PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G61830.1
Common NameARF18, F15G16.220
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: 602aa    MW: 67662.4 Da    PI: 5.9842
Description auxin response factor 18
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G61830.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3733.6e-23128228198
                  EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                  f+k+lt sd++++g +++ +k+a+e+       +   + +++l+ +d++g +W++k+i+r++++r++lt+GW+ Fv++++L +gD +vF   + +++ 
  AT3G61830.1 128 FVKILTASDTSTHGGFSVLRKHATEClpsldmtQ--ATPTQELVTRDLHGFEWRFKHIFRGQPRRHLLTTGWSTFVSSKRLVAGDAFVFL--RGENGD 221
                  89****************************9543..445569************************************************..348888 PP

                  .EEEEE- CS
           B3  92 lvvkvfr 98 
                  l+v+v+r
  AT3G61830.1 222 LRVGVRR 228
                  9***998 PP
2Auxin_resp95.86.7e-32254333183
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                  a+ha++t+++F v+Y+Pr   s+F+v v+k+++a+k+ +s+G+Rf+m+fe+e+s+er ++Gt+vg  dl++ +Wp SkWrsL+
  AT3G61830.1 254 ASHAVRTTTIFVVFYKPRI--SQFIVGVNKYMEAIKHGFSLGTRFRMRFEGEESPERIFTGTIVGSGDLSS-QWPASKWRSLQ 333
                  689***************8..9**********************************************777.*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.83E-39117257IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.3E-38122243IPR015300DNA-binding pseudobarrel domain
CDDcd100177.92E-20126228No hitNo description
PROSITE profilePS5086312.083128230IPR003340B3 DNA binding domain
SMARTSM010198.9E-21128230IPR003340B3 DNA binding domain
PfamPF023623.2E-21128228IPR003340B3 DNA binding domain
PfamPF065076.2E-29254333IPR010525Auxin response factor
PfamPF023099.2E-8481525IPR033389AUX/IAA domain
SuperFamilySSF542771.37E-12488565No hitNo description
PROSITE profilePS5174526.011489581IPR000270PB1 domain
PfamPF023094.4E-6529574IPR033389AUX/IAA 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: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:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
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: 602 aa     Download sequence    Send to blast
MASVEGDDDF GSSSSRSYQD QLYTELWKVC AGPLVEVPRA QERVFYFPQG HMEQLVASTN  60
QGINSEEIPV FDLPPKILCR VLDVTLKAEH ETDEVYAQIT LQPEEDQSEP TSLDPPIVGP  120
TKQEFHSFVK ILTASDTSTH GGFSVLRKHA TECLPSLDMT QATPTQELVT RDLHGFEWRF  180
KHIFRGQPRR HLLTTGWSTF VSSKRLVAGD AFVFLRGENG DLRVGVRRLA RHQSTMPTSV  240
ISSQSMHLGV LATASHAVRT TTIFVVFYKP RISQFIVGVN KYMEAIKHGF SLGTRFRMRF  300
EGEESPERIF TGTIVGSGDL SSQWPASKWR SLQVQWDEPT TVQRPDKVSP WEIEPFLATS  360
PISTPAQQPQ SKCKRSRPIE PSVKTPAPPS FLYSLPQSQD SINASLKLFQ DPSLERISGG  420
YSSNNSFKPE TPPPPTNCSY RLFGFDLTSN SPAPIPQDKQ PMDTCGAAKC QEPITPTSMS  480
EQKKQQTSRS RTKVQMQGIA VGRAVDLTLL KSYDELIDEL EEMFEIQGQL LARDKWIVVF  540
TDDEGDMMLA GDDPWNEFCK MAKKIFIYSS DEVKKMTTKL KISSSLENEE YGNESFENRS  600
RG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1622035617355Auxin response factor 1
4ldw_A1e-1622035617355Auxin response factor 1
4ldw_B1e-1622035617355Auxin response factor 1
4ldx_A1e-1622035617355Auxin response factor 1
4ldx_B1e-1622035617355Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.171670.0flower| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO306954900.0
Genevisible251289_at0.0
Expression AtlasAT3G61830-
AtGenExpressAT3G61830-
ATTED-IIAT3G61830-
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). 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G61830.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT2G20180 (A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G61830, AT4G23980, AT5G60450, AT1G19850, AT1G30330, AT1G34310, AT1G59750
IntActSearch Q9C5W9
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G61830
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3347170.0AF334717.1 Arabidopsis thaliana auxin response factor ARF18 (At3g61830) mRNA, complete cds.
GenBankAY0597460.0AY059746.1 Arabidopsis thaliana auxin response factor ARF18 (At3g61830) mRNA, complete cds.
GenBankAY0704630.0AY070463.1 Arabidopsis thaliana AT3g61830/F15G16_220 mRNA, complete cds.
GenBankAY0913920.0AY091392.1 Arabidopsis thaliana putative auxin response factor protein (At3g61830) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_567119.10.0auxin response factor 18
SwissprotQ9C5W90.0ARFR_ARATH; Auxin response factor 18
TrEMBLA0A178V7A70.0A0A178V7A7_ARATH; Auxin response factor
STRINGAT3G61830.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM74351841
Representative plantOGRP5501582
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. 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]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  4. 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]
  5. Remington DL,Vision TJ,Guilfoyle TJ,Reed JW
    Contrasting modes of diversification in the Aux/IAA and ARF gene families.
    Plant Physiol., 2004. 135(3): p. 1738-52
    [PMID:15247399]
  6. Nishimura T,Wada T,Okada K
    A key factor of translation reinitiation, ribosomal protein L24, is involved in gynoecium development in Arabidopsis.
    Biochem. Soc. Trans., 2004. 32(Pt 4): p. 611-3
    [PMID:15270688]
  7. Okushima Y, et al.
    Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19.
    Plant Cell, 2005. 17(2): p. 444-63
    [PMID:15659631]
  8. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  9. Lin WH, et al.
    At5PTase13 modulates cotyledon vein development through regulating auxin homeostasis.
    Plant Physiol., 2005. 139(4): p. 1677-91
    [PMID:16299182]
  10. Thilmony R,Underwood W,He SY
    Genome-wide transcriptional analysis of the Arabidopsis thaliana interaction with the plant pathogen Pseudomonas syringae pv. tomato DC3000 and the human pathogen Escherichia coli O157:H7.
    Plant J., 2006. 46(1): p. 34-53
    [PMID:16553894]
  11. Axtell MJ,Snyder JA,Bartel DP
    Common functions for diverse small RNAs of land plants.
    Plant Cell, 2007. 19(6): p. 1750-69
    [PMID:17601824]
  12. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  13. Oh E, et al.
    Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis.
    Plant Cell, 2009. 21(2): p. 403-19
    [PMID:19244139]
  14. Shin R,Jez JM,Basra A,Zhang B,Schachtman DP
    14-3-3 proteins fine-tune plant nutrient metabolism.
    FEBS Lett., 2011. 585(1): p. 143-7
    [PMID:21094157]
  15. 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]
  16. 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]
  17. Causier B,Ashworth M,Guo W,Davies B
    The TOPLESS interactome: a framework for gene repression in Arabidopsis.
    Plant Physiol., 2012. 158(1): p. 423-38
    [PMID:22065421]
  18. 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]
  19. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
    [PMID:23449474]
  20. 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]
  21. Wójcikowska B,Gaj MD
    Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis.
    Plant Cell Rep., 2017. 36(6): p. 843-858
    [PMID:28255787]