PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G60450.1
Common NameARF4, MUF9.8
Organism
Arabidopsis thaliana
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: 788aa    MW: 87284.2 Da    PI: 6.3749
Description auxin response factor 4
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G60450.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.53e-24177278199
                  EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                  f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F   +++++el
  AT5G60450.1 177 FCKTLTASDTSTHGGFSVPRRAAEDCfapldyK-QQRPSQELIAKDLHGVEWKFRHIYRGQPRRHLLTTGWSIFVSQKNLVSGDAVLFL--RDEGGEL 271
                  99****************************963.3445679************************************************..5699*** PP

                  EEEEE-S CS
           B3  93 vvkvfrk 99 
                  +++++r+
  AT5G60450.1 272 RLGIRRA 278
                  ****996 PP
2Auxin_resp122.72.7e-40302383182
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                  +a+a+stks+F+v+Y+Pra+++eFv+++ek+ ++++++v++G+Rf+m+fe++ds+err++G+v+gv dldp+rWpnSkWr+L
  AT5G60450.1 302 VANAVSTKSMFHVFYSPRATHAEFVIPYEKYITSIRSPVCIGTRFRMRFEMDDSPERRCAGVVTGVCDLDPYRWPNSKWRCL 383
                  689******************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.7E-40168291IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.53E-42171286IPR015300DNA-binding pseudobarrel domain
CDDcd100174.02E-21175277No hitNo description
SMARTSM010194.4E-23177279IPR003340B3 DNA binding domain
PfamPF023624.4E-22177278IPR003340B3 DNA binding domain
PROSITE profilePS5086313.183177279IPR003340B3 DNA binding domain
PfamPF065079.9E-34302383IPR010525Auxin response factor
SuperFamilySSF542771.47E-10660742No hitNo description
PROSITE profilePS5174523.437665747IPR000270PB1 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:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000017anatomyvascular leaf primordium
PO:0000037anatomyshoot apex
PO:0000229anatomyflower meristem
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:0020144anatomyapical meristem
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
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: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: 788 aa     Download sequence    Send to blast
MEFDLNTEIA EVEEEENDDV GVGVGGGTRI DKGRLGISPS SSSSCSSGSS SSSSSTGSAS  60
SIYSELWHAC AGPLTCLPKK GNVVVYFPQG HLEQDAMVSY SSPLEIPKFD LNPQIVCRVV  120
NVQLLANKDT DEVYTQVTLL PLQEFSMLNG EGKEVKELGG EEERNGSSSV KRTPHMFCKT  180
LTASDTSTHG GFSVPRRAAE DCFAPLDYKQ QRPSQELIAK DLHGVEWKFR HIYRGQPRRH  240
LLTTGWSIFV SQKNLVSGDA VLFLRDEGGE LRLGIRRAAR PRNGLPDSII EKNSCSNILS  300
LVANAVSTKS MFHVFYSPRA THAEFVIPYE KYITSIRSPV CIGTRFRMRF EMDDSPERRC  360
AGVVTGVCDL DPYRWPNSKW RCLLVRWDES FVSDHQERVS PWEIDPSVSL PHLSIQSSPR  420
PKRPWAGLLD TTPPGNPITK RGGFLDFEES VRPSKVLQGQ ENIGSASPSQ GFDVMNRRIL  480
DFAMQSHANP VLVSSRVKDR FGEFVDATGV NPACSGVMDL DRFPRVLQGQ EICSLKSFPQ  540
FAGFSPAAAP NPFAYQANKS SYYPLALHGI RSTHVPYQNP YNAGNQSSGP PSRAINFGEE  600
TRKFDAQNEG GLPNNVTADL PFKIDMMGKQ KGSELNMNAS SGCKLFGFSL PVETPASKPQ  660
SSSKRICTKV HKQGSQVGRA IDLSRLNGYD DLLMELERLF NMEGLLRDPE KGWRILYTDS  720
ENDMMVVGDD PWHDFCNVVW KIHLYTKEEV ENANDDNKSC LEQAALMMEA SKSSSVSQPD  780
SSPTITRV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-113504062354Auxin response factor 1
4ldw_A1e-113504062354Auxin response factor 1
4ldw_B1e-113504062354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.67970.0root
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453594840.0
Genevisible247643_at0.0
Expression AtlasAT5G60450-
AtGenExpressAT5G60450-
ATTED-IIAT5G60450-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the ARF family of transcription factors which mediate auxin responses. ARF4 appears to have redundant function with ETT(ARF3) in specifying abaxial cell identity.
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). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. {ECO:0000269|PubMed:12036261}.
Function -- GeneRIF ? help Back to Top
  1. regulation establishes the threshold at which leaves respond to a temporal signal, rather than being a component of this signal.
    [PMID: 16818444]
  2. Results indicate that auxin response factors AtARF2-AtARF4 and AtARF5 play significant roles in regulating both female and male gametophyte development.
    [PMID: 29145642]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G60450.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDauxin
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G60450, AT1G34310, AT1G59750
IntActSearch Q9ZTX9
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G60450
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0808320.0AY080832.1 Arabidopsis thaliana auxin response factor ARF4 (At5g60450) mRNA, complete cds.
GenBankAY1139770.0AY113977.1 Arabidopsis thaliana auxin response factor ARF4 (At5g60450) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_200853.10.0auxin response factor 4
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLA0A178ULQ00.0A0A178ULQ0_ARATH; Auxin response factor
STRINGAT5G60450.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95302636
Representative plantOGRP10049811
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. Hagen G,Guilfoyle T
    Auxin-responsive gene expression: genes, promoters and regulatory factors.
    Plant Mol. Biol., 2002 Jun-Jul. 49(3-4): p. 373-85
    [PMID:12036261]
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  6. Cluis CP,Mouchel CF,Hardtke CS
    The Arabidopsis transcription factor HY5 integrates light and hormone signaling pathways.
    Plant J., 2004. 38(2): p. 332-47
    [PMID:15078335]
  7. Williams L,Carles CC,Osmont KS,Fletcher JC
    A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(27): p. 9703-8
    [PMID:15980147]
  8. Pekker I,Alvarez JP,Eshed Y
    Auxin response factors mediate Arabidopsis organ asymmetry via modulation of KANADI activity.
    Plant Cell, 2005. 17(11): p. 2899-910
    [PMID:16199616]
  9. Adenot X, et al.
    DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7.
    Curr. Biol., 2006. 16(9): p. 927-32
    [PMID:16682354]
  10. Garcia D,Collier SA,Byrne ME,Martienssen RA
    Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway.
    Curr. Biol., 2006. 16(9): p. 933-8
    [PMID:16682355]
  11. Fahlgren N, et al.
    Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis.
    Curr. Biol., 2006. 16(9): p. 939-44
    [PMID:16682356]
  12. Hunter C, et al.
    Trans-acting siRNA-mediated repression of ETTIN and ARF4 regulates heteroblasty in Arabidopsis.
    Development, 2006. 133(15): p. 2973-81
    [PMID:16818444]
  13. Nakazawa Y,Hiraguri A,Moriyama H,Fukuhara T
    The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway.
    Plant Mol. Biol., 2007. 63(6): p. 777-85
    [PMID:17221360]
  14. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  15. Usami T,Horiguchi G,Yano S,Tsukaya H
    The more and smaller cells mutants of Arabidopsis thaliana identify novel roles for SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes in the control of heteroblasty.
    Development, 2009. 136(6): p. 955-64
    [PMID:19211679]
  16. Inagaki S,Nakamura K,Morikami A
    A link among DNA replication, recombination, and gene expression revealed by genetic and genomic analysis of TEBICHI gene of Arabidopsis thaliana.
    PLoS Genet., 2009. 5(8): p. e1000613
    [PMID:19696887]
  17. Yoon EK, et al.
    Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development.
    Nucleic Acids Res., 2010. 38(4): p. 1382-91
    [PMID:19969544]
  18. Marin E, et al.
    miR390, Arabidopsis TAS3 tasiRNAs, and their AUXIN RESPONSE FACTOR targets define an autoregulatory network quantitatively regulating lateral root growth.
    Plant Cell, 2010. 22(4): p. 1104-17
    [PMID:20363771]
  19. Finet C, et al.
    Parallel structural evolution of auxin response factors in the angiosperms.
    Plant J., 2010. 63(6): p. 952-9
    [PMID:20626651]
  20. 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]
  21. 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]
  22. 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]
  23. Finet C,Berne-Dedieu A,Scutt CP,Marl
    Evolution of the ARF gene family in land plants: old domains, new tricks.
    Mol. Biol. Evol., 2013. 30(1): p. 45-56
    [PMID:22977118]
  24. Bonaccorso O,Lee JE,Puah L,Scutt CP,Golz JF
    FILAMENTOUS FLOWER controls lateral organ development by acting as both an activator and a repressor.
    BMC Plant Biol., 2012. 12: p. 176
    [PMID:23025792]
  25. Takahashi H, et al.
    Meta-analyses of microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and their modifying mutants reveal a critical role for the ETT pathway in stabilization of adaxial-abaxial patterning and cell division during leaf development.
    Plant Cell Physiol., 2013. 54(3): p. 418-31
    [PMID:23396601]
  26. Wang J,Yan DW,Yuan TT,Gao X,Lu YT
    A gain-of-function mutation in IAA8 alters Arabidopsis floral organ development by change of jasmonic acid level.
    Plant Mol. Biol., 2013. 82(1-2): p. 71-83
    [PMID:23483289]
  27. Iwasaki M, et al.
    Dual regulation of ETTIN (ARF3) gene expression by AS1-AS2, which maintains the DNA methylation level, is involved in stabilization of leaf adaxial-abaxial partitioning in Arabidopsis.
    Development, 2013. 140(9): p. 1958-69
    [PMID:23571218]
  28. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  29. 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]
  30. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  31. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  32. Pashkovskiy PP,Kartashov AV,Zlobin IE,Pogosyan SI,Kuznetsov VV
    Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.
    Plant Physiol. Biochem., 2016. 104: p. 146-54
    [PMID:27031426]
  33. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  34. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  35. Liu Z, et al.
    ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis.
    Plant Cell Physiol., 2018. 59(1): p. 179-189
    [PMID:29145642]