LHWLLPVAGN SHRLLPVAKR EVSIKGYAEQ  60
NDVGARGVSC AGKVDAETAL YTELWRACAG PLVTVPREGE LVYYFPQGHI EQVEASTNQV  120
ADQQMPMYNL PSKILCRVVN VHLKAEPDTD EVYAQVTLMP VPDHDENAVK KENMPPPPPR  180
FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ PPTQELVAKD LHGNEWRFRH  240
IFRGIIPYVL NNPLPDCMMF GLSQPRRHLL QSGWSVFVSS KRLVAGDAFI FLRGENGELR  300
VGVRRAMRHQ GNAPSSVISS HSMHLGVLAT AWHAIQTKTI FTVYYKPRTS PAEFIIPYDQ  360
YMESEKSNYT IGMRFKMRFE GEEAPEQRFT GTIVGIEDGD PQRWQESKWR CLKVRWDETS  420
SVPRPDRVSP WNIEPALTPP ALNPLPVPRP KRPRSNNLPS SPDSSVLTRE GSSKLCADPS  480
PASGFSRVLH GQELSTLRGT FAESNESNSS EKPMVWPPSL EDEKIDVLSE SRRCGSDKWL  540
PLGRPEPSFT DLLSGFGTQM NSSCGFSLQP GDQTSATVSL TKRQKQYQEG SLLGKPWSIV  600
PSGLSLNLMD SGIKPHGQGS DAPYQARGDS RYGGHIECSM PPGHNVDNQQ GSWLGRQPVP  660
YLQMPAHARE RMLNPMLMQQ HEAMKPKEGN CKLFGIPLIS NSPTTDTEIL HKNTTIESGH  720
LHIGIQSHHS HVVESDQRLE QSNGSKVVDD GVTGNEEEKL FHIQPADKDR ERKVHSGSTR  780
SCTKVHKQGT ALGRSVDLTK FNNYDELLAE LDKLFDFNGE LKAMNKNWMV VYTDDEGDMM  840
LVGDDPWQEF CGMVRKIYIY TKEEVQRMNP GTLNSKDEDT SSVAEGLDTR EVKNSQIPSA  900
CSAEEC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1677943518354Auxin response factor 1
4ldw_A1e-1677943518354Auxin response factor 1
4ldw_B1e-1677943518354Auxin 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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019196152.10.0PREDICTED: auxin response factor 2-like
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLA0A328DC560.0A0A328DC56_9ASTE; 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]