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 AT2G28350.1
Common NameARF10, T1B3.13
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: 693aa    MW: 76720.9 Da    PI: 7.794
Description auxin response factor 10
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G28350.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.52.9e-24115216199
                  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   +++++ 
  AT2G28350.1 115 FAKTLTQSDANNGGGFSVPRYCAETIfprldysAEPPVQ--TVIAKDIHGETWKFRHIYRGTPRRHLLTTGWSTFVNQKKLIAGDSIVFL--RSESGD 208
                  89****************************986445444..8************************************************..458999 PP

                  .EEEEE-S CS
           B3  92 lvvkvfrk 99 
                  l+v+++r+
  AT2G28350.1 209 LCVGIRRA 216
                  9****997 PP

2Auxin_resp114.68.8e-38277360183
   Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                  a+ +a+ +++FevvY+Prast+eF+vk+++v++a++++++ GmRfkmafetedss++++ +Gtv++v+ +dp+rWpnS+Wr+L+
  AT2G28350.1 277 AVARAACGQAFEVVYYPRASTPEFCVKAADVRSAMRIRWCSGMRFKMAFETEDSSRISWfMGTVSAVQVADPIRWPNSPWRLLQ 360
                  56778899**************************************************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.2E-37108219IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.22E-29110216IPR015300DNA-binding pseudobarrel domain
CDDcd100173.86E-21114215No hitNo description
SMARTSM010191.2E-21115217IPR003340B3 DNA binding domain
PROSITE profilePS5086313.183115217IPR003340B3 DNA binding domain
PfamPF023623.7E-22115216IPR003340B3 DNA binding domain
PfamPF065072.7E-32278360IPR010525Auxin response factor
PROSITE profilePS5174519.444580668IPR000270PB1 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:0009734Biological Processauxin-activated signaling pathway
GO:0009738Biological Processabscisic acid-activated signaling pathway
GO:0009743Biological Processresponse to carbohydrate
GO:0010154Biological Processfruit development
GO:0031540Biological Processregulation of anthocyanin biosynthetic process
GO:0048366Biological Processleaf development
GO:0048441Biological Processpetal development
GO:0048442Biological Processsepal development
GO:0048589Biological Processdevelopmental growth
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: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:0009049anatomyinflorescence
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020031anatomyradicle
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:0007015developmental stageradicle emergence 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:0007131developmental stageseedling development stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 693 aa     Download sequence    Send to blast
MEQEKSLDPQ LWHACAGSMV QIPSLNSTVF YFAQGHTEHA HAPPDFHAPR VPPLILCRVV  60
SVKFLADAET DEVFAKITLL PLPGNDLDLE NDAVLGLTPP SSDGNGNGKE KPASFAKTLT  120
QSDANNGGGF SVPRYCAETI FPRLDYSAEP PVQTVIAKDI HGETWKFRHI YRGTPRRHLL  180
TTGWSTFVNQ KKLIAGDSIV FLRSESGDLC VGIRRAKRGG LGSNAGSDNP YPGFSGFLRD  240
DESTTTTSKL MMMKRNGNND GNAAATGRVR VEAVAEAVAR AACGQAFEVV YYPRASTPEF  300
CVKAADVRSA MRIRWCSGMR FKMAFETEDS SRISWFMGTV SAVQVADPIR WPNSPWRLLQ  360
VAWDEPDLLQ NVKRVSPWLV ELVSNMPTIH LSPFSPRKKI RIPQPFEFPF HGTKFPIFSP  420
GFANNGGGES MCYLSNDNNN APAGIQGARQ AQQLFGSPSP SLLSDLNLSS YTGNNKLHSP  480
AMFLSSFNPR HHHYQARDSE NSNNISCSLT MGNPAMVQDK KKSVGSVKTH QFVLFGQPIL  540
TEQQVMNRKR FLEEEAEAEE EKGLVARGLT WNYSLQGLET GHCKVFMESE DVGRTLDLSV  600
IGSYQELYRK LAEMFHIEER SDLLTHVVYR DANGVIKRIG DEPFSDFMKA TKRLTIKMDI  660
GGDNVRKTWI TGIRTGENGI DASTKTGPLS IFA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A7e-80738151388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.137300.0bud| cell culture| flower
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453604180.0
Genevisible265272_at0.0
Expression AtlasAT2G28350-
AtGenExpressAT2G28350-
ATTED-IIAT2G28350-
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
TAIRInvolved in root cap cell differentiation.
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. In root, auxin and miR160 regulate the expression of ARF10 genes independently, generating a pattern consistent with root cap development.
    [PMID: 16006581]
  2. negative regulation of ARF10 by miR160 plays a critical role in seed germination and post-embryonic developmental programs
    [PMID: 17672844]
  3. 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]
  4. miR160 negatively affects the expression of ARF10 during shoot regeneration.
    [PMID: 22335436]
  5. Auxin recruits AUXIN RESPONSE FACTOR 10 and AUXIN RESPONSE FACTOR 16 to control the expression of ABI3 during seed germination.
    [PMID: 23986496]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G28350.1
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 -- MicroRNA ? help Back to Top
Source Description
miRTarBaseRegulated by ath-miR160c, ath-miR160b, ath-miR160a
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDabscisic acid, auxin
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G60450
IntActSearch Q9SKN5
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G28350
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3250730.0AF325073.1 Arabidopsis thaliana unknown protein (At2g28350) mRNA, complete cds.
GenBankAF3369190.0AF336919.1 Arabidopsis thaliana clone C00034 (b) auxin response factor 10 (At2g28350) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_180402.10.0auxin response factor 10
SwissprotQ9SKN50.0ARFJ_ARATH; Auxin response factor 10
TrEMBLC0SV660.0C0SV66_ARATH; Auxin response factor (Fragment)
STRINGAT2G28350.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM58027130
Representative plantOGRP5261578
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. Kasschau KD, et al.
    P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction.
    Dev. Cell, 2003. 4(2): p. 205-17
    [PMID:12586064]
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  6. Jiao Y, et al.
    A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development.
    Plant Physiol., 2003. 133(4): p. 1480-93
    [PMID:14605227]
  7. 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]
  8. Chapman EJ,Prokhnevsky AI,Gopinath K,Dolja VV,Carrington JC
    Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step.
    Genes Dev., 2004. 18(10): p. 1179-86
    [PMID:15131083]
  9. 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]
  10. Souret FF,Kastenmayer JP,Green PJ
    AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets.
    Mol. Cell, 2004. 15(2): p. 173-83
    [PMID:15260969]
  11. 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]
  12. 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]
  13. 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]
  14. Axtell MJ,Bartel DP
    Antiquity of microRNAs and their targets in land plants.
    Plant Cell, 2005. 17(6): p. 1658-73
    [PMID:15849273]
  15. 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]
  16. Vergnolle C, et al.
    The cold-induced early activation of phospholipase C and D pathways determines the response of two distinct clusters of genes in Arabidopsis cell suspensions.
    Plant Physiol., 2005. 139(3): p. 1217-33
    [PMID:16258011]
  17. Cao D,Cheng H,Wu W,Soo HM,Peng J
    Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis.
    Plant Physiol., 2006. 142(2): p. 509-25
    [PMID:16920880]
  18. Lewsey M,Robertson FC,Canto T,Palukaitis P,Carr JP
    Selective targeting of miRNA-regulated plant development by a viral counter-silencing protein.
    Plant J., 2007. 50(2): p. 240-52
    [PMID:17444907]
  19. 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]
  20. Liu PP, et al.
    Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages.
    Plant J., 2007. 52(1): p. 133-46
    [PMID:17672844]
  21. Ehrenreich IM,Purugganan MD
    Sequence variation of MicroRNAs and their binding sites in Arabidopsis.
    Plant Physiol., 2008. 146(4): p. 1974-82
    [PMID:18305205]
  22. 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]
  23. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  24. Nonogaki H
    Repression of transcription factors by microRNA during seed germination and postgerminaiton: Another level of molecular repression in seeds.
    Plant Signal Behav, 2008. 3(1): p. 65-7
    [PMID:19704775]
  25. 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]
  26. Liu X, et al.
    The role of floral organs in carpels, an Arabidopsis loss-of-function mutation in MicroRNA160a, in organogenesis and the mechanism regulating its expression.
    Plant J., 2010. 62(3): p. 416-28
    [PMID:20136729]
  27. 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]
  28. 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]
  29. 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]
  30. 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]
  31. Qiao M, et al.
    Proper regeneration from in vitro cultured Arabidopsis thaliana requires the microRNA-directed action of an auxin response factor.
    Plant J., 2012. 71(1): p. 14-22
    [PMID:22335436]
  32. Qiao M,Xiang F
    A set of Arabidopsis thaliana miRNAs involve shoot regeneration in vitro.
    Plant Signal Behav, 2013. 8(3): p. e23479
    [PMID:23333958]
  33. 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]
  34. 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]
  35. 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]