PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G62000.3
Common NameARF1-BP, ARF2, HSS, MNT, MTG10.3, ORE14
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: 859aa    MW: 95700.9 Da    PI: 6.599
Description auxin response factor 2
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G62000.3genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.51.1e-22164265199
                  EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                  f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++ ++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + +++el
  AT5G62000.3 164 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHANEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGEL 258
                  99*****************************7333.34459************************************************..449999* PP

                  EEEEE-S CS
           B3  93 vvkvfrk 99 
                  +v+v+r+
  AT5G62000.3 259 RVGVRRA 265
                  ****996 PP

2Auxin_resp121.65.7e-40290372183
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                  a+ha+st+++F+v+Y+Pr+s+seF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++++dp+rWp+SkWrsLk
  AT5G62000.3 290 AWHAISTGTMFTVYYKPRTSPSEFIVPFDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEESDPTRWPKSKWRSLK 372
                  89*******************************************************************************96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.88E-40160293IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.3E-40160279IPR015300DNA-binding pseudobarrel domain
CDDcd100171.46E-20162264No hitNo description
PROSITE profilePS5086311.42164266IPR003340B3 DNA binding domain
PfamPF023621.5E-20164265IPR003340B3 DNA binding domain
SMARTSM010194.1E-22164266IPR003340B3 DNA binding domain
PfamPF065074.5E-37290372IPR010525Auxin response factor
PfamPF023093.3E-5716769IPR033389AUX/IAA domain
PROSITE profilePS5174524.819733817IPR000270PB1 domain
SuperFamilySSF542777.36E-12734810No hitNo description
PfamPF023094.6E-6779818IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009734Biological Processauxin-activated signaling pathway
GO:0009737Biological Processresponse to abscisic acid
GO:0009911Biological Processpositive regulation of flower development
GO:0010047Biological Processfruit dehiscence
GO:0010150Biological Processleaf senescence
GO:0010227Biological Processfloral organ abscission
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000005anatomycultured plant cell
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0006203anatomypericycle
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009015anatomyportion of vascular tissue
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:0020133anatomycolumella root cap initial cell
PO:0020137anatomyleaf apex
PO:0020149anatomyquiescent center
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: 859 aa     Download sequence    Send to blast
MASSEVSMKG NRGGDNFSSS GFSDPKETRN VSVAGEGQKS NSTRSAAAER ALDPEAALYR  60
ELWHACAGPL VTVPRQDDRV FYFPQGHIEQ VEASTNQAAE QQMPLYDLPS KLLCRVINVD  120
LKAEADTDEV YAQITLLPEA NQDENAIEKE APLPPPPRFQ VHSFCKTLTA SDTSTHGGFS  180
VLRRHADECL PPLDMSRQPP TQELVAKDLH ANEWRFRHIF RGQPRRHLLQ SGWSVFVSSK  240
RLVAGDAFIF LRGENGELRV GVRRAMRQQG NVPSSVISSH SMHLGVLATA WHAISTGTMF  300
TVYYKPRTSP SEFIVPFDQY MESVKNNYSI GMRFKMRFEG EEAPEQRFTG TIVGIEESDP  360
TRWPKSKWRS LKVRWDETSS IPRPDRVSPW KVEPALAPPA LSPVPMPRPK RPRSNIAPSS  420
PDSSMLTREG TTKANMDPLP ASGLSRVLQG QEYSTLRTKH TESVECDAPE NSVVWQSSAD  480
DDKVDVVSGS RRYGSENWMS SARHEPTYTD LLSGFGTNID PSHGQRIPFY DHSSSPSMPA  540
KRILSDSEGK FDYLANQWQM IHSGLSLKLH ESPKVPAATD ASLQGRCNVK YSEYPVLNGL  600
STENAGGNWP IRPRALNYYE EVVNAQAQAQ AREQVTKQPF TIQEETAKSR EGNCRLFGIP  660
LTNNMNGTDS TMSQRNNLND AAGLTQIASP KVQDLSDQSK GSKSTNDHRE QGRPFQTNNP  720
HPKDAQTKTN SSRSCTKVHK QGIALGRSVD LSKFQNYEEL VAELDRLFEF NGELMAPKKD  780
WLIVYTDEEN DMMLVGDDPW QEFCCMVRKI FIYTKEEVRK MNPGTLSCRS EEEAVVGEGS  840
DAKDAKSASN PSLSSAGNS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldx_B0.05739418354Auxin response factor 1
4ldx_A0.05739418354Auxin response factor 1
4ldw_B0.05739418354Auxin response factor 1
4ldw_A0.05739418354Auxin response factor 1
4ldv_A0.05739418354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.217040.0flower| inflorescence| leaf| root| seed| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO3341885580.0
Genevisible247468_at0.0
Expression AtlasAT5G62000-
AtGenExpressAT5G62000-
ATTED-IIAT5G62000-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the sepals and carpels of young flower buds. At stage 10 of flower development, expression in the carpels becomes restricted to the style. Also expressed in anthers and filaments. At stage 13, expressed in the region at the top of the pedicel, including the abscission zone. Expressed in developing siliques. {ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952}.
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078, ECO:0000269|PubMed:15960614}.
Functional Description ? help Back to Top
Source Description
TAIREncodes an auxin response factor. Mutants have many defects including enlarged rosette leaves, reduced fertility, later senescence, hypocotyl elongation defects, enlarged seeds and enlarged cotyledons. May not mediate auxin effects. Increase in seed size due to increased cell proliferation.
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. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Functions independently of ethylene and cytokinin response pathways. May act as a repressor of cell division and organ growth. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952, ECO:0000269|PubMed:16339187}.
Function -- GeneRIF ? help Back to Top
  1. ARF2 is a part of transcriptional complexes responsible for regulating diverse signaling pathways leading to pleiotropic developmental defects.
    [PMID: 15960614]
  2. ARF2 expression was induced in senescing leaves. ARF2 regulated leaf senescence and floral organ abscission independently of the ethylene and cytokinin response pathways
    [PMID: 16176952]
  3. mutant phenotype and gene expression studies provide evidence that MNT/ARF2 is a repressor of cell division and organ growth
    [PMID: 16339187]
  4. IAA28 overexpressing and knock-down lines showed no major morphological changes, whereas IAA13 and ARF2 overexpressing plants grew more slowly than the wild type.
    [PMID: 18596113]
  5. study describes a direct connection between the brassinosteroid-regulated BIN2 kinase and ARF2; phosphorylation by BIN2 results in loss of ARF2 DNA binding and repression activities
    [PMID: 18599455]
  6. Data suggest that ARF2 positively regulates leaf senescence in Arabidopsis.
    [PMID: 20164142]
  7. ARF2 and HB33 are novel regulators in the abscissic acid signal pathway, which has crosstalk with auxin signal pathway in regulating plant growth.
    [PMID: 21779177]
  8. Data indicate that CARBON-METABOLISM INVOLVED (GNC) and GNC-LIKE (GNL)/CYTOKININ-RESPONSIVE GATA FACTOR1 (CGA1) expression is repressed by AUXIN RESPONSE FACTO ARF2 and ARF7.
    [PMID: 23878229]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00574DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G62000.3
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 AT1G01480(A), AT2G33310(A), AT4G11280(A), AT4G37750(R), AT4G37770(A), AT5G25890(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDauxin, brassinosteroid
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G34310, AT1G69120
IntActSearch Q94JM3
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Large, dark green rosette leaves, delayed flowering, thick and long inflorescence, abnormal flower morphology and sterility in early formed flowers, but fertility in late-formed flowers. Delayed senescence and abscission. Increased seed size and weight, and extra cell division and expansion in many organs. {ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16339187}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G62000
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0007840.0BT000784.1 Arabidopsis thaliana clone RAFL07-10-G12 (R10939) auxin response factor (At5g62000) mRNA, complete cds.
GenBankAK2213050.0AK221305.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-31-F22.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_201006.20.0auxin response factor 2
RefseqNP_851244.10.0auxin response factor 2
RefseqNP_974980.10.0auxin response factor 2
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLF4K5360.0F4K536_ARATH; Auxin response factor
STRINGAT5G62000.10.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Ulmasov T,Hagen G,Guilfoyle TJ
    Dimerization and DNA binding of auxin response factors.
    Plant J., 1999. 19(3): p. 309-19
    [PMID:10476078]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  3. 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]
  4. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  5. Li H,Johnson P,Stepanova A,Alonso JM,Ecker JR
    Convergence of signaling pathways in the control of differential cell growth in Arabidopsis.
    Dev. Cell, 2004. 7(2): p. 193-204
    [PMID:15296716]
  6. 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]
  7. Okushima Y,Mitina I,Quach HL,Theologis A
    AUXIN RESPONSE FACTOR 2 (ARF2): a pleiotropic developmental regulator.
    Plant J., 2005. 43(1): p. 29-46
    [PMID:15960614]
  8. 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]
  9. 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]
  10. Schruff MC, et al.
    The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs.
    Development, 2006. 133(2): p. 251-61
    [PMID:16339187]
  11. D
    A model of the ethylene signaling pathway and its gene response in Arabidopsis thaliana: pathway cross-talk and noise-filtering properties.
    Chaos, 2006. 16(2): p. 023112
    [PMID:16822015]
  12. Falkenberg B, et al.
    Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism.
    J. Exp. Bot., 2008. 59(10): p. 2831-46
    [PMID:18596113]
  13. Vert G,Walcher CL,Chory J,Nemhauser JL
    Integration of auxin and brassinosteroid pathways by Auxin Response Factor 2.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(28): p. 9829-34
    [PMID:18599455]
  14. Hughes R, et al.
    Yield assessment of integument-led seed growth following targeted repair of auxin response factor 2.
    Plant Biotechnol. J., 2008. 6(8): p. 758-69
    [PMID:18643948]
  15. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  16. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  17. Krizek B
    AINTEGUMENTA and AINTEGUMENTA-LIKE6 act redundantly to regulate Arabidopsis floral growth and patterning.
    Plant Physiol., 2009. 150(4): p. 1916-29
    [PMID:19542297]
  18. Lim PO, et al.
    Auxin response factor 2 (ARF2) plays a major role in regulating auxin-mediated leaf longevity.
    J. Exp. Bot., 2010. 61(5): p. 1419-30
    [PMID:20164142]
  19. Wu B, et al.
    Over-expression of mango (Mangifera indica L.) MiARF2 inhibits root and hypocotyl growth of Arabidopsis.
    Mol. Biol. Rep., 2011. 38(5): p. 3189-94
    [PMID:20182802]
  20. 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]
  21. 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]
  22. 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]
  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. Wang L, et al.
    Auxin Response Factor2 (ARF2) and its regulated homeodomain gene HB33 mediate abscisic acid response in Arabidopsis.
    PLoS Genet., 2011. 7(7): p. e1002172
    [PMID:21779177]
  25. Rademacher EH, et al.
    A cellular expression map of the Arabidopsis AUXIN RESPONSE FACTOR gene family.
    Plant J., 2011. 68(4): p. 597-606
    [PMID:21831209]
  26. Stotz HU, et al.
    Jasmonate-dependent and COI1-independent defense responses against Sclerotinia sclerotiorum in Arabidopsis thaliana: auxin is part of COI1-independent defense signaling.
    Plant Cell Physiol., 2011. 52(11): p. 1941-56
    [PMID:21937677]
  27. Cui H, et al.
    Genome-wide direct target analysis reveals a role for SHORT-ROOT in root vascular patterning through cytokinin homeostasis.
    Plant Physiol., 2011. 157(3): p. 1221-31
    [PMID:21951467]
  28. 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]
  29. Smaczniak C, et al.
    Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(5): p. 1560-5
    [PMID:22238427]
  30. Rosado A,Li R,van de Ven W,Hsu E,Raikhel NV
    Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(48): p. 19537-44
    [PMID:23144218]
  31. Jiang WB, et al.
    Brassinosteroid regulates seed size and shape in Arabidopsis.
    Plant Physiol., 2013. 162(4): p. 1965-77
    [PMID:23771896]
  32. Richter R,Behringer C,Zourelidou M,Schwechheimer C
    Convergence of auxin and gibberellin signaling on the regulation of the GATA transcription factors GNC and GNL in Arabidopsis thaliana.
    Proc. Natl. Acad. Sci. U.S.A., 2013. 110(32): p. 13192-7
    [PMID:23878229]
  33. 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]
  34. 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]
  35. 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]