PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G59750.4
Common NameARF1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family ARF
Protein Properties Length: 660aa    MW: 73216.1 Da    PI: 6.1534
Description auxin response factor 1
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G59750.4genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B367.81.5e-21124225199
                  EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                  f+k+lt sd++++g +++ +++a+++       +++    ++l+ +d+++ +W +++i+r++++r++lt+GW+ Fv++++L +gD ++F   + +++e
  AT1G59750.4 124 FCKTLTASDTSTHGGFSVLRRHADDClppldmsQQP--PWQELVATDLHNSEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFL--RGENEE 217
                  99****************************964333..4459************************************************..348888 PP

                  .EEEEE-S CS
           B3  92 lvvkvfrk 99 
                  l+v+v+r+
  AT1G59750.4 218 LRVGVRRH 225
                  9****996 PP

2Auxin_resp112.34.6e-37250332183
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                  aaha++t+++F+v+Y+Pr+s+seF+v+v+++++a ++k+svGmRfkm+fe+e+++e+r+sGt+vgv++ +++ W++S+WrsLk
  AT1G59750.4 250 AAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGEEAPEKRFSGTIVGVQENKSSVWHDSEWRSLK 332
                  79*******************************************************************************96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019365.23E-44113253IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.108.4E-40121239IPR015300DNA-binding pseudobarrel domain
CDDcd100176.10E-19122224No hitNo description
PROSITE profilePS5086310.518124226IPR003340B3 DNA binding domain
PfamPF023622.2E-19124225IPR003340B3 DNA binding domain
SMARTSM010191.6E-20124226IPR003340B3 DNA binding domain
PfamPF065073.4E-34250332IPR010525Auxin response factor
PfamPF023093.4E-11532627IPR033389AUX/IAA domain
PROSITE profilePS5174530.767537630IPR000270PB1 domain
SuperFamilySSF542772.62E-11539614No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009733Biological Processresponse to auxin
GO:0009734Biological Processauxin-activated signaling pathway
GO:0010150Biological Processleaf senescence
GO:0015031Biological Processprotein transport
GO:0016192Biological Processvesicle-mediated transport
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005768Cellular Componentendosome
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042802Molecular Functionidentical protein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 660 aa     Download sequence    Send to blast
MAASNHSSGK PGGVLSDALC RELWHACAGP LVTLPREGER VYYFPEGHME QLEASMHQGL  60
EQQMPSFNLP SKILCKVINI QRRAEPETDE VYAQITLLPE LDQSEPTSPD APVQEPEKCT  120
VHSFCKTLTA SDTSTHGGFS VLRRHADDCL PPLDMSQQPP WQELVATDLH NSEWHFRHIF  180
RGQPRRHLLT TGWSVFVSSK KLVAGDAFIF LRGENEELRV GVRRHMRQQT NIPSSVISSH  240
SMHIGVLATA AHAITTGTIF SVFYKPRTSR SEFIVSVNRY LEAKTQKLSV GMRFKMRFEG  300
EEAPEKRFSG TIVGVQENKS SVWHDSEWRS LKVQWDEPSS VFRPERVSPW ELEPLVANST  360
PSSQPQPPQR NKRPRPPGLP SPATGPSDGV WKSPADTPSS VPLFSPPAKA ATFGHGGNKS  420
FGVSIGSAFW PTNADSAAES FASAFNNEST EKKQTNGNVC RLFGFELVEN VNVDECFSAA  480
SVSGAVAVDQ PVPSNEFDSG QQSEPLNINQ SDIPSGSGDP EKSSLRSPQE SQSRQIRSCT  540
KVHMQGSAVG RAIDLTRSEC YEDLFKKLEE MFDIKGELLE STKKWQVVYT DDEDDMMMVG  600
DDPWNEFCGM VRKIFIYTPE EVKKLSPKNK LAVNARMQLK ADAEENGNTE GRSSSMAGSR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A0.013591359Auxin response factor 1
4ldw_A0.013591359Auxin response factor 1
4ldw_B0.013591359Auxin response factor 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1371375KRPRP
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.748320.0bud| flower| leaf| root
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible262914_at0.0
Expression AtlasAT1G59750-
AtGenExpressAT1G59750-
ATTED-IIAT1G59750-
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the auxin response factor family. ARFs bind to the cis element 5'-TGTCTC-3' ARFs mediate changes in gene expression in response to auxin. ARF's form heterodimers with IAA/AUX genes. ARF1 enhances mutant phenotypes of ARF2 and may act with ARF2 to control aspects of maturation and senescence.ARF1:LUC and 3xHA:ARF1 proteins have a half-life of ~3-4 hours and their degradation is reduced by proteasome inhibitors. 3xHA:ARF1 degradation is not affected by a pre-treatment with IAA. A nuclear-targeted fusion protein containing the middle region of ARF1 linked to LUC:NLS has a similar half-life to the full-length ARF1:LUC construct. The degradation of 3xHA:ARF1 is not affected in an axr6-3 mutant grown at room temperature, although the degradation of AXR2/IAA7 is slowed under these conditions.
UniProtAuxin response factors (ARFs) are transcriptional factors that binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). {ECO:0000256|RuleBase:RU004561}.
Function -- GeneRIF ? help Back to Top
  1. unlike arf2 mutations, an arf1 mutation increased transcription of Aux/IAA genes in Arabidopsis flowers, supporting previous biochemical studies that indicated that ARF1 is a transcriptional repressor
    [PMID: 16176952]
  2. The half-life of degradation of ARF1, and its role in auxin metabolism, are reported.
    [PMID: 18088308]
  3. Data show that IAA8 is involved in lateral root formation, and that this process is regulated through the interaction with the TIR1 auxin receptor and ARF transcription factors in the nucleus.
    [PMID: 22912871]
  4. The authors showed that Arf1 interacted with the viral p27 replication protein within the virus-induced large punctate structures of the endoplasmic reticulum membrane.
    [PMID: 23097452]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00097PBM26531826Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G59750.4
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDauxin
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G59750
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G59750
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY1337230.0AY133723.1 Arabidopsis thaliana auxin response factor 1 (At1g59750) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001185266.10.0auxin response factor 1
SwissprotQ8L7G00.0ARFA_ARATH; Auxin response factor 1
TrEMBLF4ID310.0F4ID31_ARATH; Auxin response factor
STRINGAT1G59750.10.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Ulmasov T,Hagen G,Guilfoyle TJ
    Activation and repression of transcription by auxin-response factors.
    Proc. Natl. Acad. Sci. U.S.A., 1999. 96(10): p. 5844-9
    [PMID:10318972]
  2. Ulmasov T,Hagen G,Guilfoyle TJ
    Dimerization and DNA binding of auxin response factors.
    Plant J., 1999. 19(3): p. 309-19
    [PMID:10476078]
  3. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  4. Ouellet F,Overvoorde PJ,Theologis A
    IAA17/AXR3: biochemical insight into an auxin mutant phenotype.
    Plant Cell, 2001. 13(4): p. 829-41
    [PMID:11283339]
  5. Ellis CM, et al.
    AUXIN RESPONSE FACTOR1 and AUXIN RESPONSE FACTOR2 regulate senescence and floral organ abscission in Arabidopsis thaliana.
    Development, 2005. 132(20): p. 4563-74
    [PMID:16176952]
  6. Min MK, et al.
    Overexpression of Arabidopsis AGD7 causes relocation of Golgi-localized proteins to the endoplasmic reticulum and inhibits protein trafficking in plant cells.
    Plant Physiol., 2007. 143(4): p. 1601-14
    [PMID:17307897]
  7. Matheson LA, et al.
    Multiple roles of ADP-ribosylation factor 1 in plant cells include spatially regulated recruitment of coatomer and elements of the Golgi matrix.
    Plant Physiol., 2007. 143(4): p. 1615-27
    [PMID:17307898]
  8. Shin R, et al.
    The Arabidopsis transcription factor MYB77 modulates auxin signal transduction.
    Plant Cell, 2007. 19(8): p. 2440-53
    [PMID:17675404]
  9. Salmon J,Ramos J,Callis J
    Degradation of the auxin response factor ARF1.
    Plant J., 2008. 54(1): p. 118-28
    [PMID:18088308]
  10. Langhans M, et al.
    In vivo trafficking and localization of p24 proteins in plant cells.
    Traffic, 2008. 9(5): p. 770-85
    [PMID:18266912]
  11. Fortunati A,Tassone P,Damasso M,Migliaccio F
    Neutron irradiation affects the expression of genes involved in the response to auxin, senescence and oxidative stress in Arabidopsis.
    Plant Signal Behav, 2010. 5(8): p. 959-67
    [PMID:20505355]
  12. Van Leene J, et al.
    Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.
    Mol. Syst. Biol., 2010. 6: p. 397
    [PMID:20706207]
  13. Varaud E, et al.
    AUXIN RESPONSE FACTOR8 regulates Arabidopsis petal growth by interacting with the bHLH transcription factor BIGPETALp.
    Plant Cell, 2011. 23(3): p. 973-83
    [PMID:21421811]
  14. Robert-Seilaniantz A, et al.
    The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates.
    Plant J., 2011. 67(2): p. 218-31
    [PMID:21457368]
  15. Vernoux T, et al.
    The auxin signalling network translates dynamic input into robust patterning at the shoot apex.
    Mol. Syst. Biol., 2011. 7: p. 508
    [PMID:21734647]
  16. Li JF,Bush J,Xiong Y,Li L,McCormack M
    Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation.
    PLoS ONE, 2011. 6(11): p. e27364
    [PMID:22096563]
  17. Arase F, et al.
    IAA8 involved in lateral root formation interacts with the TIR1 auxin receptor and ARF transcription factors in Arabidopsis.
    PLoS ONE, 2012. 7(8): p. e43414
    [PMID:22912871]
  18. Hyodo K, et al.
    ADP ribosylation factor 1 plays an essential role in the replication of a plant RNA virus.
    J. Virol., 2013. 87(1): p. 163-76
    [PMID:23097452]
  19. Boer DR, et al.
    Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors.
    Cell, 2014. 156(3): p. 577-89
    [PMID:24485461]
  20. Piya S,Shrestha SK,Binder B,Stewart CN,Hewezi T
    Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis.
    Front Plant Sci, 2014. 5: p. 744
    [PMID:25566309]
  21. Ulmasov T,Hagen G,Guilfoyle TJ
    ARF1, a transcription factor that binds to auxin response elements.
    Science, 1997. 276(5320): p. 1865-8
    [PMID:9188533]
  22. Kim J,Harter K,Theologis A
    Protein-protein interactions among the Aux/IAA proteins.
    Proc. Natl. Acad. Sci. U.S.A., 1997. 94(22): p. 11786-91
    [PMID:9342315]
  23. Ulmasov T,Murfett J,Hagen G,Guilfoyle TJ
    Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements.
    Plant Cell, 1997. 9(11): p. 1963-71
    [PMID:9401121]