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 AT4G30080.1
Common NameARF16, F6G3.110
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: 670aa    MW: 73978.8 Da    PI: 7.3381
Description auxin response factor 16
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G30080.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.31.7e-24120221199
                  EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                  f k+lt+sd+++ g +++p+ +ae++        +++ +  t+  +d +g +W++++iyr++++r++lt+GW++Fv++++L +gD++vF+  + +++ 
  AT4G30080.1 120 FAKTLTQSDANNGGGFSVPRYCAETIfprldynAEPPVQ--TILAKDVHGDVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLVAGDSIVFM--RAENGD 213
                  89****************************985444444..8999*********************************************..448899 PP

                  .EEEEE-S CS
           B3  92 lvvkvfrk 99 
                  l+v+++r+
  AT4G30080.1 214 LCVGIRRA 221
                  9****997 PP

2Auxin_resp113.71.7e-37279362183
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                  aa+ a ++ +FevvY+PrastseF+vk+ + ++a++++++ GmRfkmafetedss++++ +Gtv++v+ +dp+rWpnS+Wr+L+
  AT4G30080.1 279 AATLAISGRPFEVVYYPRASTSEFCVKALDARAAMRIPWCSGMRFKMAFETEDSSRISWfMGTVSAVNVSDPIRWPNSPWRLLQ 362
                  67788899**************************************************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.105.5E-39112227IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019367.72E-30115223IPR015300DNA-binding pseudobarrel domain
CDDcd100172.25E-22118220No hitNo description
SMARTSM010197.1E-23120222IPR003340B3 DNA binding domain
PROSITE profilePS5086313.352120222IPR003340B3 DNA binding domain
PfamPF023621.8E-22120221IPR003340B3 DNA binding domain
PfamPF065072.7E-31279362IPR010525Auxin response factor
PROSITE profilePS5174518.27584664IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007389Biological Processpattern specification process
GO:0009733Biological Processresponse to auxin
GO:0009734Biological Processauxin-activated signaling pathway
GO:0048829Biological Processroot cap development
GO:0051301Biological Processcell division
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0035198Molecular FunctionmiRNA 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:0009049anatomyinflorescence
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020130anatomycentral root cap
PO:0020131anatomylateral root cap
PO:0020137anatomyleaf apex
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: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: 670 aa     Download sequence    Send to blast
MINVMNPMKG GTEKGLDPQL WHACAGGMVR MPPMNSKVFY FPQGHAENAY DCVDFGNLPI  60
PPMVLCRVLA IKYMADAESD EVFAKLRLIP LKDDEYVDHE YGDGEDSNGF ESNSEKTPSF  120
AKTLTQSDAN NGGGFSVPRY CAETIFPRLD YNAEPPVQTI LAKDVHGDVW KFRHIYRGTP  180
RRHLLTTGWS NFVNQKKLVA GDSIVFMRAE NGDLCVGIRR AKRGGIGNGP EYSAGWNPIG  240
GSCGYSSLLR EDESNSLRRS NCSLADRKGK VTAESVIEAA TLAISGRPFE VVYYPRASTS  300
EFCVKALDAR AAMRIPWCSG MRFKMAFETE DSSRISWFMG TVSAVNVSDP IRWPNSPWRL  360
LQVAWDEPDL LQNVKRVNPW LVELVSNVHP IPLTSFSPPR KKMRLPQHPD YNNLINSIPV  420
PSFPSNPLIR SSPLSSVLDN VPVGLQGARH NAHQYYGLSS SDLHHYYLNR PPPPPPPSSL  480
QLSPSLGLRN IDTKNEKGFC FLTMGTTPCN DTKSKKSHIV LFGKLILPEE QLSEKGSTDT  540
ANIEKTQISS GGSNQNGVAG REFSSSDEGS PCSKKVHDAS GLETGHCKVF MESDDVGRTL  600
DLSVLGSYEE LSRKLSDMFG IKKSEMLSSV LYRDASGAIK YAGNEPFSEF LKTARRLTIL  660
TEQGSESVVV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A3e-77238337388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.33650.0root| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453494250.0
Genevisible253662_at0.0
Expression AtlasAT4G30080-
AtGenExpressAT4G30080-
ATTED-IIAT4G30080-
Functional Description ? help Back to Top
Source Description
TAIRInvolved in root cap cell differentiation. Gene expression is regulated by mir160.Located in the nucleus.
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). 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. ARF10 and ARF16 control root cap formation in root. Auxin and micro RNA 160(miR160) regulate the expression of ARF10 and ARF16 genes independently.
    [PMID: 16006581]
  2. Phenotypic plasticity of adventitious rooting is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Repressor/Activator Balance Is Unaltered by Disruptions to ARF10 and ARF16.
    [PMID: 19820192]
  3. Auxin recruits AUXIN RESPONSE FACTOR 10 and AUXIN RESPONSE FACTOR 16 to control the expression of ABI3 during seed germination.
    [PMID: 23986496]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00461DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G30080.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT3G11260(R)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDauxin
Interaction ? help Back to Top
Source Intact With
IntActSearch Q93YR9
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G30080
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0597920.0AY059792.1 Arabidopsis thaliana putative transcription factor (At4g30080) mRNA, complete cds.
GenBankAY0911980.0AY091198.1 Arabidopsis thaliana putative transcription factor (At4g30080) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_567841.10.0auxin response factor 16
SwissprotQ93YR90.0ARFP_ARATH; Auxin response factor 16
TrEMBLD7MC880.0D7MC88_ARALL; Auxin response factor
STRINGAT4G30080.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM58027130
Representative plantOGRP5261578
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. Goda H, et al.
    Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis.
    Plant Physiol., 2004. 134(4): p. 1555-73
    [PMID:15047898]
  5. Tepperman JM, et al.
    Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation.
    Plant J., 2004. 38(5): p. 725-39
    [PMID:15144375]
  6. 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]
  7. Nemhauser JL,Mockler TC,Chory J
    Interdependency of brassinosteroid and auxin signaling in Arabidopsis.
    PLoS Biol., 2004. 2(9): p. E258
    [PMID:15328536]
  8. 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]
  9. Mallory AC,Bartel DP,Bartel B
    MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes.
    Plant Cell, 2005. 17(5): p. 1360-75
    [PMID:15829600]
  10. Sorin C, et al.
    Auxin and light control of adventitious rooting in Arabidopsis require ARGONAUTE1.
    Plant Cell, 2005. 17(5): p. 1343-59
    [PMID:15829601]
  11. Axtell MJ,Bartel DP
    Antiquity of microRNAs and their targets in land plants.
    Plant Cell, 2005. 17(6): p. 1658-73
    [PMID:15849273]
  12. Weijers D, et al.
    Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators.
    EMBO J., 2005. 24(10): p. 1874-85
    [PMID:15889151]
  13. Wang JW, et al.
    Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis.
    Plant Cell, 2005. 17(8): p. 2204-16
    [PMID:16006581]
  14. Vanneste S, et al.
    Cell cycle progression in the pericycle is not sufficient for SOLITARY ROOT/IAA14-mediated lateral root initiation in Arabidopsis thaliana.
    Plant Cell, 2005. 17(11): p. 3035-50
    [PMID:16243906]
  15. Nemhauser JL,Hong F,Chory J
    Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses.
    Cell, 2006. 126(3): p. 467-75
    [PMID:16901781]
  16. 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]
  17. Ehrenreich IM,Purugganan MD
    Sequence variation of MicroRNAs and their binding sites in Arabidopsis.
    Plant Physiol., 2008. 146(4): p. 1974-82
    [PMID:18305205]
  18. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  19. Gutierrez L, et al.
    Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance.
    Plant Cell, 2009. 21(10): p. 3119-32
    [PMID:19820192]
  20. Ding Z,Friml J
    Auxin regulates distal stem cell differentiation in Arabidopsis roots.
    Proc. Natl. Acad. Sci. U.S.A., 2010. 107(26): p. 12046-51
    [PMID:20543136]
  21. 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]
  22. Liu Z,Jia L,Wang H,He Y
    HYL1 regulates the balance between adaxial and abaxial identity for leaf flattening via miRNA-mediated pathways.
    J. Exp. Bot., 2011. 62(12): p. 4367-81
    [PMID:21610018]
  23. 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]
  24. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  25. Liu X, et al.
    Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2013. 110(38): p. 15485-90
    [PMID:23986496]
  26. We
    Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life.
    Cell Host Microbe, 2014. 16(3): p. 364-75
    [PMID:25211078]
  27. 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]