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 GSVIVT01004942001
Common NameLOC100250592, VIT_01s0244g00150
Organism
Vitis vinifera
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
Family ARF
Protein Properties Length: 768aa    MW: 86054.6 Da    PI: 6.8932
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01004942001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.18.1e-24116217199
                        EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                 B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                        f+k+lt sd++++g +++ +++a+e+      + k++ +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   +
  GSVIVT01004942001 116 FCKTLTASDTSTHGGFSVLRRHADEClppldmS-KQPPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSLFVSSKKLVAGDAFIFL--R 204
                        99*****************************63.4445569************************************************..4 PP

                        SSEE..EEEEE-S CS
                 B3  87 rsefelvvkvfrk 99 
                         +++el+v+v+r+
  GSVIVT01004942001 205 GENGELRVGVRRA 217
                        49999*****996 PP
2Auxin_resp1201.8e-39242324183
         Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                        a+ha+st+++F+v+Y+Pr+s++eF+++++++++a+k+++s+GmRfkm+fe+e+++e+r++Gtv+g++d+dp+rWp+SkWr+Lk
  GSVIVT01004942001 242 AWHAVSTGTIFTVYYKPRTSPAEFIIPFDQYMEAVKNHYSIGMRFKMKFEGEEAPEQRFTGTVIGTEDADPMRWPGSKWRCLK 324
                        89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.66E-40105245IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.1E-40109231IPR015300DNA-binding pseudobarrel domain
CDDcd100171.84E-21114216No hitNo description
PROSITE profilePS5086311.984116218IPR003340B3 DNA binding domain
PfamPF023627.9E-22116217IPR003340B3 DNA binding domain
SMARTSM010191.8E-23116218IPR003340B3 DNA binding domain
PfamPF065071.6E-36242324IPR010525Auxin response factor
PfamPF023092.0E-10627728IPR033389AUX/IAA domain
SuperFamilySSF542773.73E-11636715No hitNo description
PROSITE profilePS5174524.764638731IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 768 aa     Download sequence    Send to blast
MDFVDSEDAL YKELWHACAG PLVTVPRVGE RVFYFPQGHL EQVEASTNQV ADQQMPAYDL  60
RAKILCRVIN VHLKAESDTD EVFAQVTLLP EPKQDENSAE KEDVLTPTPR PRVHSFCKTL  120
TASDTSTHGG FSVLRRHADE CLPPLDMSKQ PPTQELVAKD LHGNEWRFRH IFRGQPRRHL  180
LQSGWSLFVS SKKLVAGDAF IFLRGENGEL RVGVRRAMRQ LSNGPSSVIS SHSMHLGVLA  240
TAWHAVSTGT IFTVYYKPRT SPAEFIIPFD QYMEAVKNHY SIGMRFKMKF EGEEAPEQRF  300
TGTVIGTEDA DPMRWPGSKW RCLKVRWDET SSVPRPECVS PWNIEVALTP PSLNPLPVSR  360
SKRPRANMMS SSTESSVLTR EGLSKVTIDH SPGSGFSRAL QGQEISTLRG IFMENNNDLV  420
TTQKSIVQPR SQVVDQMDSA STKRSFMSED WVPQLRQGVQ CANLISGPQS MMHSSTVLNM  480
ESNVKLSEGA KGKPYPTPAN VRYSGFSGYG GLHDLGAEQC PGNWLLPLLP HSYSETTPHL  540
MGLKPQPLYV QEEVVKSKGD GNCKLFGISL ISKPAANPMH RPQGEIQLTM ENPARHPEQS  600
KSSKYMEIGG FEHEKPFQAL EQQLSRDDQS KLHSGSTRSC IKVHKQGIAV GRSVDLTKFN  660
GYTELISELD QIFEFNGELI SLNKDWLIVF TDDEGDMMLV GDDPWPEFCS MVRKIFVYTR  720
EEIQRMDPRP LNPKSWRHPS AVSLWGRASL PELTMEHLFV TSGCEGS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-171834517353Auxin response factor 1
4ldw_A1e-171834517353Auxin response factor 1
4ldw_B1e-171834517353Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.171390.0cell culture| flower| fruit
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}.
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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankFQ3802690.0FQ380269.1 Vitis vinifera clone SS0ACG7YK15.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002268849.10.0PREDICTED: auxin response factor 2
RefseqXP_010656858.10.0PREDICTED: auxin response factor 2
SwissprotQ2LAJ30.0ARF2A_SOLLC; Auxin response factor 2A
TrEMBLF6HWQ30.0F6HWQ3_VITVI; Auxin response factor
STRINGVIT_01s0244g00150.t010.0(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP5501582
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]