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 AT4G23980.2
Common NameARF9, T19F6.20, T32A16.150
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: 636aa    MW: 72063.7 Da    PI: 7.0886
Description auxin response factor 9
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G23980.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.11.9e-24116217199
                  EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                  f kvlt sd++++g +++ +k+a+e+       +  ++ +++l+ ed +g +W++k+i+r++++r++lt+GW+ Fv +++L +gD++vF   + +++e
  AT4G23980.2 116 FSKVLTASDTSTHGGFSVLRKHATEClppldmtQ--QTPTQELVAEDVHGYQWKFKHIFRGQPRRHLLTTGWSTFVTSKRLVAGDTFVFL--RGENGE 209
                  88****************************9643..445569************************************************..449999 PP

                  .EEEEE-S CS
           B3  92 lvvkvfrk 99 
                  l+v+v+r+
  AT4G23980.2 210 LRVGVRRA 217
                  ******97 PP
2Auxin_resp112.44.3e-37242321183
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                  a ha++tk++F v+Y+Pr+  s+F+++++k+++a+++k+svGmRfkm+fe+eds+err+sGtv+gv+d++p +W++SkWr+L+
  AT4G23980.2 242 ARHATQTKTMFIVYYKPRT--SQFIISLNKYLEAMSNKFSVGMRFKMRFEGEDSPERRYSGTVIGVKDCSP-HWKDSKWRCLE 321
                  6799**************6..9*************************************************.*********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.94E-38108245IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.6E-41110231IPR015300DNA-binding pseudobarrel domain
CDDcd100171.00E-20114216No hitNo description
PfamPF023623.6E-22116217IPR003340B3 DNA binding domain
PROSITE profilePS5086312.731116218IPR003340B3 DNA binding domain
SMARTSM010194.6E-24116218IPR003340B3 DNA binding domain
PfamPF065075.4E-33242320IPR010525Auxin response factor
PfamPF023091.5E-12499609IPR033389AUX/IAA domain
SuperFamilySSF542771.81E-13516597No hitNo description
PROSITE profilePS5174525.774521621IPR000270PB1 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: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: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: 636 aa     Download sequence    Send to blast
MANRGGEYLY DELWKLCAGP LVDVPQAQER VYYFPQGHME QLEASTQQVD LNTMKPLFVL  60
PPKILCNVMN VSLQAEKDTD EVYAQITLIP VGTEVDEPMS PDPSPPELQR PKVHSFSKVL  120
TASDTSTHGG FSVLRKHATE CLPPLDMTQQ TPTQELVAED VHGYQWKFKH IFRGQPRRHL  180
LTTGWSTFVT SKRLVAGDTF VFLRGENGEL RVGVRRANLQ QSSMPSSVIS SHSMHLGVLA  240
TARHATQTKT MFIVYYKPRT SQFIISLNKY LEAMSNKFSV GMRFKMRFEG EDSPERRYSG  300
TVIGVKDCSP HWKDSKWRCL EVHWDEPASI SRPNKVSPWE IEPFVNSENV PKSVMLKNKR  360
PRQVSEVSAL GITASNLWSS VLTQPHEFAQ SCITSQWSSP QQCHRDANED AKKSDWLNNS  420
YSVSNVAKDS TLNDQMVSPV EQKKPETTAN YRLFGIDLMS SSLAVPEEKT APMRPINISK  480
PTMDSHSDPK SEISKVSEEK KQEPAEGSPK EVQSKQSSST RSRTKVQMQG VPVGRAVDLN  540
ALKGYNELID DIEKLFDIKG ELRSRNQWEI VFTDDEGDMM LVGDDPWPEF CNMVKRIFIW  600
SKEEVKKMTP GNQLRMLLRE VETTLTTTSK TDNHSN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-160934419355Auxin response factor 1
4ldw_A1e-160934419355Auxin response factor 1
4ldw_B1e-160934419355Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.33960.0inflorescence| root| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible254194_at0.0
Expression AtlasAT4G23980-
AtGenExpressAT4G23980-
ATTED-IIAT4G23980-
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 auxin response factor 9 (ARF9).
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
PlantRegMapAT4G23980.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G23980, AT5G60450, AT1G19850, AT1G30330, AT1G34310, AT1G35240, AT1G59750
IntActSearch Q9XED8
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G23980
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF0821760.0AF082176.1 Arabidopsis thaliana auxin response factor 9 (ARF9) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001031706.10.0auxin response factor 9
SwissprotQ9XED80.0ARFI_ARATH; Auxin response factor 9
TrEMBLA0A178V4030.0A0A178V403_ARATH; Auxin response factor
STRINGAT4G23980.10.0(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. 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. 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]
  8. 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]
  9. 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]
  10. Gifford ML,Dean A,Gutierrez RA,Coruzzi GM,Birnbaum KD
    Cell-specific nitrogen responses mediate developmental plasticity.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(2): p. 803-8
    [PMID:18180456]
  11. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  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. Rademacher EH, et al.
    Different auxin response machineries control distinct cell fates in the early plant embryo.
    Dev. Cell, 2012. 22(1): p. 211-22
    [PMID:22264733]
  18. 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]
  19. 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]